Xiaolin Liao

Characterization of novel microsatellite loci in rare minnow (Gobiocypris rarus) and amplification in closely related species in Gobioninae

Rare minnow (Gobiocypris rarus) is an endangered small fish endemic to upper reach of the Yangtze River. From a (GT)n enriched genomic library, 32 microsatellites were isolated and characterized. Nineteen of these loci were polymorphic in a test population with alleles ranging from 2–7, and observed and expected heterozygosities from zero to 0.8438, and 0.2679 to 0.8264, respectively. In the cross-species amplifications, 13 out of 19 polymorphic loci were found to be also polymorphic in at least one of the 7 closely related species of the subfamily Gobioninae. These polymorphic microsatellite loci should provide sufficient level of genetic diversity to evaluate the fine-scale population structure in rare minnow and its closely related species for the conservation purpose.

Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (HO) and expected (HE) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.

Development of EST-SSRs by an Efficient FIASCO-Based Strategy: A Case Study in Rare Minnow (Gobiocyrpis Rarus)

Type I markers are useful for comparative mapping and other genetic analyses, but relatively difficult to develop. In the present study a microsatellite (SSR)-enriched cDNA library was constructed for the first time using the fast isolation by AFLP of sequences containing repeats (FIASCO) method in a small fish, Chinese rare minnow (Gobiocypris rarus). A total of 97.4% of the expressed sequence tags (ESTs) contained targeted CA-repeats, in which 29 unique EST-SSRs were identified. Ten out of the 28 loci for which primer pairs were designed were polymorphic with alleles ranging from three to seven (mean 4.50). Some of these EST-SSRs can be amplified in other species. These results proved that cDNA-FIASCO is an efficient way to isolate novel EST-SSRs in a fish.

The complete mitochondrial genome of Chinese sturgeon (Acipenser sinensis)

Abstract The complete mitochondrial genome of Chinese sturgeon (Acipenser sinensis) was determined by direct sequencing of PCR products. The Chinese sturgeon mitochondrial DNA is a circular molecule (16,688 bp in length) with the typical gene arrangement of vertebrate mtDNA, containing 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region. Its control region contains 4.5 copies of unit with 82 bp long at 5′ end, which has been reported before for this species. Phylogenetic tree based on 13 protein-coding genes confirmed that the complete mtDNA sequence of Chinese sturgeon was reported here for the first time.

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 the ratmouth barbell, Ptychidio jordani (Cypriniformes Cyprnidae)

Abstract The complete mitochondrial genome of an endemic fish Ptychidio jordani is a circular molecular of 16,602 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 940 bp in length and is 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 Ptychidio jordani and related taxa in future.

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 Sinibrama taeniatus (Cyprinidae: Cultrinae).

Abstract In this study, the complete mitochondrial DNA genome sequence of Sinibrama taeniatus was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of S. taeniatus was a circular molecule of 16,623 bp in length. It consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of S. taeniatus was 31.3% A, 26.8% C, 16.1% G, and 25.8% T, with a relatively high A + T content (57.1%). The results could provide useful data for studying genetic diversity and phylogenetics in S. taeniatus and related species.