Yanfu Que

Identification and characterization of seventeen novel microsatellite markers for Dabry’s sturgeon (Acipenser dabryanus)

Dabry’s sturgeon, Acipenser dabryanus, is a critical endangered species in the Red List in IUCN since 1996 (IUCN 2013). In the present study, we report 17 novel microsatellites loci isolated from A. dabryanus. All 17 loci were amplified in a sample of 22 individuals. Sixteen loci were polymorphic and only one locus showed monomorphism. At these 16 polymorphic loci, 91 alleles were observed, with an average of 5.69 alleles per locus. The number of alleles, mean expected heterozygosity (HE) and Shannon–Wiener diversity indices (H′) varied from 2 to 11, 0.127 to 0.852 and 0.247 to 2.064, respectively. These markers will be useful for population genetics and conservation management in A. dabryanus. Dabry’s sturgeon is also an endemic freshwater fish and does not undertake long distance migrations except for spawning (The Yangtze Aquatic Resources Survey Group 1988). Historically, it has widely inhabited the upper and middle sections of the Yangtze River and its large tributaries (Zhuang et al. 1997). A. dabryanus was an important species in commercial fisheries of the upper reaches of the Yangtze River before the 1980s (Zhu et al. 2009). However, due to construction of dam, overfishing and pollution, natural populations have declined sharply in the past decades (Zhu et al. 2008). Natural production of A. dabryanus is so small and scattered that no exact account of total production has been reported since 1995 (Zhang et al. 2011). To save A. dabryanus, its commercial capture was prohibited in the early 1980s, and it was listed nationally as class I state protected animal since 1989 (Wang and Xie 2009). Moreover, the biggest national reserve, three months seasonal fishing

Isolation and characterization of 15 microsatellite loci in an endemic Chinese cyprinid fish, Pseudogyrincheilus prochilus , and their cross-species amplification in two related species

Fifteen polymorphic microsatellite loci were developed for an endemic Chinese cyprinid fish, Pseudogyrincheilus prochilus. The number of observed alleles per locus ranged from 2 to 17. The observed and expected heterozygosities ranged from 0.067 to 1.000 and from 0.066 to 0.932, respectively. No significant linkage disequilibrium was detected among the loci. Two loci showed significant deviation from Hardy–Weinberg equilibrium, and one of them had evidence for null alleles. Fourteen primer pairs cross-amplified in Garra pingi pingi, and 13 primer pairs cross-amplified in Onychostoma sima. These microsatellite loci should prove highly informative for future studies of genetic diversity conservation.

The complete mitochondrial genome sequence of Triplophysa anterodorsalis (Teleostei, Balitoridae, Nemacheilinae)

Abstract Triplophysa anterodorsalis is an endemic fish in the upper stream of the Yangtze River, Jinsha River and its tributaries. However, wild populations of T. anterodorsalis declined sharply due to cascade hydropower stations constructed successively in the Jinsha River during the past decades. In the present study, the complete mitochondrial DNA genome sequence of T. anterodorsalis was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial genome sequence of T. anterodorsalis is a circular molecule of 16,567 bp in size. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of T. anterodorsalis is 27.37% A, 25.68% C, 18.37% G, and 28.57% T, with a relatively a relatively high A + T content (55.94%). The results could provide useful data for studies on genetic structure and diversity and rational resource conservation in T. anterodorsalis.

The complete mitochondrial genome of the spotted longbarbel catfish, Hemibagrus guttatus (Siluriformes, Bagridae)

Abstract Spotted longbarbel catfish, Hemibagrus guttatus (Siluriformes, Bagridae), is regarded as one of the “four famous fish” in the Pearl River system in China. So far, very few genomic resources from this species were available. In the present study, the complete mitochondrial genome of H. guttatus was determined to be 16,528 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. It includes 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a non-coding control region (D-loop). The complete mtDNA genome sequence obtained in this study would be useful for studying genetic diversity and phylogenetics in H. guttatus and related taxa in future.

The complete mitochondrial genome of Jinshaia sinensis (Teleostei, Balitoridae, Balitorinae)

Abstract Jinshaia sinensis is an endemic and typical fish which is successfully adaptive to mountain torrents in the upper stream of the Yangtze River and its tributaries. In this study, the complete mitogenome sequence of J. sinensis has been first sequenced by DNA sequencing based on the PCR fragments. The mitogenome, consisting of 16,567 base pairs (bp), had typical vertebrate mitochondrial gene arrangement, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNA genes and a noncoding control region (CR). The overall base composition of J. sinensis is 30.37% A, 28.82% C, 16.59% G, and 24.22% T, with a relatively a slight AT bias of 54.59%. CR of 903 bp length is located between tRNAPro and tRNAPhe. The complete mitochondrial genome may provide fundamental informative data not only for unravel the population structure and differentiation, but also for further conservation genetics studies on this balitorid species.

