Journal Sciences News
The Kaohsiung Journal of Medical Sciences
March 2018
Genome-wide identification, phylogenetic analysis, and expression profiles of ATP-binding cassette transporter genes in the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Lin-Fan Xiao, Wei Zhang, Tian-Xing Jing, Meng-Yi Zhang, Ze-Qing Miao, Dan-Dan Wei, Guo-Rui Yuan, Jin-Jun Wang The ATP-binding cassette (ABC) is the largest transporter gene family and the genes play key roles in xenobiotic resistance, metabolism, and development of all phyla. However, the specific functions of ABC gene families in insects is unclear. We report a genome-wide identification, phylogenetic, and transcriptional analysis of the ABC genes in the oriental fruit fly, Bactrocera dorsalis (Hendel). We identified a total of 47 ABC genes (BdABCs) from the transcriptomic and genomic databases of B. dorsalis and classified these genes into eight subfamilies (A-H), including 7 ABCAs, 7 ABCBs, 9 ABCCs, 2 ABCDs, 1 ABCE, 3 ABCFs, 15 ABCGs, and 3 ABCHs. Comparative phylogenetic analysis of the ABCs suggests an orthologous relationship between B. dorsalis and other insect species in which these genes have been related to pesticide resistance and essential biological processes. Comparison of transcriptome and relative expression patterns of BdABCs indicated diverse multifunctions within different B. dorsalis tissues. The expression of 4, 10, and 14 BdABCs from 18 BdABCs was significantly upregulated after exposure to LD50s of malathion, avermectin, and beta-cypermethrin, respectively. The maximum expression level of most BdABCs (including BdABCFs, BdABCGs, and BdABCHs) occurred at 48h post exposures, whereas BdABCEs peaked at 24h after treatment. Furthermore, RNA interference-mediated suppression of BdABCB7 resulted in increased toxicity of malathion against B. dorsalis. These data suggest that ABC transporter genes might play key roles in xenobiotic metabolism and biosynthesis in B. dorsalis.
March 2018
Label-free based quantitative proteomic analysis identifies proteins involved in the testis maturation of Bactrocera dorsalis (Hendel)
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Dong Wei, Meng-Yi Zhang, Pei-Ming Gu, Guy Smagghe, Jin-Jun Wang Complex structural and biochemical processes take place in insect testis maturation, but the mechanisms by which functional proteins induce and regulate male fertility are unknown. Proteomics has been widely used to identify functional proteins involved in such complex physiological processes. In this study, we performed a label-free based quantitative proteomic analysis of developing testis of Bactrocera dorsalis with the aim of shedding light on spermatogenesis, sperm formation and also tissue development. A total of 1912 reliable proteins were identified, including 1589, 1705 and 1723 proteins in 1-, 5- and 9-d-old testis, respectively. Most of these proteins (76.68%) were identified by two to ten peptides, and the mean number of peptides was 7.46 with an average sequence coverage of 30.71%. Quantitative proteomic analysis showed that there were 141 and 111 proteins which were abundant in the 5- and 9-d-old testis, respectively. The Gene Ontology (GO) and Clusters of Orthologous Groups (COG) analyses showed that many of these proteins function in cellular and metabolic processes, including binding and catalytic activities in molecular function analysis, and energy production, cell division, and cell motility in COG analysis. Potential functional proteins, such as heat shock proteins, glutathione S-transferase, transferrin, metalloproteinase and energy metabolism-related proteins, were found to be abundant in the intermediate and sexual maturity stages of testis. The findings in this study help us to better understand the molecular mechanisms behind testis development and spermatogenesis, which is essential for manipulating male fertility for ecological regulation and potential control of this species.
March 2018
Fatty acid-binding protein genes of the ancient, air-breathing, ray-finned fish, spotted gar (Lepisosteus oculatus)
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Ananda B. Venkatachalam, Quenton Fontenot, Allyse Farrara, Jonathan M. Wright With the advent of high-throughput DNA sequencing technology, the genomic sequence of many disparate species has led to the relatively new discipline of genomics, the study of genome structure, function and evolution. Much work has been focused on the role of whole genome duplications (WGD) in the architecture of extant vertebrate genomes, particularly those of teleost fishes which underwent a WGD early in the teleost radiation >230 million years ago (mya). Our past work has focused on the fate of duplicated copies of a multigene family coding for the intracellular lipid-binding protein (iLBP) genes in the teleost fishes. To define the evolutionary processes that determined the fate of duplicated genes and generated the structure of extant fish genomes, however, requires comparative genomic analysis with a fish lineage that diverged before the teleost WGD, such as the spotted gar (Lepisosteus oculatus), an ancient, air-breathing, ray-finned fish. Here, we describe the genomic organization, chromosomal location and tissue-specific expression of a subfamily of the iLBP genes that code for fatty acid-binding proteins (Fabps) in spotted gar. Based on this work, we have defined the minimum suite of fabp genes prior to their duplication in the teleost lineages ~230–400 mya. Spotted gar, therefore, serves as an appropriate outgroup, or ancestral/ancient fish, that did not undergo the teleost-specific WGD. As such, analyses of the spatio-temporal regulation of spotted gar genes provides a foundation to determine whether the duplicated fabp genes have been retained in teleost genomes owing to either sub- or neofunctionalization.
March 2018
Genome-wide identification of 31 cytochrome P450 (CYP) genes in the freshwater rotifer Brachionus calyciflorus and analysis of their benzo[
March 2018
Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Libin Zhang, Qiming Feng, Lina Sun, Kui Ding, Da Huo, Yan Fang, Tao Zhang, Hongsheng Yang Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of
March 2018
The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Shao'e Sun, Ming Hui, Minxiao Wang, Zhongli Sha Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi & Hashimoto, 2000) was determined through Illumina sequencing. The mitogenome of S. leurokolos was 15,903bp in length, containing 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of sequenced alvinocaridids. It has the longest concatenated sequences of protein-coding genes, tRNAs and shortest pooled rRNAs among the alvinocaridids. The control regions (CRs) of alvinocaridid were significantly longer (p <0.01) than those of the other caridaen. The alignment of the alvinocaridid CRs revealed two conserved sequence blocks (CSBs), and each of the CSBs included a noncanonical open reading frame (ORF), which may be involved in adjusting mitochondrial energy metabolism to adapt to the hydrothermal environment. Phylogenetic analysis supported that the deep-sea hydrothermal vent shrimps may have originated from those living in shallow area. Positive selection analysis reveals the evidence of adaptive change in the mitogenome of Alvinocarididae. Thirty potentially important adaptive residues were identified, which were located in atp6, cox1, cox3, cytb and nad1–5. This study explores the mitochondrial genetic basis of hydrothermal vent adaptation in alvinocaridid for the first time, and provides valuable clues regarding the adaptation.
