Dataset Information

Siberian sturgeon multi-tissue reference transcriptome database.

ABSTRACT: Motivation:Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies.

Results:We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic and pre-larval tissues. It will facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology. This database represents a major contribution to the publicly available sturgeon transcriptome reference datasets.

Availability:The database is publicly available at http://siberiansturgeontissuedb.sigenae.org Supplementary information: Supplementary data are available at Database online.

SUBMITTER: Klopp C

PROVIDER: S-EPMC7687680 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Publications

Siberian sturgeon multi-tissue reference transcriptome database.

Klopp Christophe C Cabau Cédric C Greif Gonzalo G Lasalle André A Di Landro Santiago S Vizziano-Cantonnet Denise D

Database : the journal of biological databases and curation 20201101

<h4>Motivation</h4>Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies.<h4>Results</h4>We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, hea ...[more]

PMID: 33238003

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Project description:BackgroundEvolution of sturgeons and paddlefishes (order Acipenseriformes) is inherently connected with polyploidization events which resulted in differentiation of ploidy levels and chromosome numbers of present acipenseriform species. Moreover, allopolyploidization as well as autopolyploidization seems to be an ongoing process in these fishes and individuals with abnormal ploidy levels were occasionally observed within sturgeon populations. Here, we reported occurrence of Siberian sturgeon (Acipenser baerii) male with abnormal ploidy level for this species, accessed its ploidy level and chromosome number and investigate its potential sterility or fertility in comparison with normal individuals of sterlet (A. ruthenus), Russian sturgeon (A. gueldenstaedtii) and Siberian sturgeon (A. baerii).ResultsAcipenser ruthenus possessed 120 chromosomes, exhibiting recent diploidy (2n), A. gueldenstaedtii and A. baerii had ~245 chromosomes representing recent tetraploidy (4n), and A. baerii male with abnormal ploidy level had ~ 368 chromosomes, indicating recent hexaploidy (6n). Genealogy assessed from the mtDNA control region did not reveal genome markers of other sturgeon species and this individual was supposed to originate from spontaneous 1.5 fold increment in number of chromosome sets with respect to the number most frequently found in nature for this species. Following hormone stimulation, the spontaneous hexaploid male produced normal sperm with ability for fertilization. Fertilization of A. baerii and A. gueldenstaedtii ova from normal 4n level females with sperm of the hexaploid male produced viable, non-malformed pentaploid (5n) progeny with a ploidy level intermediate to those of the parents.ConclusionThis study firstly described occurrence of hexaploid individual of A. baerii and confirmed its autopolyploid origin. In addition to that, the first detailed evidence about fertility of spontaneous hexaploid sturgeon was provided. If 1.5 fold increment in number of chromosome sets occurring in diploids, resulted triploids possess odd number of chromosome sets causing their sterility or subfertility due to interference of gametogenesis. In contrast, 1.5 fold increment in number of chromosome sets in naturally tetraploid A. baerii resulted in even number of chromosome sets and therefore in fertility of the hexaploid specimen under study.

Dataset Information

Siberian sturgeon multi-tissue reference transcriptome database.

Publications

Siberian sturgeon multi-tissue reference transcriptome database.

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