Xufa Ma

The complete mitochondrial genome of Cottus sibiricus altaicus (Scorpaeniformes: Cottidae).

Abstract In this study, the complete sequence of the 16,527 base pairs Cottus sibiricus altaicus mitochondrial genome was presented. The composition of the whole mitochondrial DNA was 26.93% for A, 26.30% for T, 29.70% for C, 17.07% for G. The genes found in C. sibiricus altaicus and other vertebrate mtDNA were the same, which contained the genes for 13 proteins, 22 transfer RNAs, 2 ribosomal RNAs and 2 main non-coding genes (the control region (CR) and the origin of the light strand replication (OL). The sequence showed high economy of organization in that there were few nucleotides between individual genes except for the control region.

The complete mitochondrial genome of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae)

Abstract As reported, previous studies of Phoxinus phoxinus ujmonensis (Cypriniformes: Cyprinidae) have focused primarily on morphology and ecology. In this study, we cloned and sequenced the complete nucleotide sequence of the mitochondrial genome for P. phoxinus ujmonensis. The mitogenome was 17,738 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was 28.50% for A, 28.24% for T, 25.32% for C and 17.94% for G. The control region was revealed to contain tandem repeats. The mitogenome data of P. phoxinus ujmonensis should contribute to phylogenetic analysis and studies of population genetics of Phoxinus fishes.

The complete mtDNA genome of Triplophysa dorsalis (Cypriniformes, Balitoridae, Cobitoidea): genome characterization and phylogenetic analysis

Abstract Based upon the morphological characters, the genus Triplophysa (plateau Loach) is a highly diverse group in the family Balitoridae (or Cypriniformes, Cobitoidea) with 133 valid species. Therefore, the taxonomic relationship of this species at the genetic level remains ambiguous. In the present study, we sequenced the complete mitochondrial genome of Triplophysa dorsalis. In order to understand its position and genetic background at the gene level, the characteristics of mitochondrial DNA sequences and phylogenetic relationship were examined. The mitochondrial genome of T. dorsalis is similar to those of the typical vertebrates, 16 572 bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop). All genes were encoded on the heavy strand except for ND6 and 8 tRNA genes. The overall base composition of the heavy strand was 28.16%, 28.41%, 25.62% and 17.82% for A, T, C and G, respectively. Phylogenetic analyses showed that the seven Triplophysa species clustered together with T. dorsalis to form a sister group with Triplophysa strauchii, T. bleekeri, T. stoliczkai and T. bombifrons. The two genera Triplophysa and Barbatula formed a sister-group relationship, the species Homatula potanini located in the intermediate position, and the genus Leptobotia elongata was in the basal position in the subfamily Nemacheilidae. Further investigations with more Triplophysa species need to be performed for better understanding of the evolutionary history of this fascinating genus.

Reproductive biology of bream Abramis brama (L.) in the lower reaches of the Irtysh River, China

The reproductive biology of bream Abramis brama (L.) was studied from 546 fish collected from the lower reaches of the Irtysh River in Xinjiang, north-west China, from March to November 2013. The overall sex ratio (M/F) was 1.06:1, and was not significantly different from the theoretical 1:1 ratio (P>0.5). However, there was a dominance of males during the pre-spawning season (1.33 in March and 1.56 in April, P<0.5), while females were dominant during the peak spawning season (0.88 in June, P<0.5). The monthly variation in gonadosomatic index (GSI) and proportion of gonads at each macroscopic maturity stage, indicated that A. brama spawned once a year with peak spawning occurring from late May to June. The unimodal distribution of oocyte diameter each month indicated that A. brama is a single spawner, with a high degree of spawning synchronicity. The standard lengths (SL50) and ages (A50) at first maturity for males and females, were 178 and 204 mm, and 5.6 and 6.8 years, respectively. The mean absolute fecundity (AF) was 77 311 eggs per fish, and mean relative fecundity (RF) was 162 eggs per gram of body weight (BW). The AF of A. brama increased linearly with increasing of gonad weight (GW), eviscerated weight (EW) and standard length (SL), but was not significantly correlated with age. As, A. brama in the lower reaches of the Irtysh River reaches reproductive maturity relatively late in their life span, is mature for a short period and spawns in aggregations, this fish is vulnerable to overexploitation.

The complete mitochondrial genome of Leuciscus idus (Cypriniformes: Cyprinidae)

Abstract In this study, we determined the complete nucleotide sequence of the mitochondrial genome for a cold water fish, Leuciscus idus. The complete mitochondrial genome was sequenced and analyzed using the primer walking method and 30 pairs of newly designed primers were used. Direct sequencing of the PCR products demonstrated that the genome contained the same 37 mitochondrial genes (two ribosomal RNA, 22 transfer RNA and 13 protein-coding genes) and two main non-coding regions (the control region and the origin of the light strand replication) as those found in other vertebrates. Nearly all the protein-coding genes’ start codons were ATG except COX 1, meanwhile, the termination codons of which varied with TAA, TA, T, or TAG.

The complete mitochondrial genome of Lucioperca lucioperca (Perciformes: Percidae)

Abstract The complete nucleotide sequence of the mitochondrial genome of Lucioperca lucioperca was cloned and sequenced in this study, which contained 16,542 bp. Results showed that the sequence was made up of 13 proteins, 22 transfer RNAs and 2 ribosomal RNA genes. The control region and the origin of the light strand replication were similar to other vertebrates. All protein-coding genes began with ATG except for COX1 and COX2, the COX1 genes started with ATC and COX2 genes started with ATT, while all of those ended with TAA, TA, T or TAG. The result could be used in related studies such as molecular ecology and evolutionary biology.

The complete mitochondrial genome of Leuciscus leuciscus baicalensis (Cypriniformes: Cyprinidae)

Abstract The complete mitochondrial genome of Leuciscus leuciscus baicalensis was cloned and sequenced in the present study. The genome which had a mostly conserved structural organization in comparison with that of other teleost fish was 16,606 bp in size. 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 COX 1, which began with GTG. However, the termination codons of 13 protein-coding genes varied with TAA, TA, T or TAG. The complete mitochondrial genome sequence provided useful information for phylogenetic analysis and studies of population genetics of L. leuciscus baicalensis.

The complete mitochondrial genome of Barbatula nuda (Cypriniformes: Nemacheilidae).

Abstract In this study, we cloned and sequenced the complete mitochondrial genome of Barbatula nuda. The genome was found to be 16,619 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). 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 varied with TAA, TA, T or TAG. The complete mitochondrial genome sequence is useful for phylogenetic analysis and studies of population genetics of B. nuda.

The complete mtDNA genome of Triplophysa strauchii (Cypriniformes, Balitoridae, Cobitoidea): genome charaterization and phylogenetic analysis

Abstract In the present work, the complete mitochondrial genome of the Triplophysa strauchii (Cypriniformes: Cyprinidae, Balitoridae, Cobitoidea) is sequenced and placed, the phylogenetic analysis with another individual of Triplophysa fishes was carried out. The mitogenome is 16,590 bp in length, consisting 13 protein genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The total base composition is 28.26%, 28.49%, 25.42% and 17.82% for A, T, C and G, respectively. All genes were encoded on the heavy strand except for ND6 and 8 tRNA genes. These results will provide useful data for species identification and genetic study of Triplophysa fishes.