March 2018
Divergence of insulin superfamily ligands, receptors and Igf binding proteins in marine versus freshwater stickleback: Evidence of selection in known and novel genes
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Tim Pellissier, Hend Al Nafea, Sara V. Good Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations. Next, we analysed genome-wide transcriptome data from eight tissues to assess differential gene expression. Two Igfbp's (Igfbp2a and Igfbp5a) show evidence of divergent adaptation between life-history types, and a cluster of nonsynonymous mutations in Igfbp5a exhibit high Fst in exons apparently alternatively spliced in gill. We find evidence of selection on the relaxin family ligand-receptor gene pair, Insl3-Rxfp2, known to be involved in male spermatogenesis and bone metabolism, and in the 5
March 2018
Effect of abiotic and biotic stress factors analysis using machine learning methods in zebrafish
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Rajasekar Gutha, Suresh Yarrappagaari, Lavanya Thopireddy, Kesireddy Sathyavelu Reddy, Rajeswara Reddy Saddala In order to understand the mechanisms underlying stress responses, meta-analysis of transcriptome is made to identify differentially expressed genes (DEGs) and their biological, molecular and cellular mechanisms in response to stressors. The present study is aimed at identifying the effect of abiotic and biotic stress factors, and it is found that several stress responsive genes are common for both abiotic and biotic stress factors in zebrafish. The meta-analysis of micro-array studies revealed that almost 4.7% i.e., 108 common DEGs are differentially regulated between abiotic and biotic stresses. This shows that there is a global coordination and fine-tuning of gene regulation in response to these two types of challenges. We also performed dimension reduction methods, principal component analysis, and partial least squares discriminant analysis which are able to segregate abiotic and biotic stresses into separate entities. The supervised machine learning model, recursive-support vector machine, could classify abiotic and biotic stresses with 100% accuracy using a subset of DEGs. Beside these methods, the random forests decision tree model classified five out of 8 stress conditions with high accuracy. Finally, Functional enrichment analysis revealed the different gene ontology terms, transcription factors and miRNAs factors in the regulation of stress responses.
March 2018
Identification and characterization of chemosensory gene families in the bark beetle, Tomicus yunnanensis
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Nai-Yong Liu, Zong-Bo Li, Ning Zhao, Qi-Sheng Song, Jia-Ying Zhu, Bin Yang The bark beetle, Tomicus yunnanensis (Coleoptera: Scolytinae), is a seriously destructive pest of Yunnan pine (Pinus yunnanensis) and is distributed solely in Southwestern China. It has been a challenge to control this pest owing to its resistance to chemical pesticides, which have been used as the main control strategy of this species in recent years. Since this approach will continue until an alternative mitigation strategy is implemented, it is essential to develop novel or improved biocontrol approaches. In the current study, we aimed to identify most, if not all, of the bark beetle's chemosensory genes, and to address their respective phylogenetic relationships and expression characteristics. Digital gene expression (DGE) profiling and a comparison of the profiles at three developmental stages yielded 40,287,265 clean reads and a large number of differentially expressed genes (DEGs), with 21 up- and 20 down-regulated DEGs involved in chemoreception. Transcriptome of the three mixed stages revealed a total of 80 transcripts encoding chemosensory-related proteins comprising 45 odorant-binding proteins (OBPs), 12 chemosensory proteins (CSPs), 20 receptor proteins [9 odorant receptors (ORs), 8 gustatory receptors (GRs) and 3 ionotropic receptors (IRs)] and 3 sensory neuron membrane proteins (SNMPs). As many as 38 full-length sequences were acquired with a combination of transcriptomic analysis and rapid amplification of cDNA ends (RACE) strategy. Phylogenetic analysis showed that T. yunnanensis OBPs were clustered into four sub-groups: 27 Minus-C OBPs, 5 antennal binding proteins (ABPIIs), 10 Classic OBPs and one Plus-C OBP; meanwhile, the ORs were grouped into four clades (1, 2, 7b and Orco). Expression profiles revealed that 66 of 80 genes were detected in the three DGE libraries, and 15 soluble olfactory proteins were antennae-predominant, possibly guiding olfactory-associated behaviors of this beetle. Taken together, our study has provided valuable data for further functional studies of this beetle and will facilitate the identification of potential molecular targets associated with chemosensory reception for use in biocontrol strategies.
March 2018
Physiological and proteomic responses to corticosteroid treatments in Eurasian perch, Perca fluviatilis: Investigation of immune-related parameters
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Sylvain Milla, Sophie Massart, C
December 2017
Comparative analysis of the transcriptome responses of zebrafish embryos after exposure to low concentrations of cadmium, cobalt and copper
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Laura Sonnack, Thorsten Klawonn, Ralf Kriehuber, Henner Hollert, Christoph Sch
December 2017
Editorial Board
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24

December 2017
Transcriptomic analysis of the hepatopancreas induced by eyestalk ablation in shrimp, Litopenaeus vannamei
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Ji-Hyun Lee, Indyaswan T. Suryaningtyas, Tae-Ho Yoon, Jeong Min Shim, Hyun Park, Hyun-Woo Kim Although eyestalk ablation (ESA) is currently considered the most effective method to facilitate molting and maturation, its physiological responses are still not clearly explained in decapod crustaceans. In this study, we analyzed the hepatopancreatic transcriptomes of Litopenaeus vannamei after ESA using the Illumina Miseq platform. After screening 53,029 contigs with high cutoff values (fold change>|10|; P-value<0.05; RPKM>1), we were able to identify 105 differentially expressed genes (DEGs), of which 100 were up-regulated and five were down-regulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that many DEGs were involved in the synthetic pathways for glycerol and trehalose, which are known to function as the major protectants under conditions of low temperature and osmotic stress in arthropods. Additional analysis of the other DEGs enabled us to classify them in four categories: immunity; cellular trafficking; transcriptional regulation; molting and maturation. Many DEGs were involved in immunity and stress responses, in particular the proPO activation system, which is the major immune and wound-healing system in arthropods. In addition to immunity and stress responses, we were also able to identify DEGs involved in molting and maturation processes (e.g., group I chitinase), as well as those involved in hormone metabolism and trafficking. Collectively, based on the transcriptomic analysis, ESA causes not only stress and immune responses, but also molting and maturation in L. vannamei. The DEGs identified in this study could be useful markers to understand the physiological responses that ESA induces in shrimp, such as molting, maturation, and immunity.
