Extensive search of genetic sex markers in Siberian (Acipenser baerii) and Atlantic (A. oxyrinchus) sturgeons - RNAseq data sets

The file Panagiotopoulou_etal_Abaerii_sex_markers_RNAseq_search.bz2 contains results of RNAseq analyses of the female and male transcriptomes of Siberian Sturgeon (Acipenser baerii). Total RNAs were isolated from fin tissues and subjected to Whole Transcriptome Sequencing (WTS) on Illumina platform. Compressed file contains assemblies of the sequences, their annotations and results of the differential expression analyses of the two transcriptomes representing both sexes. Files were designated respectively to the origin of RNAs (female sequences are in files containing in their names string “Aci_2”, male sequences are in files containing in their names string “Aci_I”). File designated All-Unigene.fa contains full transcriptome of Siberian Sturgeon – joined female and male transcriptomes without redundant sequences. All sub-folders contains text and html files to facilitate data exploration.Sturgeons belong to an extraordinarily old and highly endangered group of fish. Although the sex determining region in this taxon was recently discovered, there is still a great need for the development of reliable gene expression markers for sturgeon sexing in their different life stages which could be easily applied in field conditions. In this study an extensive screening of the Atlantic sturgeon genome was performed using: AFLP (202 PC) and MS-AFLP (256 PC) markers likewise the Siberian sturgeon transcripts deriving from the Whole Transcriptome Sequencing (WTS) and cDNA-AFLP (128 PC). Genetic material extracted from female and male fins was used. AFLP reactions were minimized and automatized and a novel method for SCAR identification was proposed (SCAR-NGS). The 204 primary selected markers were subjected to gDNA or cDNA PCR amplifications, semi- and RT-qPCRs in order to confirm the presence of unique sex-marker sequences in the genomes or sex-linked expression differences. We identified eleven loci in the Atlantic sturgeon genome which exhibited sex-linked polymorphisms of the restriction sites (SNP based). In case of the Siberian sturgeon, 41 transcripts were confirmed to be expressed in a sex specific manner; three of which were also significantly differentially amplified in the female and male genomes. Six of those markers were highly overexpressed in males, which was quantified using RT-qPCRs. The approach enabled the discovery of DNA and RNA candidate sequences suitable for application in sturgeon sexing, being important both for commercial aquaculture optimization and genetic variability maintenance of sturgeons.