Microbiome analyses of pacific white shrimp (Litopenaeus vannamei) collected from disparate geographical locations

In this study, the tail muscle microbiota of pacific white shrimp (Litopenaeus vannamei) sourced from five countries across Central and South America and Southeast Asia were determined and compared. The genomic DNA was sequenced at around 10 × coverage for each geographical location and was assembled de novo for comparative analysis. The assembled sequences for all the lines were classified based on their similarity to the sequences in the public database. We found that there is high correlation among the microbiota of shrimp from disparate regions, as well as the presence of some DNA from bacteria known to cause food poisoning in humans. Sequencing data has been deposited at NCBI-SRA database and can be found under the BioProject ID PRJNA282154

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation.</p> <p>Results</p> <p>The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the <it>Glycine max </it>genome.</p> <p>Conclusions</p> <p>This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of <it>Glycine max </it>can be explored at <url>http://www.soybase.org/soyseq</url>.</p