Xiujie Zhang

The complete mitochondrial genomes of natural diploid and tetraploid loaches Misgurnus anguillicaudatus (Cypriniformes: Cobitidae)

Abstract Dojo loach Misgurnus anguillicaudatus, a small-sized freshwater fish species, is not only one of the most important cultured fish in East Asia, but also a promising model animal to study evolutionary biology for polyploidy. We sequenced the complete mitochondrial genomes from the natural diploid and tetraploid individuals of this species. The two different cytotypes loaches share the same length (16,646 bp) and structural organization of mitochondrial genome. The two genomes have 98.3% nucleotide sequence similarity, and the biggest nucleotide sequence divergence between homologous genes is observed in CYTB gene.

The complete mitochondrial genome of natural Misgurnus bipartitus (Cypriniformes: Cobitidae)

Abstract Misgurnus bipartitus, a small sized freshwater fish species, is one of the most important cultured fish in East Asia. In this study, the complete mitochondrial genome of M. bipartitus is sequenced to be 16,636 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of M. bipartitus in descending order is A 29.79 %, T 27.95%, C 25.90% and G 16.36%, with a slight A + T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of M. bipartitus and the elucidation of evolutionary mechanisms in Cobitidae.

The complete nucleotide sequence of white Amur bream (Parabramis pekinensis) mitochondrial genome

Abstract White Amur bream, Parabramis pekinensis (Cypriniformes: Cyprinidae), a freshwater cyprinid fish, is an important economic fish in several countries, especially in China. The complete sequence of P. pekinensis mitochondrial genome has been determined. The genome is 16,622 bp in length, and consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and the noncoding control region, with the genomic organization being identical to that of typical vertebrates. Three conserved sequence blocks (CSB1 to CSB3) were identified in the control region. The complete mitochondrial genome sequence is useful for phylogenetic analysis and studies of population genetics of P. pekinensis.

Organization of the mitochondrial genome of Odontobutis sinensis (Perciformes: Odontobutidae): rearrangement of tRNAs and additional non-coding regions

Abstract In this study, we cloned and sequenced the complete mitochondrial genome of Odontobutis sinensis. The genome was found to be 17,441 bp in size with a mostly conserved structural organization when compared with that of other teleost fish. It contained 37 genes (13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes) and two main non-coding regions (the control region and the origin of the light strand replication). Rearrangements of tRNAs (tRNA-Ser, tRNA-Leu, tRNA-His) and three additional longer non-coding regions (51 bp, 622 bp and 66 bp, respectively) were present between the ND4 and ND5 genes. Within the control region, one 322 bp long tandem repeat area (7*46 bp) and some typical conserved domains were identified. The molecular data here we presented could play a useful role to study the evolutionary relationships and population genetics of the Odontobutidae.

Complete mitochondrial genome of the freshwater goby Odontobutis potamophila (Perciformes: Odontobutidae)

Abstract In this study, we cloned and sequenced the complete mitochondrial genome of Odontobutis potamophila. The genome was found to be 16,932 bp in size with a mostly conserved structural organization when compared with that of other teleost fish. It contained 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and 2 main non-coding regions (the control region and the origin of the light strand replication). Rearrangements of tRNAs (tRNA-Ser, tRNA-Leu, tRNA-His) and three additional longer non-coding regions (43 bp, 336 bp and 76 bp, respectively) were present between the ND4 and ND5 genes. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified. This mitogenome sequence data would contribute to better understanding population genetics and phylogenetic analysis of the Odontobutidae.

The complete mitochondrial genome of Culter dabryi (Cyprinidae: Cultrinae)

Abstract Culter dabryi, a medium-sized economic cyprinid fish, is widely distributed in East Asia. We sequenced the complete mitochondrial genome of this species. The genome is 16,622 bp in length, and consists of 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and the non-coding control region with a structural organization conserved relative to that of other fishes. The overall base composition of C. dabryi in descending order is A 31.51%, C 27.60%, T 24.95% and G 15.94%, with a slight A + T bias. The mitogenome sequence data may provide useful information to the population genetics analysis of C. dabryi and the elucidation of evolutionary mechanisms in the endemic clade of East Asian Cyprinidae.

The complete mitochondrial genome of Schizothorax pseudaksaiensis (Cypriniformes: Cyprinidae).

Abstract The complete mitochondrial genome of Schizothorax pseudaksaiensis was cloned and sequenced in the present study. The genome was 16,582 bp in size, which had a mostly conserved structural organization in comparison with that of other teleost fish. It consisted of 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes), and 2 main non-coding regions (the control region and the origin of the light strand replication). All protein-coding genes started with ATG except for COX1, which began with GTG. However, the termination codons of 13 protein-coding genes varied with TAA, TA, T or TAG. The overall base composition of S. pseudaksaiensis in descending order was A 30.18%, C 27.08%, T 25.37% and G 17.37%, with a slight A + T bias. The complete mitochondrial genome sequence may provide useful information for phylogenetic analysis and studies of population genetics of S. pseudaksaiensis.

The complete mitochondrial genome of Micropercops swinhonis (Perciformes: Gobioidei: Odontobutidae)

Abstract For understanding the phylogenetic position of Micropercops swinhonis within the family Odontobutidae, the complete nucleotide sequence of M. swinhonis mitochondrial genome was firstly determined. The genome is 16,493 bp in length, and consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes) and 2 main noncoding regions (the control region and the origin of the light strand replication). The gene composition and order of which were similar to most other vertebrates. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified.

The complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Megalobrama skolkovii (♂)

Abstract The complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Megalobrama skolkovii (♂) was characterized first in this study. The total length of the genome was identical to the female parent as 16 623 bp, and the overall base composition was 31.23% A, 24.69% T, 27.89% C, and 16.19% G, with a slight A + T bias. It contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions (the control region and the origin of the light-strand replication). This study discovered the 99.88% sequence identity between the hybrid and its female parent, which confirmed the maternal inheritance pattern followed by the mitochondrial genome of the hybrid. However, the sequence alignment of mitochondrial genomes between the hybrid and its female parent revealed a total of 20 variable sites in 10 genes or regions, especially 4 sense mutations in 2 PCGs (COX1 and ATPase6). The complete mitochondrial genome sequence of this hybrid bream may provide an important dataset for further study in mitochondrial inheritance mechanism.

Species identification and evolutionary inference of the genera Megalobrama and Parabramis (Cyprinidae: Cultrinae) in China

Abstract The species boundaries and evolutionary relationships of two closely related genera, Megalobrama and Parabramis, were inferred from the partial mitochondrial cytochrome oxidase subunit I (COI) gene, NADH dehydrogenase subunit 2 (ND2) gene and their concatenated segment. Phylogenetic reconstructions showed that among the three breams, Megalobrama amblycephala and Megalobrama skolkovii are more closely related to each other than either is to Megalobrama terminalis. The taxonomy of M. pellegrini should be reconsidered. The divergence time estimation based on the assumption of a global molecular clock indicated that speciation and dispersal of the two genera might have occurred at approximately Pliocene to Late Pleistocene, due to major paleo-environmental events associated with monsoon evolution and the formation of the Three Gorges of the Yangtze River.