December 2017
Identification and comparison of candidate odorant receptor genes in the olfactory and non-olfactory organs of Holotrichia oblita Faldermann by transcriptome analysis
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Kebin Li, Hongshuang Wei, Changlong Shu, Shuai Zhang, Yazhong Cao, Chen Luo, Jiao Yin A sophisticated olfactory system is part of the explanation for the prominence of insects among animals because of the essential roles of the olfactory system in foraging, host seeking, mating, ovipositing and avoiding toxic substances. In this study, we sequenced and analysed the transcriptomes of olfactory tissue (antennae) and non-olfactory tissue (legs) of the scarab beetle, Holotrichia oblita Faldermann, which is a serious underground pest in China. We obtained approximately 80.2 million 150bp reads that were assembled into 61,038 unigenes with an average length of 890bp. Among the transcripts, 70% of the unigenes were annotated. A total of 44 odorant receptors (ORs) and 9 ionotropic receptors (IRs) were identified based on homology searches. Then, quantitative real-time PCR experiments were performed to investigate the expression patterns of 32 putative chemosensory genes. The results showed that these genes were highly expressed in olfactory organs (antennae) and might play a key role in the olfaction-related behaviours in H. oblita. Based on the results of our phylogenetic analysis and the detailed tissue and sex-biased expression characteristics, the different roles of the receptor proteins in the olfactory system were also indicated. The results of this study will provide the foundation for further understanding of the olfactory odorant receptors of H. oblita at the molecular level and ultimately help to develop novel targets for manipulating this pest.
December 2017
Digital gene expression analysis of Takifugu rubripes brain after acute hypoxia exposure using next-generation sequencing
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Jie-Lan Jiang, Ming-Guang Mao, Hui-Qian L
December 2017
Global gene expression analysis of the muscle tissues of medaka acclimated to low and high environmental temperatures
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Daisuke Ikeda, Hiroki Koyama, Nanami Mizusawa, Nobuhiro Kan-no, Engkong Tan, Shuichi Asakawa, Shugo Watabe Medaka (Oryzias latipes) is a temperate eurythermal fish that is able to survive over a wide range of water temperatures ranging from near zero to over 30°C throughout the year; it maintains its normal physiological and biochemical processes through temperature acclimation. To determine the mechanisms involved in temperature acclimation of fish, the fast skeletal muscle tissues of medaka underwent global gene expression analysis using next-generation sequencing. Ten individuals were placed into two aquariums at 24°C. While the water temperature of one aquarium was decreased to 10°C, that of the other aquarium was increased to 30°C; these temperatures were subsequently maintained for 5weeks. RNA sequencing (RNA-Seq) analyses revealed that 11 genes involved in energy metabolism and muscle atrophy were significantly highly expressed in the 10°C-acclimated fish. Meanwhile, significantly higher expression levels were observed for 20 genes encoding myofibrillar proteins and heat shock proteins in the 30°C-acclimated fish. Moreover, 1103 genes had at least fourfold differential expression between the acclimation groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses provided important information: although the expression of genes related to metabolic processes were activated, muscle atrophy occurred in the 10°C-acclimated fish, and muscle cells divided actively in the 30°C-acclimated fish and avoided thermal stress by expressing heat shock proteins. Therefore, RNA-Seq analyses with the available genome database will be useful for better understanding the molecular mechanisms involved in the temperature acclimation of fish.
December 2017
Concentration dependent transcriptome responses of zebrafish embryos after exposure to cadmium, cobalt and copper
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Laura Sonnack, Thorsten Klawonn, Ralf Kriehuber, Henner Hollert, Christoph Sch
December 2017
Profiles of soluble proteins in chemosensory organs of three members of the afro-tropical Anopheles gambiae complex
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Immacolata Iovinella, Beniamino Caputo, Maria Calzetta, Laurence J. Zwiebel, Francesca Romana Dani, Alessandra della Torre In female mosquitoes, host-seeking and preference as well as several other important behaviors are largely driven by olfaction. Species of the Afrotropical Anopheles gambiae complex display divergent host-preference that are associated with significant differences in their vectorial capacity for human malaria. Olfactory sensitivity begins with signal transduction and activation of peripheral sensory neurons that populate the antennae, maxillary palps and other appendages. We have used shotgun proteomics to characterize the profile of soluble proteins of antennae and maxillary palps of three different species: An. coluzzii, An. arabiensis and An. quadriannulatus that display remarkable differences in anthropophilic behavior. This analysis revealed interspecific differences in the abundance of several proteins that comprise cuticular components, glutathione S-transferase and odorant binding proteins, the latter of which known to be directly involved in odor recognition.
December 2017
De novo assembly and characterization of seabass Lateolabrax japonicus transcriptome and expression of hepatic genes following different dietary phosphorus/calcium levels
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Kang-Le Lu, Zhong-Li Ji, Samad Rahimnejad, Chun-Xiao Zhang, Ling Wang, Kai Song Fish farming seriously influences the aquatic environment because most dietary phosphorus (P) is excreted in the effluent. To increase the P utilization in fish, molecular techniques should be explored given the remarkable development of these techniques. Thus, to identify the candidate genes related to P utilization and molecular alterations following administration of a P-deficient diet in seabass Lateolabrax japonicus, we assessed the de novo pituitary, gill, intestine, liver, kidney, scales and vertebra transcriptomes, and we compared the expression of hepatic genes with three diets varying in P and Ca levels: diet I (0.4% P, 0.3% Ca), diet II (0.8% P, 0.3% Ca), and diet III (0.8% P, 3% Ca). In total, we identified 99,392 unigenes, and 37,086 (37.31%) unigenes were annotated. The results showed that 48 unigenes were significantly (P <0.05) up-regulated, while 55 genes were significantly down-regulated in the liver of group I compared with group II. Offering the P-sufficient and high Ca diet, diet III significantly up-regulated 24 unigenes and down-regulated 46 genes in the liver. There were significant differences in the regulation of 8 unigenes (3 up-regulated and 5 down-regulated) between groups II and III. Gene ontology (GO) functional enrichment and KEGG pathway analysis of differently expressed genes were performed for each pair of groups. The GO analysis showed that a large number of biological processes were significantly altered between P-deficient and P-sufficient treatments (I vs II and I vs III). Comparing group I and group II, seven KEGG terms were enriched significantly: glycine, serine and threonine metabolism, one carbon pool by folate, arginine and proline metabolism, the biosynthesis of unsaturated fatty acids, fatty acid elongation, drug metabolism-cytochrome P450, and fatty acid metabolism. There was no significantly enriched KEGG pathway between groups II and III. In conclusion, our study revealed that a P-deficient diet could increase catabolism and decrease anabolism of protein, as highlighted by low protein efficiency in fish fed the P-deficient diet. Furthermore, P-deficiency could motivate the biosynthesis of fatty acids. However, the dietary Ca level had no significant effect on the growth and expression of hepatic genes in L. japonicus.
