Journal Sciences News
The Kaohsiung Journal of Medical Sciences
June 2018
De novo transcriptome of the pallial gland of the date mussel (Lithophaga lithophaga)
Publication date: June 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 26 Author(s): Ur
June 2018
iTRAQ-based proteomic analysis identifies proteins involved in limb regeneration of swimming crab Portunus trituberculatus
Publication date: June 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 26 Author(s): Yuanyuan Fu, Fang Zhu, Lei Liu, Shaokun Lu, Zhiming Ren, Changkao Mu, Ronghua Li, Weiwei Song, Ce Shi, Yangfang Ye, Chunlin Wang The swimming crab (Portunus trituberculatus) has a striking capacity for limb regeneration, which has drawn the interest of many researchers. In this study, isobaric tag for relative and absolute quantitation (iTRAQ) approach was utilised to investigate protein abundance changes during limb regeneration in this species. A total of 1830 proteins were identified, of which 181 were significantly differentially expressed, with 94 upregulated and 87 downregulated. Our results highlight the complexity of limb regeneration and its regulation through cooperation of various biological processes including cytoskeletal changes, extracellular matrix (ECM) remodelling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism. Additionally, real-time PCR confirmed that mRNA levels of differentially expressed genes were correlated with protein levels. Our results provide a basis for studying the regulatory mechanisms associated with crab limb regeneration.
June 2018
Proteomic analysis reveals the distinct energy and protein metabolism characteristics involved in myofiber type conversion and resistance of atrophy in the extensor digitorum longus muscle of hibernating Daurian ground squirrels
Publication date: June 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 26 Author(s): Hui Chang, Shanfeng Jiang, Xiufeng Ma, Xin Peng, Jie Zhang, Zhe Wang, Shenhui Xu, Huiping Wang, Yunfang Gao Previous hibernation studies demonstrated that such a natural model of skeletal muscle disuse causes limited muscle atrophy and a significant fast-to-slow fiber type shift. However, the underlying mechanism as defined in a large-scale analysis remains unclarified. Isobaric tags for relative and absolute quantification (iTRAQ) based quantitative analysis were used to examine proteomic changes in the fast extensor digitorum longus muscles (EDL) of Daurian ground squirrels (Spermophilus dauricus). Although the wet weights and fiber cross-sectional area of the EDL muscle showed no significant decrease, the percentage of slow type fiber was 61% greater (P
June 2018
Baseline levels of metabolites in different tissues of mussel Mytilus galloprovincialis (Bivalvia: Mytilidae)
Publication date: June 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 26 Author(s): Tiziana Cappello, Alessia Giannetto, Vincenzo Parrino, Maria Maisano, Sabrina Oliva, Giuseppe De Marco, Giulia Guerriero, Angela Mauceri, Salvatore Fasulo The Mediterranean mussel Mytilus galloprovincialis (Lamarck 1819) is a popular shellfish commonly included in human diet and is routinely used as bioindicator in environmental monitoring programmes worldwide. Recently, metabolomics has emerged as a powerful tool both in food research and ecotoxicology for monitoring mussels' freshness and assessing the effects of environmental changes. However, there is still a paucity of data on complete metabolic baseline of mussel tissues. To mitigate this knowledge gap, similarities and differences in metabolite profile of digestive gland (DG), gills (G), and posterior adductor muscle (PAM) of aquaculture-farmed M. galloprovincialis were herein investigated by a proton nuclear magnetic resonance (1H NMR)-based metabolomic approach and discussed considering their physiological role. A total of 44 metabolites were identified in mussel tissues and grouped in amino acids, energy metabolites, osmolytes, neurotransmitters, nucleotides, alkaloids, and miscellaneous metabolites. A PCA showed that mussel tissues clustered separately from each other, suggesting a clear differentiation in their metabolic profiles. A Venn diagram revealed that mussel DG, G and PAM shared 27 (61.36%) common metabolites, though with different concentrations. Osmolytes were found to dominate the metabolome of all tissues. The DG exhibited higher level of glutathione and carbohydrates. The G showed greater level of osmolytes and the exclusive presence of neurotransmitters, namely acetylcholine and serotonin. In PAM higher levels of energetics-related metabolites were found. Overall, findings from this study are helpful for a better understanding of mussel tissue-specific physiological functions as well as for future NMR-based metabolomic investigations of marine mussel health and safety.
