Dataset Information

Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis).

ABSTRACT: The Chinese sturgeon (Acipenser sinensis) 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 de novo transcriptome assembly of the gonad tissue to create a comprehensive dataset for A. sinensis.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 A. sinensis. 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 (sox, apolipoprotein and cyclin) were found in A. sinensis compared to their orthologs in the diploid Danio rerio. In addition, 12,151 putative simple sequence repeats (SSRs) were detected.This study provides the first de novo transcriptome analysis currently available for A. sinensis. 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.

SUBMITTER: Yue H

PROVIDER: S-EPMC4452307 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis).

Yue Huamei H Li Chuangju C Du Hao H Zhang Shuhuan S Wei Qiwei Q

PloS one 20150601 6

<h4>Background</h4>The Chinese sturgeon (Acipenser sinensis) 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 de novo transcriptome assembly of the gonad tissue to create a comprehensive dataset for A. sinensis.<h4>Results</h4>The Illumina se ...[more]

PMID: 26030930

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Project description:In this study, the effects of different feeding frequencies on the growth and the expression of genes in the GH/IGF axis were assessed in juvenile Chinese sturgeon. The newly hatched Chinese sturgeons were bred for 38 days at three different feeding frequencies groups (feeding frequency of two times a day, TWD; three times a day, THD; and four times a day, FOD), and the expression levels of the GH/IGF axis responses to feeding frequency were determined by quantitative real-time PCR. In addition, the full-length of the Coding Sequences of IGF I and IGF II genes (489-bp and 660-bp, respectively), were cloned and analyzed from Chinese sturgeon the first time. Multiple sequence alignments of IGFs revealed that Chinese sturgeon are high sequence identity to IGFs from other species. The phylogenetic relationships based on the IGF I and IGF II amino acid sequences were consistent with the traditional classification. After 38 days of growth, the three different feeding frequencies groups of Chinese sturgeon had no significant difference of body length, body weight, specific growth rate, the survival rate, the rate of weight gain and the condition factor. However, the relative expression of Chinese sturgeon GH in the pituitary decreased with increasing feeding frequency. The relative expression of Chinese sturgeon GHR in liver and skeletal muscle was deceased with increasing feeding frequency, while the relative expression of GHR in stomach and intestines at THD group was significantly higher than that of at TWD group and FOD group (p?<?0.05). The relative expression of Chinese sturgeon IGF I in liver increased significantly with increasing feeding frequency (p?<?0.05). The relative expression of IGF I in stomach and skeletal muscle was similar at the three groups. The relative expression of IGF I in intestines was significantly higher at FOD group than at TWD group and THD group (p?<?0.05). The relative expression of Chinese sturgeon IGF II in liver at TWD group was significantly higher than that at THD group and FOD group (p?<?0.05). However, the relative expression of IGF II in stomach, intestines and skeletal muscle at THD group was higher than that at TWD group and FOD group. Based on these previous studies that liver IGF I is regarded as a biomarker of growth performance, this result suggested that the juvenile Chinese sturgeon is better for growth when feeding four times daily compared to twice and thrice daily.

Project description:BACKGROUND: Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The intense fishing pressure on wild stocks to harvest caviar has caused in the last decades a dramatic decline of their distribution and abundance leading the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, the characterization of the genes involved in sex determination could provide relevant information for the selective farming of the more profitable females. RESULTS: The 454 sequencing of two cDNA libraries from the gonads and brain of one male and one female full-sib A. naccarii, yielded 182,066 and 167,776 reads respectively, which, after strict quality control, were iterative assembled into more than 55,000 high quality ESTs. The average per-base coverage reached by assembling the two libraries was 4X. The multi-step annotation process resulted in 16% successfully annotated sequences with GO terms. We screened the transcriptome for 32 sex-related genes and highlighted 7 genes that are potentially specifically expressed, 5 in male and 2 in females, at the first life stage at which sex is histologically identifiable. In addition we identified 21,791 putative EST-linked SNPs and 5,295 SSRs. CONCLUSIONS: This study represents the first large massive release of sturgeon transcriptome information that we organized into the public database AnaccariiBase, which is freely available at http://compgen.bio.unipd.it/anaccariibase/. This transcriptomic data represents an important source of information for further studies on sturgeon species. The hundreds of putative EST-linked molecular makers discovered in this study will be invaluable for sturgeon reintroduction and breeding programs.