December 2017
Preliminary profiling of microRNA in the normal and regenerating liver of Chiloscyllium plagiosum
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Dandan Cheng, Yanna Chen, Conger Lu, Yuezhong Qian, Zhengbing Lv Liver is a vital organ present in animals for detoxification, protein synthesis, digestion and other functions and its powerful regenerative capacity is well known. C. plagiosum is an abundant fish that is representative of the cartilaginous class in the southeast coastal region of China and its liver accounts for >70% of the fish's visceral weight and contains many bioactive substances. MicroRNAs (microRNAs) play important roles in a wide range of biological processes in eukaryotes, including cell proliferation, differentiation, apoptosis. However, microRNAs in response to liver regeneration has not been well studied. This study aimed to identify the microRNAs that participate in liver regeneration and other liver-related diseases and to improve our understanding of the mechanisms of liver regeneration in sharks. To this end, normal and regenerating liver tissues from C. plagiosum were harvested 0, 3, 6, 12 and 24h after partial hepatectomy (pH) and were sequenced using the Illumina/Solexa platform. In total, 309 known microRNAs and 590 novel microRNAs were identified in C. plagiosum. There were many microRNAs differentially expressed in the normal and regenerating livers between time points. Using target prediction and GO analysis, most of the differentially expressed microRNAs were assigned to functional categories that may be involved in regulating liver regeneration, such as cell proliferation, differentiation and apoptosis. The microRNA expression profile of liver regeneration will pave the way for the development of effective strategies to fight against liver disease and other related disease.
December 2017
Transcriptome sequencing reveals potential mechanisms of diapause preparation in bivoltine silkworm Bombyx mori (Lepidoptera: Bombycidae)
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Yan-rong Chen, Tao Jiang, Juan Zhu, Yu-chen Xie, Zhi-cheng Tan, Yan-hua Chen, Shun-ming Tang, Bi-fang Hao, Sheng-peng Wang, Jin-shan Huang, Xing-jia Shen In the bivoltine strain of the silkworm, Bombyx mori, embryonic diapause is induced transgenerationally as a maternal effect. Progeny diapause ability is determined by the environmental condition such as temperature and lightness that mothers experience during their own embryonic development. Diapause preparation is a crucial phase of this process; diapause-destined individuals undergo a series of preparatory events before the entry into developmental arrest. However, the molecular regulatory mechanisms of diapause preparation have largely remained unknown. In the present study, we sequenced the transcriptome of bivoltine silkworm Qiufeng's ovaries resulted in laying of diapause destined or non-diapause eggs, using high-throughput RNA-Seq technology. Differential expression analyses identified 183 genes with higher expression, and 106 with lower expression under diapause-inducing conditions. GO and KEGG analysis revealed that the enrichment of several functional terms related to peroxisome, glycerolipid metabolism, steroid biosynthesis, longevity regulating pathway - multiple species, three signaling transductions, insect hormone biosynthesis, and cytoskeleton components. We conducted a detailed comparison of transcript profile data of ovaries from diapause-inducing and non-diapause conditions, the results imply up-regulation of peroxisomal metabolism, triacylglycerides accumulation, cryoprotectant production, and ecdysteroid biosynthesis in diapause-inducing group. Differential expression of genes related to actin cytoskeleton implies the occurrence of shifts in cellular structure and composition between diapause-inducing and non-diapause-inducing groups. The Hippo and FOXO signaling pathways may play an important role in preparing for entering diapause. This study provides an insight into the molecular events of insect diapause, in particular for the preparatory phase.
December 2017
Comparative transcriptome analysis of fast twitch muscle and slow twitch muscle in Takifugu rubripes
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Kailun Gao, Zhicheng Wang, Xiaoxu Zhou, Haoze Wang, Derong Kong, Chen Jiang, Xiuli Wang, Zhiqiang Jiang, Xuemei Qiu Fast twitch muscle and slow twitch muscle are two important organs of Takifugu rubripes. Both tissues are of ectodermic origin, and the differences between the two muscle fibers reflect the differences in their myofibril protein composition and molecular structure. In order to identify and characterize the gene expression profile in the two muscle fibers of T. rubripes, we generated 54 million and 44 million clean reads from the fast twitch muscle and slow twitch muscle, respectively, using RNA-Seq and identified a total of 580 fast-muscle-specific genes, 1533 slow-muscle-specific genes and 11,806 genes expressed by both muscles. Comparative transcriptome analysis of fast and slow twitch muscles allowed the identification of 1508 differentially expressed genes, of which 34 myosin and 30 ubiquitin family genes were determined. These differentially expressed genes (DEGs) were also analyzed by Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. In addition, alternative splicing analysis was also performed. The generation of larger-scale transcriptomic data presented in this work would enrich the genetic resources of Takifugu rubripes, which could be valuable to comparative studies of muscles.
December 2017
Genome-wide characterization of Toll-like receptor gene family in common carp (Cyprinus carpio) and their involvement in host immune response to Aeromonas hydrophila infection
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Yiwen Gong, Shuaisheng Feng, Shangqi Li, Yan Zhang, Zixia Zhao, Mou Hu, Peng Xu, Yanliang Jiang The Toll-like receptor (TLR) gene family is a class of conserved pattern recognition receptors, which play an essential role in innate immunity providing efficient defense against invading microbial pathogens. Although TLRs have been extensively characterized in both invertebrates and vertebrates, a comprehensive analysis of TLRs in common carp is lacking. In the present study, we have conducted the first genome-wide systematic analysis of common carp (Cyprinus carpio) TLR genes. A set of 27 common carp TLR genes were identified and characterized. Sequence similarity analysis, functional domain prediction and phylogenetic analysis supported their annotation and orthologies. By examining the gene copy number of TLR genes across several vertebrates, gene duplications and losses were observed. The expression patterns of TLR genes were examined during early developmental stages and in various healthy tissues, and the results showed that TLR genes were ubiquitously expressed, indicating a likely role in maintaining homeostasis. Moreover, the differential expression of TLRs was examined after Aeromons hydrophila infection, and showed that most TLR genes were induced, with diverse patterns. TLR1, TLR4-2, TLR4-3, TLR22-2, TLR22-3 were significantly up-regulated at minimum one timepoint, whereas TLR2-1, TLR4-1, TLR7-1 and TLR7-2 were significantly down-regulated. Our results suggested that TLR genes play critical roles in the common carp immune response. Collectively, our findings provide fundamental genomic resources for future studies on fish disease management and disease-resistance selective breeding strategy development.