June 2018
Transcriptome-wide analysis of differential gene expression in response to light:dark cycles in a model cnidarian
Publication date: June 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 26 Author(s): W.B. Leach, J. Macrander, R. Peres, A.M. Reitzel Animals respond to diurnal shifts in their environment with a combination of behavioral, physiological, and molecular changes to synchronize with regularly-timed external cues. Reproduction, movement, and metabolism in cnidarians have all been shown to be regulated by diurnal lighting, but the molecular mechanisms that may be responsible for these phenotypes remain largely unknown. The starlet sea anemone, Nematostella vectensis, has oscillating patterns of locomotion and respiration, as well as the molecular components of a putative circadian clock that may provide a mechanism for these light-induced responses. Here, we compare transcriptomic responses of N. vectensis when cultured under a diurnal lighting condition (12
June 2018
iTRAQ-based quantitative proteomic analysis of the androgenic glands of the oriental river prawn, Macrobrachium nipponense, during nonreproductive and reproductive seasons
Publication date: June 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 26 Author(s): Shubo Jin, Hongtuo Fu, Shengming Sun, Sufei Jiang, Yiwei Xiong, Yongsheng Gong, Hui Qiao, Wenyi Zhang, Yan Wu The androgenic gland produces hormones that play crucial roles in driving male sexual development. In this study, we investigated the regulatory proteins and pathways affecting male sexual development of M. nipponense, by analyzing the proteomes of their androgenic glands during their reproductive and nonreproductive seasons using isobaric tags for relative and absolute quantitation (iTRAQ). A total of 13 sex-related protein homologs out of 999 total proteins were identified in the proteome of M. nipponense based on comparisons with the published literature. A total of 32 proteins were differentially expressed in the androgenic gland between the reproductive and nonreproductive seasons of M. nipponense. However, only 10 differentially expressed proteins (DEPs) were annotated in the Nr, COG, GO, and KEGG databases. Other non-annotated DEPs may also play vital roles in the male sexual development of M. nipponense. The qPCR analysis indicated that the mRNA expression patterns of the 10 annotated DEPs were consistent with that determined by iTRAQ analysis. Additional qPCR analysis of the 10 DEPs in testes, ovaries, and androgenic glands showed that Gem, Ferritin, and Rev3 were highly expressed in the androgenic gland, implying importance in male sexual development, given the important role of the androgenic gland in male differentiation and development in many crustacean species. Our study provided valuable information about DEPs in androgenic glands between reproductive and nonreproductive seasons for M. nipponense and identified their potential roles in male sexual development, which will improve our understanding of the development process in both M. nipponense and other crustaceans.
Available online 14 April 2018
Identification and evolution of olfactory genes in the small poplar longhorn beetle Saperda populnea
Publication date: June 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 26 Author(s): Yinliang Wang, Jian Zhang, Qi Chen, Hanbo Zhao, Jiatong Wang, Ming Wen, Jinghui Xi, Bingzhong Ren Saperda populnea is a serious pest of poplar and willow trees in the Palaearctic region, causing extensive damage to forests and the lumber industry. Until recently, there is no safe and effective chemical method to control this pest due to the lack of sufficient knowledge on the molecular basis of its olfactory genes, moreover, the evolutionary history of the olfactory gene family in subfamily Lamiinae is still fully unknown. Our RNA sequencing of the antennae of S. populnea identified 43 odorant binding proteins (OBPs), 15 chemosensory proteins (CSPs), 56 odorant receptors (ORs) and 24 inotropic receptors (IRs) in S. populnea. The RT-PCR results showed several genes were expressed in a sex specific manner, suggesting that these genes might play key role in their olfactory-sensing and sex-related behaviors. Further evolutionary studies were performed on these olfactory genes, overall comparison of the Ka/Ks values of orthologous genes in S. populnea and two other Lamiinae species showed three main conclusions: 1. olfactory genes have evolved more rapidly than the non-olfactory genes in the tested long horn beetles; 2. the IR gene family are under a strong purifying selection; 3. the OBPs of Monochamus alternatus evolved more rapidly than the other two species, which is speculated to be correlated with differentiation of selective pressure in different geographic origins. Detailed evolutionary studies on each olfactory genes showed that several OBPs and ORs are under significantly purifying/relaxed selective pressure, and several positive selection sites were also detected, modeling of SpopOR14 and SpopOBP4/5 showed that most of the positive selection sites were distributed at the N-terminus of SpopOR14, while the positive selection sites in SpopOBP4/5 were located in H-bond donors, results suggest that these sites are more likely to be linked with the selectivity of modeled olfactory genes. The research provided a better understanding of the molecular basis and evolutionary history of the olfactory genes in Lamiinae, through elaborating the mechanism whereby amino structural evolution affects specific variants in OBPs and ORs.
