Comparative Biochemistry and Physiology Part D: Genomics and Proteomics This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Transcriptome profiling of the low-salinity stress responses in the gills of the juvenile Pseudopleuronectes yokohamae
This study is the first transcriptomic study conducted on marbled flounder, and it revealed many novel sequences for further biological analyses. In addition, the candidate genes identified in the gene expression analysis provided insights into responses to salinity change and molecular mechanisms underlying osmoregulation in the gills of marbled flounder.Graphical abstract (Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics)
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - July 27, 2019 Category: Genetics & Stem Cells Source Type: research

Thermal acclimation and gene expression in rainbow smelt: Changes in the myotomal transcriptome in the cold
Publication date: Available online 20 July 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): D.J. Coughlin, L.K. Nicastro, P.J. Brookes, M.A. Bradley, J.L. Shuman, E.R. Steirer, H.L. MistryAbstractRainbow smelt, Osmerus mordax, have an impressive ability to acclimate to very cold water. Rainbow smelt exposed to cold (<5 °C) for an extended period of time have faster sustained swimming speeds and increased contraction kinetics in their myotomal muscle compared to warm acclimated fish. We used RNA Sequencing reactions (RNA-Seq) to explore how gene expression underlies therma...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - July 21, 2019 Category: Genetics & Stem Cells Source Type: research

Rapid evolution of piRNA pathway and its transposon targets in Japanese flounder (Paralichthys olivaceus)
This study illustrated the evolutionary significance of piRNA pathway via a systematic comparative analysis on diverse teleosts, including flatfish lineages. Molecular evolution of piRNA pathway and microRNA/small interfering RNA pathway genes indicated a faster evolution of piRNA pathway in teleosts than in mammals. Positive selection was detected at the PAZ (Piwi-Argonaute-Zwille) domain involved in Piwi–piRNA interaction, thereby suggesting that the amino acid substitutions were adaptive to their functions in teleost piRNA pathway. Notably, Piwil1 evolved faster in Japanese flounder than in other teleosts, and the piR...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - July 21, 2019 Category: Genetics & Stem Cells Source Type: research

Effects of oxidative stress on sex-specific gene expression in the copepod Tigriopus californicus revealed by single individual RNA-seq
In this study, we used comparative transcriptomic analyses to assess sex-specific transcriptional responses to oxidative stress. Male and female individuals were maintained separately in one of three treatments: 1) control conditions with an algae diet, 2) pro-oxidant (H2O2) conditions with an algae diet or 3) decreased antioxidant conditions (reduced carotenoid due to a yeast diet). Single individual RNA-seq was then conducted for twenty-four libraries using Ligation Mediated RNA sequencing (LM-Seq). Variance in gene expression was partitioned into 62.3% between sexes, 26.85% among individuals and 10.85% among treatments....
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - July 11, 2019 Category: Genetics & Stem Cells Source Type: research

Identification of glutathione-S-transferase genes by transcriptome analysis in Meteorus pulchricornis (Hymenoptera: Braconidae) and their expression patterns under stress of phoxim and cypermethrin
We present the first body transcriptome dataset for M. pulchricornis. In total, 50,781,796 clean reads were obtained and 33,144 unigenes were assembled; 15,458 unigenes showed a significant similarity (E value < 10−5) to known proteins in the NCBI non-redundant protein database. Gene ontology and cluster of orthologous group analyses were performed to classify the functions of genes. To better understand the role of glutathione-S-transferases (GSTs) in detoxification mechanism in M. pulchricornis, we identified seventeen GST genes (MpulGSTs) from the body transcriptome. Among these, fifteen MpulGSTs belonged to c...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - July 10, 2019 Category: Genetics & Stem Cells Source Type: research

Genome-wide identification and expression profiling of odorant-binding proteins in the oriental fruit fly, Bactrocera dorsalis
In this study, we expanded the repository of B. dorsalis OBPs to 49. Phylogenetic analysis of BdorOBPs with other species revealed that these proteins grouped into four subfamilies. Furthermore, we determined the expression profiles in six body parts (namely, the legs, wing, antenna, cuticles of the head, thorax, and abdomen) and five internal tissues (namely, the fat body, midgut, Malpighian tubule, testes, and ovary). The results indicated that 21 BdorOBPs showed high expression levels in the antenna, legs, and head cuticles and may thus perform olfactory functions, which corroborates previous evidence. Two BdorOBPs were...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - July 9, 2019 Category: Genetics & Stem Cells Source Type: research

Identification and characterization of microRNAs in the gonads of Crassostrea hongkongensis using high-throughput sequencing
Publication date: Available online 5 July 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Pinyuan Wei, Pingping He, Xingzhi Zhang, Wei Li, Li Zhang, Junliang Guan, Xiaohan Chen, Yong Lin, Xiaofei Zhuo, Qiongzhen Li, Jinxia PengAbstractCrassostrea hongkongensis is one of the three most-commonly cultivated oyster species in China. Although microRNAs (miRNAs) expression in the gonads have been widely investigated, few studies of miRNAs in mollusk gonads are available, particularly in oyster. In the present study, we analyzed the miRNAs expressed in the ovaries and testes of C. hon...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - July 7, 2019 Category: Genetics & Stem Cells Source Type: research