December 2017
RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis)
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): V
December 2017
NMR-based untargeted metabolomic study of hydrogen peroxide-induced development and diapause termination in brine shrimp
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Ming-Chang Hong, Shangwu Ding, Cheng-Chi Lin, Tah-Wei Chu, Kuo-Hsun Chiu Artemia diapause has been extensively studied in embryonic biology for a long time. It has been demonstrated that hydrogen peroxide (H2O2) can increase the hatching rate in the development and diapause termination of Artemia cysts. This study used an untargeted 1H NMR-based metabolomic approach to explore the physiological regulation of H2O2 in initiating the development and terminating the diapause of Artemia cysts. This experiment was divided into two parts. In the first part, we analyzed three groups with or without H2O2 as control-0h, control-5h and H2O2 (180
December 2017
Identification of differentially expressed reproductive and metabolic proteins in the female abalone (Haliotis laevigata) gonad following artificial induction of spawning
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Omar Mendoza-Porras, Natasha A. Botwright, Antonio Reverter, Mathew T. Cook, James O. Harris, Gene Wijffels, Michelle L. Colgrave Inefficient control of temperate abalone spawning prevents pair-wise breeding and production of abalone with highly marketable traits. Traditionally, abalone farmers have used a combination of UV irradiation and application of temperature gradients to the tank water to artificially induce spawning. Proteins are known to regulate crucial processes such as respiration, muscle contraction, feeding, growth and reproduction. Spawning as a pre-requisite of abalone reproduction is likely to be regulated, in part, by endogenous proteins. A first step in elucidating the mechanisms that regulate spawning is to identify which proteins are directly involved during spawning. The present study examined protein expression following traditional spawning induction in the Haliotis laevigata female. Gonads were collected from abalone in the following physiological states: (1) spawning; (2) post-spawning; and (3) failed-to-spawn. Differential protein abundance was initially assessed using two-dimensional difference in-gel electrophoresis coupled with mass spectrometry for protein identification. A number of reproductive proteins such as vitellogenin, vitelline envelope zona pellucida domain 29 and prohibitin, and metabolic proteins such as thioredoxin peroxidase, superoxide dismutase and heat shock proteins were identified. Differences in protein abundance levels between physiological states were further assessed using scheduled multiple reaction monitoring mass spectrometry. Positive associations were observed between the abundance of specific proteins, such as heat shock cognate 70 and peroxiredoxin 6, and the propensity or failure to spawn in abalone. These findings have contributed to better understand both the effects of oxidative and heat stress over abalone physiology and their influence on abalone spawning.
September 2017
Odorant-binding and chemosensory proteins identified in the antennal transcriptome of Adelphocoris suturalis Jakovlev
Publication date: December 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 24 Author(s): Huan-Huan Cui, Shao-Hua Gu, Xiao-Qiang Zhu, Yu Wei, Hang-Wei Liu, Hussain Dhiloo Khalid, Yu-Yuan Guo, Yong-Jun Zhang Adelphocoris suturalis Jakovlev (Hemiptera: Miridae) is an insect pest that causes severe agricultural damage to cotton and many other important crops. In insects, olfaction is very important throughout their lifetime. There are two groups of small soluble proteins, named odorant binding proteins (OBPs) and chemosensory proteins (CSPs), which are suggested to participate in the initial biochemical recognition steps of insect olfactory signal transduction. In this study, a total of 16 OBPs (12 classical OBPs and 4 plus-C OBPs) and 8 CSPs, were identified in the antennal transcriptome of A. suturalis. The sex- and tissue-specific profiles of these binding protein genes showed that 13 of the 16 OBP transcripts were highly expressed in the antennae of both sexes, and 4 OBPs (AsutOBP1, 4, 5 and 9) were expressed higher in the male antennae compared to the female antennae. Three CSPs (AsutCSP1, 4 and 5) were expressed specifically in the antennae of both sexes, and AsutCSP1 was expressed higher in the male antennae than in the female antennae. Our findings identify several novel OBP and CSP genes for further investigation of the olfactory system of A. suturalis at the molecular level.
September 2017
Editorial Board
Publication date: September 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 23

September 2017
Identification of 28 cytochrome P450 genes from the transcriptome of the marine rotifer Brachionus plicatilis and analysis of their expression
Publication date: September 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 23 Author(s): Hui-Su Kim, Jeonghoon Han, Hee-Jin Kim, Atsushi Hagiwara, Jae-Seong Lee Whole transcriptomes of the rotifer Brachionus plicatilis were analyzed using an Illumina sequencer. De novo assembly was performed with 49,122,780 raw reads using Trinity software. Among the assembled 42,820 contigs, 27,437 putative open reading frame contigs were identified (average length 1235bp; N50=1707bp). Functional gene annotation with Gene Ontology and InterProScan, in addition to Kyoto Encyclopedia of Genes and Genomes pathway analysis, highlighted the metabolism of xenobiotics by cytochrome P450 (CYP). In addition, 28 CYP genes were identified, and their transcriptional responses to benzo[
September 2017
Exposure to Deepwater Horizon oil and Corexit 9500 at low concentrations induces transcriptional changes and alters immune transcriptional pathways in sheepshead minnows
Publication date: September 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 23 Author(s): Elizabeth R. Jones, Christopher J. Martyniuk, Jeffrey M. Morris, Michelle O. Krasnec, Robert J. Griffitt The 2010 Deepwater Horizon (DWH) oil spill caused the release of 4.9 million barrels of crude oil into the Gulf of Mexico, followed by the application of 2.9 million L of the dispersant, Corexit™ to mitigate the spread of oil. The spill resulted in substantial shoreline oiling, potentially exposing coastal organisms to polyaromatic hydrocarbon (PAH) and dispersant contaminants. To investigate molecular effects in fish following exposure to environmentally relevant concentrations of DWH oil and dispersants, we exposed adult sheepshead minnows (Cyprinodon variegatus) to two concentrations of high-energy water-accommodated fraction (HEWAF), chemically enhanced water-accommodated fraction (CEWAF) or Corexit 9500™ for 7 and 14days. Resulting changes in hepatic gene expression were measured using 8
September 2017
IBT-based quantitative proteomics identifies potential regulatory proteins involved in pigmentation of purple sea cucumber, Apostichopus japonicus
Publication date: September 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 23 Author(s): Lili Xing, Lina Sun, Shilin Liu, Xiaoni Li, Libin Zhang, Hongsheng Yang Sea cucumbers are an important economic species and exhibit high yield value among aquaculture animals. Purple sea cucumbers are very rare and beautiful and have stable hereditary patterns. In this study, isobaric tags (IBT) were first used to reveal the molecular mechanism of pigmentation in the body wall of the purple sea cucumber. We analyzed the proteomes of purple sea cucumber in early pigmentation stage (Pa), mid pigmentation stage (Pb) and late pigmentation stage (Pc), resulting in the identification of 5580 proteins, including 1099 differentially expressed proteins in Pb: Pa and 339 differentially expressed proteins in Pc: Pb. GO and KEGG analyses revealed possible differentially expressed proteins, including“melanogenesis”, “melanosome”, “melanoma”, “pigment-biosynthetic process”, “Epidermis development”, “Ras-signaling pathway”, “Wnt-signaling pathway”, “response to UV light”, and “tyrosine metabolism”, involved in pigment synthesis and regulation in purple sea cucumbers. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying pigmentation in sea cucumbers. Furthermore, these results may also provide the base for further identification of proteins involved in resistance mechanisms against melanoma, albinism, UV damage, and other diseases in sea cucumbers.
