Zuogang Peng

The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes)

The Chinese rare minnow, Gobiocypris rarus, which is endemic to China, is an attractive aquatic laboratory animal in China. In the present study, the complete mitogenome sequence of G. rarus has been determined using long polymerase chain reaction (PCR) method. It was 16,601 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, the gene composition and order of which are similar to most other vertebrates. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand is 29.5% A, 27.6% T, 25.7% C, and 17.2% G, with a slight AT bias of 57.1%. There are 10 regions of gene overlap totaling 27 bp and 13 intergenic spacer regions totaling 63 bp. The mitogenome sequence of G. rarus could contribute to a better solution of its phylogenetic position within cyprinid fishes based on the whole mitogenomic data.

The complete mitochondrial genome of the spotted steed, Hemibarbus maculatus (Teleostei, Cypriniformes).

The complete mitogenome sequence of the spotted steed (Hemibarbus maculatus) was determined using long PCR reactions. The genome is 16,611 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene order and composition of H. maculatus was similar to that of most other vertebrates. The base composition of H-strand in descending order is A (29.16%), C (27.41%), T (25.93%), and G (17.50%), with an AT content of 55.09%. The Kimura two-parameter distances between mitogenome sequences of H. maculatus and Hemibarbus labeo, Hemibarbus barbus, Hemibarbus longirostris, Hemibarbus mylodon were 2.09%, 2.35%, 12.77%, and 13.92%, respectively. The phylogenetic relationships among the five Hemibarbus species based on the whole mitogenome sequence data were (((H. barbus, H. labeo), H. maculatus), (H. longirostris, H. mylodon)).

Mitochondrial genome of Onychostoma lini (Teleostei, Cypriniformes)

The complete mitogenome sequence of a vulnerable species Onychostoma lini was determined using polymerase chain reaction and directly sequenced with primer walking method. The complete mitogenome was 16,595 bp in length, containing 37 genes of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene order and composition of O. lini was similar to most other fishes. The descending order of the base composition on heavy strand was 31.6% A, 27.9% C, 24.6% T, and 15.9% G, with a relatively lower level of G and a slight AT bias of 56.2%. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The complete mitogenome sequence of O. lini provides fundamental data for further conversation genetics and captive breeding studies on this species.

The complete mitogenome sequence of a cave loach Triplophysa rosa (Teleostei, Balitoridae, Nemacheilinae)

China is very rich in cavefishes and some detailed studies on their taxonomy and biology have been carried out, but many other aspects such as genetics and evolution need further investigation. Here, we sequenced the complete mitogenome sequence of the Rose Blind Plateau Loach, Triplophysa rosa, and combined with other 27 ostariophysan complete mitogenome sequences, the phylogenetic position of T. rosa was estimated. The 16,585 bp mitogenome of T. rosa was a typical vertebrate mitochondrial genome containing 13 protein-coding, 2 rRNA, 22 tRNA genes, and 1 control region (CR). The CR of T. rosa was characterized by one termination-associated sequence and seven conserved sequence blocks (CSB-B, D, E, F, and CSB I, II, III). Phylogenetic analyses showed that T. rosa belongs to the subfamily Nemacheilinae and formed a sister-group relationship with the genus Barbatula. Further analyses based on the concatenated mitochondrial cyt b and D-loop sequences showed that T. rosa clustered with other Triplophysa species, and it was located in the basal position within the genus. In addition, the molecular clock estimations showed that T. rosa might have diverged from other Triplophysa species at about 48.3 million years ago during the rapid uplift period of the Qinghai-Tibetan Plateau.

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

The genus Triplophysa (plateau loach) is a highly diverse group in the family Balitoridae with 133 valid species, and they play an important role in zoogeographic study of the Qinghai-Tibet Plateau. In this study, we sequenced the complete mitochondrial genome of a Triplophysa species, Triplophysa bleekeri. Combined with the complete mitogenome sequences of other 10 balitorids, the phylogenetic position of T. bleekeri was estimated. The mitochondrial genome of T. bleekeri is similar to those of the typical vertebrates, 16,568 bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding control region (D-loop). In the D-loop region, two pair of motifs, “TACAT” and its reverted and complemented sequence “ATGTA”, can be found in the domain of termination-associated sequence; six conserved sequences (CSB-F, CSB-E, CSB-D, and CSB I–III) can be identified by searching some conserved motifs. Phylogenetic analyses showed that the three Triplophysa species clustered together, with T. bleekeri sister to Triplophysa stoliczkai. The two genera Triplophysa and Barbatula formed a sister-group relationship, the genus Lefua located in the intermediate position, and the genus Schistura was in the basal position in the subfamily Nemacheilinae. Further investigations with more Triplophysa species included need to be performed to better understand the evolutionary history of this intriguing genus.