Transcriptional comparison between pheromone gland-ovipositor and tarsi in the corn earworm moth Helicoverpa zea
In this study, we compared the transcriptome between female pheromone glands (including the ovipositor) and female and male tarsi to identify differences between these tissues, particularly the genes involved in sex pheromone biosynthesis and chemosensation. We found transcripts encoding 11 fatty acyl-CoA desaturases, 20 fatty acyl-CoA reductases, 8 alcohol oxidases, some G protein-coupled receptors and many transcripts involved in signal transduction and pheromone transportation. Also we found gustatory and olfactory receptors associated with the tarsi and ovipositor. Differential expression analysis showed that there wer...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - June 26, 2019 Category: Genetics & Stem Cells Source Type: research

Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production
This article serves as an introduction to a Virtual Special Issue of Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics (CBPD), with the objective to showcase the state-of-the-science for Omics in aquaculture. In this editorial, we describe the role that Omics can play in aquaculture, and provide a synopsis for each of the Special Issue articles that use these technologies to improve aquaculture practices. Current genomic resources available for some aquaculture species are also described. The number of datasets is impressive for species such as Atlantic salmon and rainbow trout, totaling in the thou...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - June 19, 2019 Category: Genetics & Stem Cells Source Type: research

Hepatopancreas and ovarian transcriptome response to different dietary soybean lecithin levels in Portunus trituberculatus
This study compared the transcriptome in the ovary and the hepatopancreas of female P. trituberculatus fed two different diets containing 0% (SL0) and 4% soybean lecithin (SL4), respectively during the growth and ovarian maturation stages by Illumina HiSeq4000 sequencer. The differences between ovary and hepatopancreas of P. trituberculatus were also compared at transcriptional level. A total of 55,667 unigenes were obtained with mean length of 962 bps across the four treatment groups (SL0_O, SL4_O, SL0_H and SL4_H). In ovary, there were 257 differentially expressed genes (DEGs) between SL0_O and SL4_O, with 145 down- an...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - June 14, 2019 Category: Genetics & Stem Cells Source Type: research

Insights into hypoxic adaptation in Tibetan chicken embryos from comparative proteomics
This study aimed to identify differently abundant proteins (DAPs) and elucidate the mechanisms involved in hypoxic adaptation in the Tibetan chicken. In this study, we obtained proteome data for the embryonic heart tissues of Tibetan and Chahua chickens incubated under hypoxia (TCH and CHH) and normoxia (TCN and CHN) using isobaric tags for relative and absolute quantitation (iTRAQ) technology. We identified 4210 proteins from 53,352 unique peptides in the heart tissue of chicken embryos. Pairwise TCH vs. CHH, TCH vs. TCN, CHH vs. CHN, and TCN vs. CHN comparisons revealed 118, 176, 103, and 162 differently abundant protein...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - June 13, 2019 Category: Genetics & Stem Cells Source Type: research

Candidate genes involved in spiroacetal biosynthesis in the oriental fruit fly, Bactrocera dorsalis
Publication date: Available online 8 June 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Zhong-Zhen Wu, He Zhang, Meng-Qiu Qu, Yang Cui, Ming-Shun Chen, Shu-Ying Bin, Jin-Tian LinAbstractSpiroacetals are widespread in nature as components of volatile semiochemical secretions from many insect species. The general pathway for spiroacetal biosynthesis in Bactrocera sp. is preliminarily established, but many genes involved in this pathway remain to be characterized. By analyzing transcriptomes of the rectal glands (RGs) from immature and mature females of the oriental fruit fly, B...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - June 9, 2019 Category: Genetics & Stem Cells Source Type: research

A first step towards building spectral libraries as complementary tools for snake venom proteome/peptidome studies
Publication date: Available online 31 May 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): André Zelanis, Débora A. Silva, Eduardo S. Kitano, Tarcísio Liberato, Isabella Fukushima, Solange M.T. Serrano, Alexandre K. TashimaAbstractSnake venoms are complex mixtures of a large number of distinct proteins and peptides with biological activity. Peptide spectral libraries are compilations of previously identified MS/MS spectra obtained from proteomics experiments. Here we present the generation and use of a Venom Peptidome and a Venom Proteome spectral library for the analysis of ...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - June 1, 2019 Category: Genetics & Stem Cells Source Type: research

Transcriptome analysis of shell color-related genes in the hard clam Mercenaria mercenaria
In this study, RNA-seq was performed to exploit the related shell color genes and determine the genetic basis of the different shell colors. Nine sequence libraries with those three shell colors of hard clam were constructed; 406,377 transcripts and 248,251 unigenes were obtained with N50 values of 1365 and 1682 base pairs, respectively. Cluster analysis identified 363, 392, and 220 genes exclusively highly expressed in red, white, and mottled clams, respectively. We further classified differentially expressed genes (DEGs), the genes involved in lipid binding and transport, signal transduction, ATP synthesis, and other pro...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - May 31, 2019 Category: Genetics & Stem Cells Source Type: research

Whole transcriptome analysis of the Atlantic cod vaccine response reveals subtle changes in adaptive immunity
Publication date: Available online 28 May 2019Source: Comparative Biochemistry and Physiology Part D: Genomics and ProteomicsAuthor(s): Monica Hongrø Solbakken, Sissel Jentoft, Trond Reitan, Helene Mikkelsen, Kjetill S. Jakobsen, Marit SeppolaAbstractAtlantic cod has lost the Major Histocompatibility complex class II pathway – central to pathogen presentation, humoral response and immunity. Here, we investigate the immunological response of Atlantic cod subsequent to dip vaccination with Vibrio anguillarum bacterin using transcriptome sequencing. The experiment was conducted on siblings from an Atlantic cod family found...
Source: Comparative Biochemistry and Physiology Part D: Genomics and Proteomics - May 29, 2019 Category: Genetics & Stem Cells Source Type: research