September 2017
De novo transcriptome sequencing and comparative analysis to discover genes involved in ovarian maturity in Strongylocentrotus nudus
Publication date: September 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 23 Author(s): Zhiying Jia, Qiai Wang, Kaikai Wu, Zhenlin Wei, Zunchun Zhou, Xiaolin Liu Strongylocentrotus nudus is an edible sea urchin, mainly harvested in China. Correlation studies indicated that S. nudus with larger diameter have a prolonged marketing time and better palatability owing to their precocious gonads and extended maturation process. However, the molecular mechanism underlying this phenomenon is still unknown. Here, transcriptome sequencing was applied to study the ovaries of adult S. nudus with different shell diameters to explore the possible mechanism. In this study, four independent cDNA libraries were constructed, including two from the big size urchins and two from the small ones using a HiSeq™2500 platform. A total of 88,581 unigenes were acquired with a mean length of 1354bp, of which 66,331 (74.88%) unigenes could be annotated using six major publicly available databases. Comparative analysis revealed that 353 unigenes were differentially expressed (with log2(ratio)
September 2017
Dietary cholesterol-induced transcriptome differences in the intestine, hepatopancreas, and muscle of Oriental River prawn Macrobrachium nipponense
Publication date: September 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 23 Author(s): Xizhang Gu, Hongtuo Fu, Shengming Sun, Hui Qiao, Wenyi Zhang, Sufei Jiang, Yiwei Xiong, Shubo Jin, Yongsheng Gong, Yan Wu Cholesterol is an important nutrient for crustaceans. In this study, we performed comparative transcriptome analyses to explore the transcriptome differences in the intestine, hepatopancreas, and muscle of Macrobrachium nipponense fed either a low cholesterol (LC) or high cholesterol (HC) diet (2.8 or 17.1g cholesterol per kg diet). High-throughput RNA-Seq was conducted, resulting in 7.65, 5.88, and 7.59G clean bases from the intestine, hepatopancreas, and muscle of the LC group, respectively, and 7.59, 6.73, and 6.70G clean bases from the same tissues of the HC group. Assembly of clean reads resulted in 230,946 unigenes. The following enriched pathways were identified: xenobiotic and drug metabolism by cytochrome P450; chloroalkane and chloroalkene degradation; metabolic and biosynthetic pathways; fatty acid metabolism and biosynthesis; and immune-related pathways. To the best of our knowledge, this is the first study to describe how functional unigenes and biosynthetic and metabolic pathways are affected by dietary cholesterol in aquatic crustaceans. Thus, these results contribute to our understanding of the molecular mechanisms underlying the cholesterol requirement of crustaceans.
June 2017
Genome-wide identification of 52 cytochrome P450 (CYP) genes in the copepod Tigriopus japonicus and their B[
June 2017
Editorial Board
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22

June 2017
Understanding regulation of microRNAs on intestine regeneration in the sea cucumber Apostichopus japonicus using high-throughput sequencing
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Lina Sun, Jingchun Sun, Xiaoni Li, Libin Zhang, Hongsheng Yang, Qing Wang The sea cucumber, as a member of the Echinodermata, has the capacity to restore damaged organs and body parts, which has always been a key scientific issue. MicroRNAs (miRNAs), a class of short noncoding RNAs, play important roles in regulating gene expression. In the present study, we applied high-throughput sequencing to investigate alterations of miRNA expression in regenerative intestine compared to normal intestine. A total of 73 differentially expressed miRNAs were obtained, including 59 up-regulated miRNAs and 14 down-regulated miRNAs. Among these molecules, Aja-miR-1715-5p, Aja-miR-153, Aja-miR-252a, Aja-miR-153-5p, Aja-miR-252b, Aja-miR-2001, Aja-miR-64d-3p, and Aja-miR-252-5p were differentially expressed over 10-fold at 3days post-evisceration (dpe). Notably, real-time PCR revealed that Aja-miR-1715-5p was up-regulated 1390-fold at 3dpe. Moreover, putative target gene co-expression analyses, gene ontology, and pathway analyses suggest that these miRNAs play important roles in specific cellular events (cell proliferation, migration, and apoptosis), metabolic regulation, and energy redistribution. These results will provide a basis for future studies of miRNA regulation in sea cucumber regeneration.
June 2017
Proteomic analysis of liver tissue from rainbow trout (Oncorhynchus mykiss) under high rearing density after administration of dietary vitamin E and selenium nanoparticles
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Mahdi Naderi, Saeed Keyvanshokooh, Amir Parviz Salati, Alireza Ghaedi The aim of the present study was to investigate the effects of dietary vitamin E (vit E) and selenium nanoparticles (nanoSe) on liver proteome profile of rainbow trout under high density condition. To correlate the proteome modifications with physiological aspects, growth, serum metabolites (cortisol, glucose, lactate, ALT, AST, and ALP), and liver antioxidant-related parameters (SOD, GPx, CAT, and MDA) were also examined. A total of 1275 fish (average weight of 42.6±2.3g) were stocked into 12 tanks at a density of 80kgm
June 2017
Candidate chemosensory genes identified in the endoparasitoid Meteorus pulchricornis (Hymenoptera: Braconidae) by antennal transcriptome analysis
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Sheng Sheng, Cheng-Wu Liao, Yu Zheng, Yu Zhou, Yan Xu, Wen-Miao Song, Peng He, Jian Zhang, Fu-An Wu Meteorus pulchricornis is an endoparasitoid wasp which attacks the larvae of various lepidopteran pests. We present the first antennal transcriptome dataset for M. pulchricornis. A total of 48,845,072 clean reads were obtained and 34,967 unigenes were assembled. Of these, 15,458 unigenes showed a significant similarity (E-value <10
June 2017
Metabolic responses to intestine regeneration in sea cucumbers Apostichopus japonicus
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Lina Sun, Jingchun Sun, Qinzeng Xu, Xiaoni Li, Libin Zhang, Hongsheng Yang Sea cucumbers are excellent models for studying organ regeneration due to their striking capacity to regenerate most of their viscera after evisceration. In this study, we applied NMR-based metabolomics to determine the metabolite changes that occur during the process of intestine regeneration in sea cucumbers. Partial least-squares discriminant analysis showed that there was significant differences in metabolism between regenerative intestines at 3, 7, and 14days post evisceration (dpe) and normal intestines. Changes in the concentration of 13 metabolites related to regeneration were observed and analyzed. These metabolites included leucine, isoleucine, valine, arginine, glutamate, hypotaurine, dimethylamine, N,N-dimethylglycine, betaine, taurine, inosine, homarine, and histidine. Three important genes (betaine-aldehyde dehydrogenase, betaine-homocysteine S-methyltransferase 1, and dimethylglycine dehydrogenase) were differentially expressed to regulate the levels of betaine and N,N-dimethylglycine during intestine regeneration. These results provide an important basis for studying regenerative mechanisms and developing regenerative matrixes.
