Ruibin Yang

Complete mitochondrial genome of Rhinogobius giurinus (Perciformes: Gobiidae: Gobionellinae).

Abstract In this study, we present the complete mitochondrial gene for the freshwater goby Rhinogobius giurinus. The genome is a circular molecule of 16,520 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 2 main non-coding regions (the control region and the origin of the light strand replication). The overall base composition of R. giurinus is 26.08% for T, 29.56% for C, 27.73% for A and 16.63% for G, with a slight A + T bias of 53.81%. It has the typical vertebrate mitochondrial gene arrangement.

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.

Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations

To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis. Additionally, the present gene order and the positions of associated intergenic spacers of these Odontobutis mitogenomes indicate that this unusual gene rearrangement results from tandem duplication and random loss of large-scale gene regions. Moreover, these mitogenomes exhibit a high level of sequence variation, mainly due to the differences of corresponding intergenic sequences in gene rearrangement regions and the heterogeneity of tandem repeats in the control regions. Phylogenetic analyses support Odontobutis species with shared gene rearrangement forming a monophyletic group, and the interspecific phylogenetic relationships are associated with structural differences among their mitogenomes. The present study contributes to understanding the evolutionary patterns of Odontobutidae species.

The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae).

Abstract The complete mitochondrial DNA (mtDNA) sequence of Rhodeus fangi is 16,733 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes and 2 non-coding regions. Base composition of the genome is A (28.54%), G (17.67%), C (27.03%) and T (26.76%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes. The complete mitogenome of the R. fangi can provide a basic data for phylogenetic relationship study and useful information for taxonomic identification of the R. smithii complex in genus Rhodeus.

Complete mitochondrial genome of the Chinese bitterling Acheilognathus macropterus (Cypriniformes: cyprinidae)

Abstract Acheilognathus macropterus belongs to the family Acheilognathinae. In the present study, we obtain the complete mitochondrial genome of the Chinese bitterling A. macropterus by PCR amplification and DNA sequencing. It is a circular double-stranded DNA molecule of 16,773 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two main non-coding regions (the control region and the origin of the light strand replication). The gene composition and order of which are similar to most other vertebrates. Compared with Acanthorhodeus macropterus, they share 98.90% nucleotide sequences similarity, and the biggest nucleotide sequence discrepancy between homologous genes are observed in ND5 gene. The molecular data we presented here could provide useful information for the studies on species identification, evolutionary relationships and population genetics of the Acheilognathinae.

Complete mitochondrial genome of Macropodus ocellatus (Perciformes: Anabantidae: Macropodusinae).

Abstract In this study, we cloned and sequenced the complete mitochondrial genome of Macropodus ocellatus. The genome is a circular molecule of 16,501 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 2 main non-coding 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. All protein-coding genes are initiated with ATG except for COX 1, which begin with GTG instead. However, the termination codons of 13 protein-coding genes are varied with TAA, TA, T or AGG. This mitogenome sequenc data would contribute to better understanding species identification, evolutionary relationships and population genetics of the Macropodus.

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.

Isolation and characterization of nineteen novel polymorphic microsatellite loci for the northern snakehead Channa argus

Channa argus is one of the most important economic fish species in China. However, there is limited genetic information on its population structure and genetic diversity. Nineteen novel polymorphic microsatellite loci were isolated and characterized in 42 individuals from one natural population collected from the Poyang Lake in Jiangxi Province. The number of alleles per locus ranged from 5 to 18 with an average of 11.16. The observed and expected heterozygosities ranged from 0.214 to 1.000 and from 0.630 to 0.923, respectively. The average polymorphic information content value was 0.814. Among these polymorphic microsatellites, eleven loci conformed to Hardy–Weinberg equilibrium. These microsatellite loci are currently being used to assess the genetic diversity and population structure of C. argus and will contribute to the effective conservation and rational utilization of genetic resources of this species.

Complete mitochondrial genome of the Chinese bitterling Rhodeus sinensis (Cypriniformes: Cyprinidae)

Abstract The mitochondrial genome of the Chinese bitterling Rhodeus sinesis is a circular molecule of 16,677 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two main non-coding 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. All protein-coding genes are initiated with ATG except for COX 1, which begin with GTG instead. However, the termination codons of 13 protein-coding genes are varied with TAA, TA, T or TAG. The molecular data we presented here could provide useful information for the studies on species identification, evolutionary relationships and population genetics of the Acheilognathinae.