Available online 6 March 2018
De novo transcriptome analysis and differentially expressed genes in the ovary and testis of the Japanese mantis shrimp Oratosquilla oratoria by RNA-Seq
Publication date: Available online 14 April 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics Author(s): Hongwei Yan, Xin Cui, Xufang Shen, Lianshun Wang, Linan Jiang, Haiying Liu, Ying Liu, Qi Liu, Chen Jiang The mantis shrimp Oratosquilla oratoria is a widely distributed, commercially important crustacean species. Although its conservation and the development of successful artificial breeding technologies have recently received considerable attention, there are currently no available data regarding the molecular mechanisms in controlling reproduction. In this study, we performed transcriptome sequencing of the testis, ovary, female and male eyestalks and the androgenic gland of O. oratoria, and compared the expression pattern of transcripts from the testis and ovary libraries to identify genes involved in gonadal development. A total of 147,130,937 clean reads were retrieved after removing the adapters in reads and filtering out low-quality data. All the reads were assembled into 94,990 unigenes (23,133 in testis and ovary) with an average length of 783 base pairs (bp) and N50 of 1502 bp. A search of all-unigenes against COG, GO, KEGG, KOG, Pfam, Swiss-Prot and Nr databases resulted in a total of 19,404 annotated unigenes. Comparison of the sequences in the ovary and testis libraries revealed that 1188 unigenes were up-regulated in the ovary and 2732 were up-regulated in the testis. Twenty ovary-up-regulated and 21 testis-up-regulated unigenes were confirmed by quantitative real-time PCR. Additionally, 13,437 simple sequence repeats (SSRs) and 275,799 putative single nucleotide polymorphisms (SNPs) were identified. The important functional genes and pathways identified here provide a valuable dataset for understanding the molecular mechanisms controlling gonad development in O. oratoria, and the numerous (13,437 SSRs and 275,799 SNPs) molecular markers obtained here will provide fundamental basis for functional genomic and population genetic studies of O. oratoria.
March 2018
Genome-wide identification, phylogeny and expressional profile of the Sox gene family in channel catfish (Ictalurus punctatus)
Publication date: Available online 6 March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics Author(s): Shiyong Zhang, Xiaohui Chen, Minghua Wang, Wenyi Zhang, Jianlin Pan, Qin Qin, Liqiang Zhong, Junjie Shao, Mengling Sun, Hucheng Jiang, Wenji Bian The Sox gene family has been systematically characterized in some fish species but not in catfish Ictalurus punctatus. In this study, 25 Sox genes were identified in the channel catfish genome and classified into seven families based on their conserved domains as follows: eight genes in SoxB group (six in SoxB1 subgroup and two in SoxB2 subgroup); five genes in SoxC group; three genes in SoxD and SoxF groups; four genes in SoxE group; and one gene in SoxH and SoxK groups. The mammalian Sox groups SoxA, G, I, and J were not present in catfish. The number of introns in channel catfish Sox genes varied from zero to 13. Sox genes were distributed unevenly across 17 chromosomes. Five members of the ancestral vertebrate Sox genes (Sox1, Sox4, Sox9, Sox11 and Sox19) experienced teleost-specific whole genome duplication during evolution, and now have two copies on different chromosomes. Expression profiles analyses indicated that the accumulation of Sox genes was associated with different tissues, and the expression pattern also differed among each Sox gene group and duplicated gene. This study constitutes a comprehensive overview of the Sox gene family in channel catfish and provides new insights into the evolution of this gene family.
March 2018
Editorial Board
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25

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
March 2018
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
Available online 8 February 2018
Transcriptomic analysis of changes in gene expression of immune proteins of gill tissue in response to low environmental temperature in fathead minnows (Pimephales promelas)
Publication date: March 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 25 Author(s): Simon A. Wentworth, Katrina Thede, Varsha Aravindabose, Ian Monroe, Andrew W. Thompson, Neil Molyneaux, Christopher L. Owen, John R. Burns, Agustin Gonzalez-vicente, Jeffrey L. Garvin, Randall K. Packer In the face of ongoing climate change, it is imperative to understand better the effects of temperature on immune function in freshwater teleosts. It is unclear whether previously observed changes were caused by temperature per se. We studied changes in the gill transcriptome of fathead minnows (Pimephales promelas) at low temperature to understand better the effects of temperature on immune function. De novo assembly of the transcriptome using Trinity software resulted in 73,378 assembled contigs. Annotation using the Trinotate package yielded 58,952 Blastx hits (accessions). Expression of 194 unique mRNA transcripts changed in gill tissue of fathead minnows acclimatized to 5° compared to controls at 22
December 2017
Corrigendum to “De novo assembly and characterization of seabass Lateolabrax japonicus transcriptome and expression of hepatic genes following different dietary phosphorus/calcium levels” [Comp. Biochem. Physiol. D Genomics Proteomics 24 (2017) 51–59]
Publication date: Available online 8 February 2018
Source:Comparative Biochemistry and Physiology Part D: Genomics and Proteomics Author(s): K.L. Lu, Z.L. Ji, S. Rahimnejad, C.X. Zhang, L. Wang, K. Song
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

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
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