June 2017
iTRAQ reveals proteomic changes during intestine regeneration in the sea cucumber Apostichopus japonicus
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Lina Sun, Dongxue Xu, Qinzeng Xu, Jingchun Sun, Lili Xing, Libin Zhang, Hongsheng Yang Sea cucumbers have a striking capacity to regenerate most of their viscera after evisceration, which has drawn the interest of many researchers. In this study, the isobaric tag for relative and absolute quantitation (iTRAQ) was utilized to investigate protein abundance changes during intestine regeneration in sea cucumbers. A total of 4073 proteins were identified, and 2321 proteins exhibited significantly differential expressions, with 1100 upregulated and 1221 downregulated proteins. Our results suggest that intestine regeneration constitutes a complex life activity regulated by the cooperation of various biological processes, including cytoskeletal changes, extracellular matrix (ECM) remodeling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism. Additionally, real-time PCR showed mRNA expression of differentially expressed genes correlated positively with their protein levels. Our results provided a basis for studying the regulatory mechanisms associated with sea cucumber regeneration.
June 2017
Comparative RNA-Seq analysis of differentially expressed genes in the testis and ovary of Takifugu rubripes
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Zhicheng Wang, Xuemei Qiu, Derong Kong, Xiaoxu Zhou, Zhongbao Guo, Changfu Gao, Shuai Ma, Weiwei Hao, Zhiqiang Jiang, Shengcong Liu, Tao Zhang, Xuesong Meng, Xiuli Wang Takifugu rubripes is a classical model organism for studying the role of gonad organogenesis in such physiological processes as fertilization, sex determination, and sexual development. To explicitly investigate the mechanism associated with gonad organogenesis in T. rubripes, we obtained 44.3 million and 55.2 million raw reads from the testis and ovary, respectively, by RNA-seq and from these, 18,523 genes were identified. A total of 680 differentially expressed genes were obtained from comparison transcriptome analysis between the testis and ovary, and of these, 556 genes were up-regulated in the testis, whereas only 124 genes were upregulated in the ovary. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many of these genes encode proteins involved in signal transduction and gonad development. We mainly focused on the differentially expressed genes that have the potential to develop into the gonad. The generation of large scale transcriptomic data presented in this work would enrich the genetic resources of T. rubripes, which should be valuable to the comparative and evolutionary studies of teleosts.
June 2017
Gene expression patterns regulating embryogenesis based on the integrated de novo transcriptome assembly of the Japanese flounder
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Yuanshuai Fu, Liang Jia, Zhiyi Shi, Junling Zhang, Wenjuan Li The Japanese flounder (Paralichthys olivaceus) is one of the most important commercial and biological marine fishes. However, the molecular biology involved during embryogenesis and early development of the Japanese flounder remains largely unknown due to a lack of genomic resources. A comprehensive and integrated transcriptome is necessary to study the molecular mechanisms of early development and to allow for the detailed characterization of gene expression patterns during embryogenesis; this approach is critical to understanding the processes that occur prior to mesectoderm formation during early embryonic development. In this study, more than 117.8 million 100bp PE reads were generated from pooled RNA extracted from unfertilized eggs to 41dph (days post-hatching) embryos and were sequenced using Illumina pair-end sequencing technology. In total, 121,513 transcripts (
June 2017
Triploid Atlantic salmon shows similar performance, fatty acid composition and proteome response to diploids during early freshwater rearing
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Waldo G. Nuez-Ort
June 2017
Transcriptome analysis and identification of induced genes in the response of Harmonia axyridis to cold hardiness
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Bin Tang, Xiao-Jun Liu, Zuo-Kun Shi, Qi-Da Shen, Yan-Xia Xu, Su Wang, Fan Zhang, Shi-Gui Wang Harmonia axyridis is an important predatory lady beetle that is a natural enemy of agricultural and forestry pests. In this research, the cold hardiness induced genes and their expression changes in H. axyridis were screened and detected by the way of the transcriptome and qualitative real-time PCR under normal and low temperatures, using high-throughput transcriptome and digital gene-expression-tag technologies. We obtained a 10Gb transcriptome and an 8Mb gene expression tag pool using Illumina deep sequencing technology and RNA-Seq analysis (accession number SRX540102). Of the 46,980 non-redundant unigenes identified, 28,037 (59.7%) were matched to known genes in GenBank, 21,604 (46.0%) in Swiss-Prot, 19,482 (41.5%) in Kyoto Encyclopedia of Genes and Genomes and 13,193 (28.1%) in Gene Ontology databases. Seventy-five percent of the unigene sequences had top matches with gene sequences from Tribolium castaneum. Results indicated that 60 genes regulated the entire cold-acclimation response, and, of these, seven genes were always up-regulated and five genes always down-regulated. Further screening revealed that six cold-resistant genes, E3 ubiquitin-protein ligase, transketolase, trehalase, serine/arginine repetitive matrix protein 2, glycerol kinase and sugar transporter SWEET1-like, play key roles in the response. Expression from a number of the differentially expressed genes was confirmed with quantitative real-time PCR (HaCS_Trans). The paper attempted to identify cold-resistance response genes, and study the potential mechanism by which cold acclimation enhances the insect's cold endurance. Information on these cold-resistance response genes will improve the development of low-temperature storage technology of natural enemy insects for future use in biological control.
June 2017
Oligomeric protein complexes of apolipoproteins stabilize the internal fluid environment of organism in redfins of the Tribolodon genus [Pisces; Cypriniformes, Cyprinidae]
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Alla M. Andreeva, Marina V. Serebryakova, Nina E. Lamash One of the most important functions of plasma proteins in vertebrates is their participation in osmotic homeostasis in the organism. Modern concepts about plasma proteins and their capillary filtration are based on a model of large monomeric proteins that are able to penetrate the interstitial space. At the same time, it was revealed that a considerable amount of oligomeric complexes are present in the low-molecular-weight (LM) protein fraction in the extracellular fluids of fishes. The functions of these complexes are unknown. In the present study, we investigated the LM-fraction proteins in the plasma and interstitial fluid (IF) of redfins of the genus Tribolodon. This fish alternatively spends parts of its life cycle in saline and fresh waters. We identified the protein Wap65, serpins and apolipoproteins in this fraction. By combining the methods of 2D-E under native and denaturing conditions with MALDI, we demonstrated that only apolipoproteins formed complexes. We showed that serum apolipoproteins (ÀðîÀ-I, Àðî-14) were present in the form of homooligomeric complexes that were dissociated with the release of monomeric forms of proteins in the course of capillary filtration to IF. Dissociation of homooligomers is not directly correlated with the change in salinity but is correlated with seasonal dynamics. We found that there was a significant decrease in the total protein concentration in IF relative to plasma. Therefore, we suggested that dissociation of homooligomeric complexes from various apolipoproteins supports the isoosmoticity of extracellular fluids relative to capillary wall stabilization through a fluid medium in fish.