Determination and comparison of two complete mitochondrial genomes of golden Chinese loach, Sinibotia superciliaris (Teleostei, Cypriniformes)

The golden Chinese loach, Sinibotia superciliaris (Günther, 1892) is an endemic fish in China, which is only distributed in the main river and tributaries of the upper and middle Yangtze River. In this study, we sequenced two mitochondrial genomes simultaneously from two samples of S. superciliaris collected from two different locations. Both mitogenomes were 16,572 bp in length, showing a typical vertebrate mitogenome feature with 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 major non-coding control region (CR). Alignment and comparative analyses showed that the two mitogenome sequences possessed 22 mutation sites, all of which were transitions and mainly occurred in protein-coding genes (13/22) and CR (7/22). Among the 13 mutation sites that occurred in protein-coding genes, three mutation sites occurred in the first codon position and the remaining 10 sites occurred in the third codon position. However, only one mutation that occurred in the first codon position resulted in non-synonymous substitution in COI gene. The molecular data presented in this study will contribute to further phylogenetic analyses for this group of fishes.

The complete mitochondrial genome of Percocypris pingi (Teleostei, Cypriniformes).

Percocypris pingi is an endemic and economic fish species only found in the upper Yangtze River basin in China. It has become endangered in recent years due to overfishing and/or dam construction. However, the available genetic data are still scarce for this species. Here, we sequenced the complete mitochondrial genome sequence of P. pingi using long polymerase chain reactions. The complete mitogenome sequence has 16,586 bp and contains the usual 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and 1 control region, the gene composition and order of which are similar to most of other vertebrates. Most mitochondrial genes except ND6 and eight tRNAs are encoded on the heavy strand. The overall base composition of the heavy strand is 30.9% A, 25.7% T, 26.6% C, and 16.8% G with a slight AT bias of 56.6%. There are seven regions of gene overlaps totaling 23 bp and 11 intergenic spacer regions totaling 35 bp. Combined with the COI barcoding region sequences of other 25 cyprinids, the phylogenetic position of P. pingi was estimated using neighbor-joining method. The results showed that P. pingi had a close phylogenetic relationship with the species from genus Schizothorax. This mitogenome sequence data of P. pingi would provide the fundamental genetic data for further conservation genetic studies for this endangered fish species.

High-throughput microsatellite marker development in Amur catfish (Silurus asotus) using next-generation sequencing

The Amur catfish, Silurus asotus, is an economically important fish species in East Asia, but few genetic studies have been conducted on this species, especially those based on nuclear markers. Here, we isolated and characterized 47 novel polymorphic microsatellite loci in the genome of S. asotus using 454 sequencing. We screened 70 primers and 48 of them generated amplification products. Forty-seven of the amplification products were polymorphic in a population of 40 collected from the upper Yangtze River. The number of alleles varied from 3 to 15, and the observed and expected heterozygosities varied from 0.300 to 0.800 and 0.305 to 0.866, respectively. The average polymorphic information content (PIC) of all loci was 0.682, indicating high levels of polymorphism. In addition, cross-species amplification in a congener species, Silurus meridionalis showed a high level of transferability (79.2xa0%), which confirmed that the microsatellite markers developed here could be used effectively for other related catfish species.

Mitochondrial genome of Hemibagrus macropterus (Teleostei, Siluriformes)

The complete mitochondrial genome sequence of the Chinese catfish Hemibagrus macropterus was determined using long polymerase chain reaction (PCR). The complete mtDNA sequence was 16,530 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (D-loop), the gene composition and order of which were identical to most of the other vertebrates. Two conserved sequence blocks (CSB-2 and CSB-3) in the control region can be easily identified in all available bagrid mitogenomes. The overall base composition of the heavy strand was 31.6% A, 27.7% T, 25.8% C, and 14.8% G, with an AT content of 59.3%. The mitogenome sequence of H. macropterus could be contributed to elucidate the evolutionary relationships among the bagrid catfishes, the systematics and evolution of which group remain poorly explored to date.

Mitochondrial genome of Silurus asotus (Teleostei: Siluriformes)

The complete mitogenome sequence of the Amur catfish Silurus asotus was determined using long PCRs. The genome was 16,528 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region; the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand is 30.5% A, 25.8% T, 28.0% C, and 15.8% G, with an AT content of 56.3%. The mtDNA sequence of S. asotus shared 93.6% and 90.6% sequence identity with that of Silurus meridionalis and Silurus glanis. This mitogenome sequence data would play an important role in silurid catfish phylogenetics and siluriform catfish systematics in general.