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

Summary of simple sequence repeat (SSR) types in the Chinese sturgeon transcriptome.

<p>^aNumber of SSRs detected in unigenes</p><p>^bRelative percent of SSRs with different repeat motifs among the total SSRs</p><p>Summary of simple sequence repeat (SSR) types in the Chinese sturgeon transcriptome.</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

Real-time PCR confirmation of the relative expression of genes showing differential expression between the two gonad types.

<p>^a The relative-fold expression determined by Illumina transcriptome analysis.</p><p>^b The relative-fold expression validated by qRT-PCR.</p><p>O/T: The relative transcription level of genes in ovary compared to that in testis. O, Ovary; T, Testis.</p><p>Real-time PCR confirmation of the relative expression of genes showing differential expression between the two gonad types.</p

Clusters of orthologous groups (COG) classification.

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