Ten polymorphic microsatellite loci developed from Triplophysa anterodorsalis

Triplophysa anterodorsalis is a genus Triplophysa (Rendahl) fish which belongs to the family Balitoridae, subfamily Nemacheilinae. There are 112 nominal species in the genus Triplophysa all over the world, and ∼60% of species are found in China (Chen and Yang 2005; Froese R. and Pauly D. 2008 FishBase: www.fishbase.org, ver. (06/2008)). T. anterodorsalis is an endemic fish, distributed in upper reaches of the Yangtze river, Jinsha river and its tributaries (Ding 1994). But, since 2002, four cascade hydropower stations were under construction in the lower reaches of Jinsha river (Chen et al. 2005). Fragmentation caused by these dams might disrupt the connectivity of hydro-ecosystem and the gene flow between local fish populations (Fu et al. 2003; Jiang et al. 2007; Huang et al. 2011). Due to human activities, such as overfishing, dam construction, water contamination and habitat alteration, wild fisheries of this species have declined dramatically, and the distribution ranges have been shrinking rapidly in the last decades (Gao et al. 2011). In the long run, a good understanding of the genetic diversity, population structure and differentiation of T. anterodorsalis is required in order to establish adequate management plans for the conservation of this species. While the need for restoration of T. anterodorsalis, has been recognized, a eight-year management project based on population genetics has been initiated to define the efficiency of these conservation measures since 2011 (Yu and Chen 2011). In the present study, we isolated and characterized 10 microsatellites from T. anterodorsalis. These markers will be a useful tool for studies of population demographic history, genetic structure and conservation purposes in this species.

Development and characterization of 18 microsatellite loci from the endemic elongate loach (Leptobotia elongata)

Abstract18 novel microsatellite loci were separated by the method of triplex affinity capture for Leptobotia elongate. All these 18 loci were polymorphic in L. elongate and the number of alleles per locus ranged from 5 to 14. The observed and expected heterozygosity were 0.259–0.966 and 0.486–0.918, respectively. Deviation from Hardy–Weinberg equilibrium was indicated at four loci. The significant pairwise linkage disequilibrium was found in one pair of loci. This is the first development of species-specific markers for L. elongate. These microsatellite loci would provide new opportunities for a wide range of population genetic and taxonomic studies of L. elongate.

The complete mitochondrial genome of Discogobio tetrabarbatus (Cypriniformes Cyprnidae)

Abstract The complete mitochondrial genome of a China endemic fish Discogobio tetrabarbatus is a circular molecular of 16,596 bp in size, containing 13 protein-coding genes(PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region. Most of the genes are encoded on the heavy strand, expect for ND6 and eight tRNAs. The control region is 936  bp in length and located between the tRNAPro and tRNAPhe genes. Of 13 PCGs, 7 genes (ND2, COII, ATPase 6, COIII, ND3, ND4, Cytb) had an incomplete stop codon. The complete mtDNA genome sequence obtained in this study would be useful for studying genetic diversity and phylogenetics in Discogobio tetrabarbatus and related taxa in future.

The complete mitochondrial genome of Schizothorax chongi (Fang, 1936) (Teleostei, Cyprinidae, Schizothoracinae).

Abstract Schizothorax chongi is an endemic and important polyploidy fish in the upper stream of the Yangtze River. S. chongi represents a typical model species to study historical adaptation and evolution in the Tibetan Plateau. In this study, the complete mitochondrial DNA genome sequence of S. chongi was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of S. chongi is a circular molecule of 16,584 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of S. chongi is 29.6% A, 27.1% C, 17.9% G, and 25.4% T, with a high AT content (55.0%). The results could provide useful data for further studies on phylogenetics, conservation genetics and rational resource management for S. chongi.

The complete mitochondrial genome of Lepturichthys fimbriata (Teleostei, Balitoridae, Balitorinae)

Abstract Lepturichthys fimbriata is an endemic and an important commercial fish which distributes in the upper stream of the Yangtze River. In this study, the complete mitogenome sequence of L. fimbriata has been first sequenced by DNA sequencing based on the PCR fragments. The mitogenome, consisting of 16,567 base pairs (bp), includes 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNA genes and a non-coding control region (CR). The overall base composition of L. fimbriata is 30.4% A, 28.7% C, 16.5% G, and 24.4% T, with a relatively a slight AT bias of 54.7%. CR of 903 bp length is located between tRNAPro and tRNAPhe. The complete mitochondrial genome sequence would be useful for further studies on conservation genetics and resource management in L. fimbriata.