Functional annotation of unigenes of the <i>Acipenser sinensis</i> transcriptome.

<p>Functional annotation of unigenes of the <i>Acipenser sinensis</i> transcriptome.</p

Transcriptome comparison of three sturgeon species.

<p>^a Female gonad with heterogametic sex</p><p>^b Contigs for female assembly with combined reads of the ovary and the female gonad with heterogametic sex</p><p>Transcriptome comparison of three sturgeon species.</p

Assembly statistics of the gonad transcriptome using the Trinity software package.

<p>^a Sequences constructed from Inchworm contigs by Chrysalis module and Butterfly module.</p><p>^b The longest transcripts in the cluster units.</p><p>Assembly statistics of the gonad transcriptome using the Trinity software package.</p

Comparison of orthologs from three gene families in Chinese sturgeon and zebrafish.

<p>Comparison of orthologs from three gene families in Chinese sturgeon and zebrafish.</p

Sequencing and <i>De Novo</i> Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (<i>Acipenser sinensis</i>)

<div><p>Background</p><p>The Chinese sturgeon (<i>Acipenser sinensis</i>) is endangered through anthropogenic activities including over-fishing, damming, shipping, and pollution. Controlled reproduction has been adopted and successfully conducted for conservation. However, little information is available on the reproductive regulation of the species. In this study, we conducted <i>de novo</i> transcriptome assembly of the gonad tissue to create a comprehensive dataset for <i>A</i>. <i>sinensis</i>.</p><p>Results</p><p>The Illumina sequencing platform was adopted to obtain 47,333,701 and 47,229,705 high quality reads from testis and ovary cDNA libraries generated from three-year-old <i>A</i>. <i>sinensis</i>. We identified 86,027 unigenes of which 30,268 were annotated in the NCBI non-redundant protein database and 28,281 were annotated in the Swiss-prot database. Among the annotated unigenes, 26,152 and 7,734 unigenes, respectively, were assigned to gene ontology categories and clusters of orthologous groups. In addition, 12,557 unigenes were mapped to 231 pathways in the Kyoto Encyclopedia of Genes and Genomes Pathway database. A total of 1,896 unigenes, potentially differentially expressed between the two gonad types, were found, with 1,894 predicted to be up-regulated in ovary and only two in testis. Fifty-five potential gametogenesis-related genes were screened in the transcriptome and 34 genes with significant matches were found. Besides, more paralogs of 11 genes in three gene families (<i>sox</i>, <i>apolipoprotein</i> and <i>cyclin</i>) were found in <i>A</i>. <i>sinensis</i> compared to their orthologs in the diploid <i>Danio rerio</i>. In addition, 12,151 putative simple sequence repeats (SSRs) were detected.</p><p>Conclusions</p><p>This study provides the first <i>de novo</i> transcriptome analysis currently available for <i>A</i>. <i>sinensis</i>. The transcriptomic data represents the fundamental resource for future research on the mechanism of early gametogenesis in sturgeons. The SSRs identified in this work will be valuable for assessment of genetic diversity of wild fish and genealogy management of cultured fish.</p></div

Transcriptome assembly and analysis pipeline.

<p>Clean reads were obtained by pre-processing the raw reads with WipeAadpter.pl software and Fastq_filter software. A total of 86,027 unigenes were acquired by Trinity assembly. The expression levels of the unigenes were normalized with RPKM, through which 1,896 genes differentially expressed between ovary and testis were identified. The unigenes were used for functional annotation and SSR detection.</p

The distribution of transcripts between testis and ovary.

<p>(A) The numbers of all transcripts present in the testis, ovary, or both. (B) The distribution of transcripts with potential function in sexual development in testis and ovary.</p

Table_3_Quantifying the Colonization of Environmental Microbes in the Fish Gut: A Case Study of Wild Fish Populations in the Yangtze River.XLSX

In aquatic animals, gut microbial communities shift with host development and living environments. Understanding the mechanism by which the environment impacts the gut microbial communities of aquatic animals is crucial for assessing and managing aquatic ecosystem health. Here, we proposed a simplified framework for the colonization and dynamics of gut microbial communities. Then, to quantify the colonization of environmental microbes in the wild fish gut, the current study used 16S rRNA gene amplicon sequencing to obtain the structure of the water environmental microbial community and the gut microbial community in 10 wild fish populations (Leiocassis crassilabris, Leiocassis longirostris, Pelteobagrus vachelli, Silurus asotus, Siniperca chuatsi, Coilia brachygnathus, Aristichthys nobilis, Hypophthalmichthys molitrix, Coreius heterodon, and Xenocypris argentea) from the Wuhan section of the Yangtze River, and the relationship of these microbial communities was analyzed. The results identified that in most individuals, approximately 80% of gut microbes [at the operational taxonomic unit (OTU) level] were shared with the water environmental microbial community (except for individuals of Siniperca chuatsi and Coilia brachygnathus, approximately 74%). In approximately 80% of individuals, more than 95% of microbial species (OTUs) in the gut were transient. For fish species, more than 99% of microbial species (OTUs) that were introduced into the gut were transient. Nearly 79% of OTUs and 89% of species of water environmental microbes could be introduced into the fish gut. Driven by the introduction of transient microbes, fishes with similar feeding habits had similar gut microbial communities. The results indicated that for adult wild fishes, most gut microbiota were transient from the environmental microbiota that were related to fish feeding habits. We therefore encourage future research to focus on environmental microbiota monitoring and management to promote the better conservation of aquatic animals. It was important to note that, because of various influence factors, interspecific differences and individual variations on gut microbial community characteristics, the quantification of gut microbes in the current work was approximate rather than accurate. We hope that more comparable research could be conducted to outline the quantitative characteristics of the relationship between gut microbial community and aquatic environment microbial community as soon as possible.</p

Clusters of orthologous groups (COG) classification.

<p>4,479 unigenes with Nr hits were grouped into 24 COG classifications.</p

Functional annotation of assembled sequences based on gene ontology (GO) categorization.

<p>GO analysis was performed for three main categories: cellular components, molecular function, and biological processes.</p