Nian Xu

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

Characterization of microsatellite loci in Sinilabeo rendahli and cross-amplification in four other Chinese cyprinid species

Twenty-eight microsatellite loci were isolated in Sinilabeo rendahli, an endemic cyprinid fish in China. In a test on a population of 48 individuals, 15 primer pairs exhibited polymorphism with 2–12 alleles per locus, while the rest 13 were monomorphic. Observed and expected heterozygosities ranged from 0.104 to 0.915 and 0.195 to 0.865, respectively. Four loci showed significant deviation from Hardy–Weinberg equilibrium and two of them had evidence of null alleles. Twenty-six markers successfully cross-amplified in at least one of the four additional Chinese cyprinid species (Garra pingi pingi, Pseudogyrincheilus procheilus, Discogobio yunnanensis and Onychostoma sima) examined in this study.

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.

Complete mitochondrial genome of Pareuchiloglanis sinensis (Siluriformes: Sisoridae).

Abstract The complete mitochondrial genome of Pareuchiloglanis sinensis, an endemic Chinese sisorid fish, was determined by DNA sequencing based on the PCR fragments. The complete mtDNA genome sequence of P. sinensis is 16,593 bp in length, with a gene content of 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and a typical gene arrangement identical to many other reported fishes. The overall base composition of the heavy strand was 30.6% A, 24.2% T, 16.0% G and 29.2% C, with a relatively high A + T content (54.8%). This will provide a useful tool for understanding the genetic diversity, population structure and conservation status of P. sinensis in future.

Development of sixteen novel polymorphic microsatellite markers in Rhinogobio ventralis (Teleostei, Cyprinidae, Gobioninae)

Abstract In the present study, we developed 16 polymorphic microsatellite loci in Rhinogobio ventralis, an endemic cyprinid fish in the upper reaches of the Yangtze River. The polymorphism of each locus was assessed in 32 individuals collected from Jiangjin section of the Yangtze River. A total of 126 alleles were detected and the number of alleles per locus ranged from 2 to 16. The observed and expected heterozygosities ranged from 0.161 to 0.968 and from 0.154 to 0.928, respectively. Two loci significantly deviated from Hardy–Weinberg equilibrium. No significant linkage disequilibrium was found between pairs of loci. These polymorphic microsatellites will be useful tools in the study of genetic diversity and population structure of R. ventralis.

Microsatellites development for rock carp ( Procypris rabaudi ) and cross-species testing in Onychostoma sima and Spinibarbus sinensis

A total of thirty-six microsatellite loci were isolated and characterized in the endemic and endangered fish species rock carp (Procypris rabaudi) from China. Each locus was screened in a population of natural and artificial breeding individuals. The number of alleles observed per locus ranged from 2 to 13. The observed and expected heterozygosities ranged from 0.267 to 1.000 and 0.378 to 0.910. No significant linkage disequilibrium was detected among the loci. Significant deviations from Hardy–Weinberg equilibrium were found in fifteen loci, of which seven loci had evidence of null alleles. Twenty-five primer pairs cross-amplified in Onychostoma sima while thirty-two primer pairs cross-amplified in Spinibarbus sinensis. These microsatellite loci will be useful for future investigation on genetic population structure of P. rabaudi as well as other related species.

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.

Characterization of the complete mitochondrial genome sequence of Homatula potanini (Cypriniformes, Nemacheilidae, Nemachilinae)

Abstract Homatula potanini is an endemic and one of ornamental fishes in the upper stream of the Yangtze River and its tributaries. However, wild populations of H. potanini declined sharply due to anthropological activity in the Jinsha River during the past decades. In present study, the complete mitochondrial DNA genome sequence of H. potanini was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial genome sequence is a circular molecule of 16,569 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 H. potanini is 30.1% A, 26.9% C, 16.7% G, and 26.3% T, with a relatively high A + T content (56.4%). The results could provide useful data for studies on genetic structure and rational resource conservation in H. potanini.

Identification of novel polymorphic microsatellite loci in the endangered Chinese sucker ( Myxocyprinus asiaticus )

Chinese sucker (Myxocyprinus asiaticus Bleeker), an endangered freshwater fish in China and the only representative of the family Catostomidae in Asia (Nelson 1976), is distributed mainly in the upper reaches of the Yangtze river. It is important in studies of systematics and zoogeography, and has significant economic value for its delicious taste. However, wild populations of M. asiaticus have declined dramatically since the 1970s due to overfishing, damming and other anthropogenic influences (Zhang et al. 2000). M. asiaticus was listed as second class national protected species and vulnerable in the China red data book of endangered animals (Wang 1998). Studies on artificial propagation of M. asiaticus have been carried out since the 1970s and a release programme in the Yangtze river on a large scale was first conducted in 2005. However, no genetic information was used in any of these conservation programmes, which may have led to unintended consequences. Although a few sets of microsatellite loci in M. asiaticus have been identified in recent years (Chen et al. 2010; Cheng et al. 2012; Li et al. 2012), more valid loci are needed to provide a broad knowledge of genetic structure in future studies. This paper reports characterization of 10 novel polymorphic microsatellite loci that show simple four-base-pair motifs.

Development of twenty-nine polymorphic microsatellite loci from largemouth bronze gudgeon (Coreius guichenoti

Largemouth bronze gudgeon (Coreius guichenoti) is an endemic freshwater fish in the upper reaches of the Yangtze river in China (Ding 1994). As a typical migratory river fish, broodstocks of C. guichenoti spawn in the middle and lower reaches of the Jinsha river, which is part of the upper reaches of the Yangtze river. The eggs hatch in the process of drifting downstream, then the juvenile fish is traced towards upstream of the Yangtze river to spawn (Cao 2008). The impoundment of Xiangjia dam in 2012 and Xiluodu dam in 2013 on the lower reaches of the Jinsha river have blocked the migration routes of C. guichenoti supplementary stocks because of which the number of broodstocks declined significantly. Artificial propagation of C. guichenoti has been developed to conserve the resources. Besides increasing the number ofC. guichenoti populations, maintaining the genetic diversity of populations should also be concerned in the conservation strategy. To date, 29 polymorphic microsatellites have been published for C. guichenoti, and 25 of their motifs are dinucleotide repeats (Liao et al. 2007; Xu et al. 2007). Genetic diversity in seven populations of C. guichenoti has been examined using 11 loci isolated by Liao et al. (2006, 2007). Dramatic population differentiation among populations which were seperated by dams was observed (Zhang and Tan 2010). No significant variation occurred among populations in continuous habitat (Zhang and Tan 2010), which was consistent with the study by Yuan et al. (2008). Therefore it is necessary to analyse the genetic diversity of populations seperated by Xiangjia dam and Xiluodu dam. Dinucleotide microsatellites have been demonstrated to be less polymorphic and stable than trinucleotide and