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Coilia nasus is an important economic fish species in China due to its excellent meat quality and wonderful flavor. The germplasm resources of C. nasus have recently been seriously degraded by human activities. It is urgent to develop the genetic markers of C. nasus in order to apply to conservation of this species. In this study, we used C. nasus transcriptomic data from GENBANK to identify single nucleotide polymorphism (SNP) markers for this species. From 148,156 unigenes with functional annotations, 85,454 putative SNPs were identified. Forty-one of the 61 SNP loci (including 31 loci that were associated with osmoregulation-related genes and 10 loci associated with other functions) were successfully validated and showed bi-allelic polymorphism in three rivers. Nine, six and eleven of these SNP loci deviated significantly from Hardy–Weinberg equilibrium (P

Xenocypris argentea is a cyprinid fish species and widely distributed in rivers and lakes within China. The germplasm resources of X. argentea have recently been seriously degraded by human activities. Thus, the development of sufficient molecular markers to inform conservation efforts of X. argentea is urgently needed. In this study, we used Illumina HiSeq high-throughput sequencing of X. argentea transcriptomic data to identify single nucleotide polymorphism (SNP) markers for X. argentea. From 43,346 unigenes with functional annotations, 462,621 putative SNPs were identified. Among these, we validated 32 polymorphic loci of 40 function-related SNPs from a Poyang Lake population of X. argentea. Six of these SNP loci deviated significantly from Hardy–Weinberg equilibrium (P

Bighead carp (Aristichthys nobilis) is one of the most economically and ecologically important fish species widely stocked in lakes or cultured in ponds throughout China. The natural populations are facing the stringent challenges of germplasm resources reduction because of pollution and culture. Thus, developing sufficient molecular markers for the conservation and molecular-aided selection of bighead carp is urgent. In this study, we used SNaPshot to develop single nucleotide polymorphism (SNP) markers in bighead carp. A total of 38861 putative SNP markers were identified from the RAD sequencing of bighead carp. Among the markers, 28 SNPs were randomly selected and 25 loci exhibited significant polymorphisms in genotyping by SNaPshot. To the best of our knowledge, this is the first report about SNP marker development in bighead carp based on SNaPshot. These SNP markers can provide an effective tool for the resource conservation and genetic improvement of bighead carp.

In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise F

In this paper, the complete mitochondrial DNA (mtDNA) sequence of Thryssa kammalensis was determined. The mitochondrial genome is 16,884 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region as those found in other vertebrates, with the gene identical to that of typical vertebrates. The overall base composition of the heavy strand is 31.07% A, 24.82% T, 28.33% C, and 15.78% G, with an AT bias of 55.89%. Phylogeny of T. kammalensis suggested more close relationship with Lycothrissa crocodilus and Setipinna taty. The complete mitogenome of this species can provide a basic data for the studies on population history, molecular systematics, phylogeography, stock evaluation, and conservation genetics.

Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture. However the gene discovery in this species has been limited to small-scale data collection in China. We used the next generation sequencing technology for the experiment; the transcriptome was sequenced of samples of hepatopancreas organ in individuals from 4 GFP groups (A1, A2, B1 and B2). De novo transcriptome sequencing generated 66,953 isogenes. Using BLASTX to search the Non-redundant (NR), Search Tool for the Retrieval of Interacting Genes (STRING), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases; 21,224 unigenes were annotated, 9,552 matched unigenes with the Gene Ontology (GO) classification; 5,782 matched unigenes in 25 categories of Clusters of Orthologous Groups of proteins (COG) and 20,859 unigenes were consequently assigned to 312 KEGG pathways. Between the A and B groups 147 differentially expressed genes (DEGs) were identified; between the A1 and A2 groups 6,860 DEGs were identified and between the B1 and B2 groups 5,229 DEGs were identified. After enrichment, the A and B groups identified 38 DEGs, but none of them were significantly enriched. The A1 and A2 groups identified 21,856 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function and the KEGG pathway defined 2,459 genes had a KEGG Ortholog - ID (KO-ID) and could be categorized into 251 pathways, of those, 9 pathways were significantly enriched. The B1 and B2 groups identified 5,940 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function, and the KEGG pathway defined 1,543 genes had a KO-ID and could be categorized into 240 pathways, of those, 2 pathways were significantly enriched. We investigated 99 queries (GO) which related to growth of GFP in 4 groups. After enrichment we identified 23 DEGs and 1 KEGG PATHWAY ‘ko04711’ relation with GFP growth.