Project description:BackgroundTo determine the presence and abundance of an aquatic species in large waterbodies, especially when populations are at low densities, is highly challenging for conservation biologists. Environmental DNA (eDNA) has the potential to offer a noninvasive and cost-effective method to complement traditional population monitoring, however, eDNA has not been extensively applied to study large migratory species. Chinese sturgeon (Acipenser sinensis), is the largest anadromous migratory fish in the Yangtze River, China, and in recent years its population has dramatically declined and spawning has failed, bringing this species to the brink of extinction. In this study, we aim to test the detectability of eDNA methods to determine the presence and relative abundance of reproductive stock of the species and whether eDNA can be used as a tool to reflect behavioral patterns. Chinese sturgeon eDNA was collected from four sites along the spawning ground across an eight month period, to investigate the temporal and spatial distribution using droplet digital PCR (ddPCR).ResultsWe designed a pair of specific primers for Chinese sturgeon and demonstrated the high sensitivity of ddPCR to detect and quantify the Chinese sturgeon eDNA concentration with the limit of detection 0.17 copies/μl, with Chinese sturgeon eDNA been intermittently detected at all sampling sites. There was a consistent temporal pattern among four of the sampling sites that could reflect the movement characteristics of the Chinese sturgeon in the spawning ground, but without a spatial pattern. The eDNA concentration declined by approximately 2-3 × between December 2018 and December 2019.ConclusionsThe results prove the efficacy of eDNA for monitoring reproductive stock of the Chinese sturgeon and the e decreased eDNA concentration reflect that Chinese sturgeon may survive with an extremely small number of reproductive stock in the Yangtze River. Accordingly, we suggest future conservation measures should focus on both habitat restoration and matured fish restocking to ensure successful spawning. Overall, this study provides encouraging support for the application of eDNA methods to monitor endangered aquatic species.

Project description:Background:Acipenser dabryanus, an endemic Chinese species, has been listed as a first-class protected animal in China. Sturgeons are among the oldest and most primitive group of existing fish in the world and occupy a special place in the evolutionary history of fish. Thus, a study of the reproduction and sex differentiation of sturgeon will be of great value for fish as well as the whole vertebrate group. Methods:In this study, we conducted comparative analysis of the testes and ovaries transcriptomes of A. dabryanus to screen for sex-differentiation and sexual development-related genes. Results:The transcriptome sequencing of six cDNA libraries generated 265 million clean reads, encompassing 79 Gb of sequences. The N50 and mean length of the identified 91,375 unigenes were 1,718 and 989 bp, respectively. A total of 6,306, 9,961, 13,170, 15,484, and 23,588 unigenes were annotated in the clusters of orthologous groups, gene ontology categories, Kyoto Encyclopedia of Genes and Genomes Pathway, euKaryotic orthologous groups, and NCBI non-redundant protein databases, respectively. A total of 5,396 differentially expressed genes were found between the two sexes, with 1,938 predicted to be up-regulated in ovaries and 3,458 in testes. A total of 73 candidate genes known to be involved in sex differentiation and sexual development were searched in the transcriptome of A. dabryanus of which 52 showed significant similarity. We highlighted six genes that are differentially expressed between the two sexes and may play important roles in sex differentiation and gonad maintenance. In addition, 24,271 simple sequence repeats (SSRs) and 550,519 single-nucleotide polymorphisms (SNPs) were detected. Discussion:This work represents the first transcriptome study comparing the ovary and testis in A. dabryanus. The putative differentially expressed genes between the gonads provide an important source of information for further study of the sex-differentiation related genes and the sex-differentiation mechanism in sturgeons. The SSRs or SNPs identified in this study will be helpful in the discovery of sex-related markers in A. dabryanus.

Dataset Information

Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis).

Publications

Sequencing and De Novo Assembly of the Gonadal Transcriptome of the Endangered Chinese Sturgeon (Acipenser sinensis).

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