Genetic diversity of mitochondrial control region (D-Loop) polymorphisms in Coilia ectenes taihuensis inhabiting Taihu Lake, China.

Coilia ectenes is a commercially important fishery species in China. C. ectenes taihuensis is an endemic and dominant species found in Taihu Lake of China. When compared with C. ectenes, C. ectenes taihuensis lacks anadromous behavior, and can independently grow and reproduce in Taihu Lake. In this study, the mitochondrial DNA control region (D-loop) sequences were employed to investigate the genetic diversity and population structure of C. ectenes taihuensis. Sixty-eight individuals collected from 4 localities in Taihu Lake were examined. Results indicated that in the 887-bp D-loop region, seventy-seven (8.68%) sites were variant, contributing to 53 distinct haplotypes. Although the population haplotype diversity (Hd = 0.971 to 1.000) was generally high, the nucleotide diversity (π = 0.616 to 0.731%) was relatively low among the 4 populations. Additionally, the genetic distances ranged from 0.62 to 0.74% within the populations and from 0.67 to 0.74% between the populations. The neighbor-joining tree indicated that a distinct distribution of phylogenetic structure existed among haplotypes. Analysis of molecular variance and FST statistics suggested that a divergence existed among populations in 4 localities, indicating that gene communication might have occurred among those populations. Furthermore, neutral tests and analysis of mismatch distribution reflected that C. ectenes taihuensis might have undergone a population expansion during the evolution process. Our study showed the population genetic diversity and structure of C. ectenes taihuensis. Results from this study might be helpful in the development and protection of fishery resource within the localities in Taihu Lake in future.

Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing.

RNA-Seq technology has been widely applied to transcriptomics, genomics, molecular marker development, and functional gene studies. In the genome, microsatellites are simple sequence repeats (SSR) with a high degree of polymorphism that are used as DNA markers in many molecular genetic studies. Using traditional methods such as magnetic bead enrichment, only a few microsatellite markers have been isolated. Coilia nasus is an anadromous, small-to-moderately sized fish species that is famous as an important fishery resource. Here, we have identified a large number of microsatellites from the fish brains by using Illumina sequencing. About 20 million Illumina reads were assembled into 148,845 unigenes. A total of 13,038 SSR motifs were identified via analysis of 3,958,293,117 (3.96 Gb) nucleotides to produce a comprehensive transcript dataset for the C. nasus brain, including mono-, di-, tri-, tetra-, and penta-repeat motifs. The most abundant type of repeat motif was di-nucleotide (42.97%), followed by mono-nucleotide (38.86%), tri-nucleotide (16.21%), tetra-nucleotide (1.83%), and penta-nucleotide (0.05%) repeat units, which is similar to the results obtained in studies in other species. These data provide a base of sequence information to improve molecular-assisted markers to study C. nasus genetic diversity.

Genetic diversity of the endangered scaly-sided merganser (Mergus squamatus) in the wintering habitat of central-southern China.

The scaly-sided merganser (Mergus squamatus), found in temperate East Asia, has been reduced to a very small population. Central and southern China are its main wintering habitat. However, populations have declined greatly since the 1980s due to habitat loss and degradation, and poaching. To meet the urgent need for up-to-date conservation information, we examined RAPD DNA markers from 156 specimens in 6 populations in Jiangxi Province. We found that genetic diversity (based on individual similarities) is in fact low; molecular variance between populations ranged from 0.137 to 0.347. Genetic similarity ranged from 0.683 to 0.866. In conclusion, the geographical pattern of genetic diversity supports the long-term refugial status of the scaly-sided merganser in central-southern China; strong conservation measures should be taken to maintain the merganser in this region.

A novel DDX5 gene in the freshwater crayfish Cherax quadricarinatus is highly expressed during ontogenesis and spermatogenesis.

The freshwater crayfish Cherax quadricarinatus, originally from Australia, is an invasive species that is also widely used in aquaculture. DEAD-box helicase family genes are found throughout evolution and encode RNA-binding proteins. The human DDX5 (p68) is important for normal cell growth, differentiation and proliferation. We identified a C. quadricarinatus homolog of DDX5 (Cq-DDX5); the temporal expression of Cq-DDX5 mRNA transcripts was measured during early ontogenesis, during spermatogenesis, during testes development, and during the annual cycle. The Cq-DDX5 cDNA comprises 2258 nucleotides, with an open reading frame of 1569 bp, encoding 522 amino acid residues. The deduced amino acid sequence of Cq-DDX5 has a 53 to 90% similarity to DDX5 of other eukaryotic species. mRNA transcripts of Cq-DDX5 were detected in all tissues, with high levels in the gonads. The DDX5 expression was highest in the nauplii stage, during early ontogenesis and during testes development. In adult testes, transcripts appeared at significantly higher levels in the prespawning and spawning phase than in the post-spawning or regressed phase. Eyestalk ablation resulted in upregulation of Cq-DDX5 in adult male gonads in a time-dependent manner, with a peak at about 12 days. We conclude that the Cq-DDX5 gene plays an important role in early ontogenesis and spermatogenesis, with a crucial reproductive function in germ cell differentiation in these invertebrates.