June 2017
Crenomytilus grayanus 40kDa calponin-like protein: cDNA cloning, sequence analysis, tissue expression, and post-translational modifications
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Oleg S. Matusovsky, Anna V. Dobrzhanskaya, Victoria V. Pankova, Konstantin V. Kiselev, Ulyana V. Girich, Nikolay S. Shelud'ko Calponin-like protein (CaP-40), a third major protein after actin and tropomyosin, has recently been identified by us in the Ca2+-regulated thin filaments of mussel Crenomytilus grayanus. It contains calponin homology domain, five calponin family repeats and possesses similar biochemical properties as vertebrate smooth muscle calponin. In this paper, we report a full-length cDNA sequence of CaP-40, study its expression pattern on mRNA and protein levels, evaluate CaP-40 post-translational modifications and perform protein-protein interaction analysis. The full-length sequence of CaP-40 consists of 398 amino acids and has high similarity to calponins among molluscan species. CaP-40 gene is widely expressed in mussel tissues, with the highest expression in adductor and mantle. Comparison of these data with protein content established by mass-spectrometry analysis revealed that the high mRNA content is mirrored by high protein levels for adductor smooth muscles. To provide unbiased insight into the function of CaP-40 and effect of its over-expression in adductor smooth muscle, we built protein-protein interaction network of identified Crenomytilus grayanus proteome. In addition, we showed that CaP-40 is subjected to post-translational N- and C-terminal acetylation at N127, G229 and G349 sites which potentially regulates its function in vivo.
June 2017
DExD/H-box RNA helicase genes are differentially expressed between males and females during the critical period of male sex differentiation in channel catfish
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Changxu Tian, Suxu Tan, Lisui Bao, Qifan Zeng, Shikai Liu, Yujia Yang, Xiaoxiao Zhong, Zhanjiang Liu DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and syntenic analyses. All the catfish RNA helicases contained conserved helicase signature motifs, demonstrating that the RNA helicase gene family was highly conserved. Analysis of the relative rates of synonymous (dS) and nonsynonymous (dN) substitutions revealed that the RNA helicase genes were subjected to strong negative (purifying) selection. Meta-analysis was conducted to determine expression of the RNA helicase genes during the critical period (90–110days post-fertilization, dpf) of male gonad differentiation. At 90dpf, 24 RNA helicase genes were highly differentially expressed in the gonad tissues between the males and females; similarly, 24 and 18 RNA helicase genes were found highly differentially expressed in the gonad tissues between the males and females at 100 and 110dpf, respectively (p <0.01). In general, the vast majority of the RNA helicase genes (31) were expressed at higher levels in females than in males. In the male gonad, a set of 8 RNA helicases were expressed at a significantly higher level at 110dpf than at 90dpf. These findings suggested that RNA helicases may play important roles in sex development and differentiation in teleosts.
June 2017
De novo analysis of the oriental armyworm Mythimna separata antennal transcriptome and expression patterns of odorant-binding proteins
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Xiang-Qian Chang, Xiao-Pei Nie, Zan Zhang, Fang-Fang Zeng, Liang Lv, Shu Zhang, Man-Qun Wang To better understand the olfactory mechanisms in the oriental armyworm Mythimna separate, one of the most serious pests of cereals, an antennal transcriptome was constructed in this study. A total of 130 olfactory related transcripts were identified. These transcripts were predicted to encode 32 odorant-binding proteins (OBPs), 16 chemosensory proteins (CSPs), 71 olfactory receptors (ORs), 8 ionotropic receptors (IRs), 1 gustatory receptor (GR) and 2 sensory neuron membrane proteins (SNMPs). Q-PCR analysis of the temporal expression profiles of seven OBPs in different tissues indicated that, except for MsepOBP19 which was highly expressed in the wings of 0-day-old adult and MsepOBP20 which was low expressed in all tissues, other tested MsepOBPs were significantly more highly expressed in the antenna than in the head (antenna excluded), thorax, abdomen, legs and wings. The expression levels of MsepOBPs were diverse in different life stages (differed on eclosion days). MsepOBP5 exhibited female-biased expression in 0- and 5-day-old adult, while no gender bias in 1- and 3-day-old adult was detected and similar expression profiles were found for MsepOBP7, 20, 24 and 26. In addition, we found that although the expression of MsepOBP22 was female biased in 0- and 5-day-old adult, in the 3-day-old adult it was male-biased. Our findings established a foundation for future studies of the functions of olfactory proteins in M. separata.
June 2017
Comparative analysis of the liver transcriptome of Pelteobagrus vachellii with an alternative feeding time
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Chuanjie Qin, Quan Gong, Zhengyong Wen, Yuanchao Zou, Dengyue Yuan, Ting Shao, Huatao Li Pelteobagrus vachellii, an important freshwater fish in China, shows predominantly nocturnal behavior. To better understand the growth and molecular mechanisms underlying altered feeding times in this species, we studied the growth and liver transcriptome of P. vachellii with shifted feeding times. In this study, a 9-week growth trial was conducted on male P. vachellii (mean weight±S.E.=1.05±0.36g) with commercial feed. Two triplicate groups of fish were fed either at 0800 (day group, control) or at 2000 (night group) with the same amount of feed. After nine weeks, a significant increase in growth was observed in the night group, demonstrated by the specific growth rate (SGR). Using high-throughput RNA-seq, 70,793,844 and 67,930,610 paired-end clean reads were obtained from six cDNA libraries of P. vachellii liver, and 60,069 unigenes were assembled. Gene expression comparison revealed that 122 genes were significantly up-regulated and 59 genes were significantly down-regulated in the night group. Gene pathway and GO enrichment analyses revealed metabolic responses of genes and gene networks related to protein, lipid and carbohydrate metabolism and rhythms. This study indicates that an alternative feeding time can improve growth and create metabolic alterations in the liver of P. vachellii.

Metamorphosis and transition between developmental stages in European eel (Anguilla anguilla, L.) involve epigenetic changes in DNA methylation patterns
Publication date: June 2017
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 22 Author(s): Jochen H. Trautner, Stefan Reiser, Tina Blancke, Katrin Unger, Klaus Wysujack The life history of the European eel (Anguilla anguilla, L.) is characterized by a series of metamorphoses and transitions that provoke drastic morphological changes. Most of these changes go along with the catadromous life cycle in eels, involving extensive physiologically adaptations. In this study it was investigated whether these drastic changes have an epigenetic basis by analyzing global methylation patterns in liver, gill and brain tissue from glass eels caught at the British coast as well as yellow and silver eels from River Rhine using methylation-sensitive amplified polymorphisms (MSAP). Analysis of molecular variance (AMOVA) on MSAP data derived from liver tissue revealed only minor differences in methylation patterns between glass, yellow and silver eels, reflecting uniform functioning of the liver throughout the investigated lifespan. In brain and gill tissue, however, marked differences in methylation patterns were found. Principal coordinates analysis (PCoA) revealed yellow eels being partially clustered with silver eels and a more distinct cluster of glass eels based on the methylation patterns in the brain. According to results found in the gills, glass eels were more similar to silver eels whereas yellow eels were found to be clustered separately. From these results it can be concluded that epigenetic changes in gill tissue most likely reflect and are linked with adaptation towards salt- and freshwater conditions. The observed differences in brain methylation patterns, however, might be linked to morphological and physiological changes during metamorphosis and transitions within the life history of European eels potentially affecting subsequent differential gene expression patterns required for such changes.
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