Dengqiang Wang

The complete mitochondrial genome of Liobagrus kingi (Teleostei, Siluriformes: Amblycipitidae)

Liobagrus kingi is endemic to southwest China and listed as endangered species (IUCN 2012). Genetic diversity is necessary for conservation issue. In studying this, the complete mitochondrial genome sequence of L. kingi has been obtained with PCR, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,483 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the against bias of G has a universality in different statistical results. The complete mitochondrial genome sequence of L. kingi would contribute to better understand population genetics and protect its genetic diversity.

The mitogenome of Liobagrus marginatoides (Teleostei, Siluriformes:Amblycipitidae)

Liobagrus marginatoides is endemic to southwest China (Ding, 1994), according to morphological taxonomy, and it is very similar to Liobagrus nigricauda, but its population is much smaller. In this study, the complete mitochondrial genome sequence of L. Marginatoides has been obtained with polymerase chain reaction (PCR), which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,498 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the against bias of G has a universality in different statistics results. The complete mitochondrial genome sequence of L. Marginatoides would contribute to better understand population genetics and protect its genetic diversity.

The complete mitochondrial gemone of Phoxinus lagowskii (Teleostei, Cypriniformes: Cyprinidae)

Abstract In this paper, we determined the whole mitochondrial DNA (mtDNA) sequence of Phoxinus lagowskii, a small freshwater fish that is distributed in rivers of north China, Russia and North Korea. The entire sequence of P. lagowskii mitochondrial genome is 16,699 bp in size, consisting of 13 protein-coding genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA) and 1 putative control region. Most of the genes are encoded on the heavy strand except ND6 and eight tRNA genes (Gln, Ala, Asn, Cys, Try, Ser, Glu and Pro) encoded on the light strand.

Genetic diversity and differentiation between populations of Glyptothorax zanaensis in the middle and lower reaches of the Nujiang River

The development of hydroelectricity in the Nujiang River would have adverse impacts on the populations of Glyptothorax zanaensis. In order to assess the genetic diversity and differentiation of this species, we sequenced the cytochrome b gene of the mitochondria in 102 individuals of the fish collected from 6 sampling sites (Gongshan, Gudeng and Lushui in the Nujiang Prefectural District and Daojie, Mengnuo and Mucheng in the Baoshan Municipal District). A total of 87 variation sites were detected in the fragment of 1 137 bp in length, with which the 102 samples were defined as 36 haplotypes. The haplotype diversity (h) and the nucleotide diversity (pi) of total samples were 0.851+/-0.028 and 0.01356+/-0.0008, respectively. Therefore, the genetic diversity of G. zanaensis was relatively low. However, the genetic diversity of the Nujiang population was significantly higher than that of the Baoshan population. The pairwise Fst value between the populations (0.475-0.846) was higher than that within the population (0.002-0.108), which implied that the Fst value was positively related to geographic distance. Analysis of molecular variance (AMOVA) showed that the genetic differentiation between the populations and within the populations were 53.65% and 46.35%, respectively. The fixation index (Fst value) was 0.5365, indicating that there existed significant differentiation between the Nujiang population and the Baoshan population. The phylogentic tree and networks of the haplotypes of G. zanaensis showed that there were two separate lineages: the Nujiang lineage and the Baoshan lineage. Each lineage represents at least one separated management unit, or belongs to an evolutionary significant unit. It was suggested that in the construction of hydroelectric projects the measures for protecting G. zanaensis should be adopted in fully considering the populations of G. zanaensis and the status quo of their population structure to avoid the occurrence of gene exchange among populations.

Complete mitochodrial genome of the redlip loach Leptobotia rubrilaris (Teleostei, Cypriniformes: Cobitidae)

Abstract In this study, the complete mitochondrial genome sequence of the Leptobotia rubrilaris has been obtained. The genome includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,585 bp. The gene arrangement and composition were identical to other vertebrate. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The complete mitochondrial genome sequence of L. rubrilaris would contribute to better understand population genetics and protect its genetic diversity.

The mitogenome of Leptobotia microphthalma (Teleostei, Cypriniformes: Cobitidae)

Abstract The Leptobotia microphthalma belongs to family Cobitidae, which is endemic to the upper reaches of the Yangtze River in China. In this studying, the complete mitochondrial genome sequence of L. microphthalma has been obtained with PCR, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,512 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The complete mitochondrial genome sequence of L. microphthalma would contribute to better understand population genetics and protect its genetic diversity.

Mitochondrial DNA diversity of Glyptothorax zanaensis (Wu et al., 1981) populations in Nu River, China

The hillstream fish, Glyptothorax zanaensis (Wu et al., Oceanol Limnol Sin 12:74–79, 1981) is a freshwater teleost species belonging to the order Siluriformes, endemic to Nu River and Lancang River basin. Because wild stocks of G. zanaensis have declined substantially in recent years, owing to overexploitation, pollution, illegal fishing practices and the development of hydroelectricity in the Nu River, the populations of G. zanaensis have markedly declined in recent years. We studied the mitochondrial DNA cyt b gene to assess the genetic diversity of G. zanaensis in seven tributaries of the Nu River. Seventy variable sites defined 15 haplotypes in 153 individuals. Haplotype diversity and nucleotide diversity were 0.542 ± 0.014 and 0.011 ± 0.007, respectively. The Sunzu River site had the highest haplotype diversity (Hd, 0.893 ± 0.014) and nucleotide diversity ( Pi, 0.010 ± 0.012). Genetic diversity was low in the Dong River, Fengwei River and Mengtong River. Pairwise FST values ranged from 0.00 to 1.00. Significant FST values were found for Sunzu River sampled sites paired with all other populations and Mengtong river sampled site paired with the others. Furthermore, the Nanpeng River sampled site was significantly differentiated from the Luoming River, Dong River and Fengwei River sampled sites. Such knowledge is essential for developing appropriate policies for the rational management of G. zanaensis.

The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae)

Abstract In the present study, the complete mitogenome sequence of Gnathopogon imberbis is determined using PCR amplification and DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,598 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the H-strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The overall nucleotide composition was 30.0% A, 27.0% T, 25.8% C and 17.2% G, with an A + T bias of 57.0%. The complete mitochondrial genome sequence will be useful for phylogenetic analysis and studies of population genetics of G. imberbis.

Isolation and characterization of twelve microsatellite loci of Leiocassis albomargintus (Rendhal) in the Yangtze River

Leiocassis albomargintus (Rendhal) is endemic to the Yangtze River basin in China. By using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol, we identified twelve microsatellite loci in a wild population. The number of alleles per locus ranged from 4 to 13. The observed and expected heterozygosity ranged from 0.4887 to 1.000 and from 0.5025 to 0.9180, respectively. Cross-amplification was tested in related species L. tenuifurcatus and L. crassilabris.

Species diversity of drifting fish eggs in the Yangtze River using molecular identification

The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river fish. Monitoring the species composition of drifting eggs during spawning season is important for protection issues. In this study, we have sampled drifting fish eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 fish eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the eggs, were classified in the Family Cyprinidae. Abundance and Shannon–Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some fish species. The Jaccard’s similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for fish egg identification in Yangtze River and these data are useful for conservation efforts.