The complete mitogenome sequence and organization of Parachaeturichthys polynema (Gobiiformes: Gobiidae).

In this study, the complete mitochondrial genome of Parachaeturichthys polynema was reported. The mitochondrial genome was 16,620bp in length including 13 protein-coding genes, 23 tRNAs, 2 rRNAs, and a control region. The overall contents of A, T, G, and C were 28.56%, 26.34%, 16.22%, and 28.89%, respectively. Phylogenetic analysis of 18 species in the family Gobiidae showed that P. polynema was clustered into the subfamily Gobiinae. This information will contribute to future phylogenetic studies of P. polynema and Gobiidae.

The complete mitochondrial genome sequence and phylogenetic position of Gobio coriparoides.

In this paper, we determined the complete mitochondrial DNA (mtDNA) sequence of Gobio coriparoides and analyzed its phylogenetic position. The complete mitogenome is 16,604 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Among the 37 genes, 28 were encoded on the heavy strand, while 9 were encoded on the light strand. The overall base composition was 28.97% for A, 18.06% for G, 26.54% for T, and 26.43% for C, with a higher A + T content (55.51%). There are some overlaps existing in G. coriparoides mitochondrial genome. The neighbor-joining (NJ) phylogenetic tree based on whole mitogenome sequences supported that G. coriparoides is the closest to G. cynocephalus. This result will provide a basic reference for understanding the genetic structure, molecular evolution, and phylogeny of G. coriparoides and related species.

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications.

Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.

The complete mitochondrial genome and phylogenetic position of the half-fin anchovy, Setipinna tenuifilis (Valenciennes, 1848).

Half-fin anchovy (Setipinna tenuifilis) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of S. tenuifilis. The entire mitochondrial genome is a circular-molecule of 16,215 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI-III, Cytb, ND1-6, and 4L), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (12S and 16S rRNAs), with gene arrangement and content basically identical to those of other species of Engraulidae. The result of phylogenetic analysis strongly supported that S. tenuifilis was first clustered together with Setipinna melanochir and formed a monophyly in the genus Coilia, and then they constituted a sister-group relationship with two genus Engraulis, and Stolephorus. It concluded that the S. tenuifilis should be classified into the genus Setipinna. The present study also revealed the phylogenetic relationship of this genus at molecular levels. The complete mitochondrial genome sequence of S. tenuifilis can provide basic information for the studies on molecular taxonomy and phylogeny of teleost fishes.

The development of two novel species-specific primers for identifying genus Crassostrea, with focus on C. sikamea and C. ariakensis.

Oyster reefs have important ecological functions and environmental service values, such as filtering water, providing fish habitats, maintaining biodiversity, and carbon sequestration. Oyster reef recovery has become one of the most important means for fishery resource conservation and ecosystems restoration of coastal regions. C. sikamea and C. ariakensis are two important reef oysters along the coast of China. However, it is very difficult to identify the larvae of these two oysters. To solve this problem, we developed two pairs of novel species-specific PCR primers for identifying these two oysters. The forward C. sikamea-specific primer is Cs-F: 5'-CGAAGAGGGGCATGATAAATGAGG-3', and the reverse primer is Cs-R: 5'-ATATGAACTTCTCCAACCTCCCC-3', both of them within the scope of mitochondrial ND5 gene. The forward C. ariakensis-specific primer is Ca-F: 5'-GGGCAAATAAAAGGCAAAACCC-3', located between tRNAser and tRNApro, and the reverse primer is Ca-R: 5'-CATAAACTTCTGCAAGACTCCC-3', lies between tRNApro and small subunit ribosomal RNA (ssrRNA). These two primers can identify the larvae of C. ariakensis and C. sikamea from other oysters rapidly and effectively, with extremely high accurate rate (=100%). This molecular identification method does not require prior sorting of larvae. These two specific primers are good contribution to molecular identification of C. sikamea, C. ariakensis and other oysters, and could be a useful tool for oyster larvae identification and ecological restoration.

The complete mitochondrial genome sequence of Sphyraena jello (Perciformes: Sphyraenidae) and its phylogenetic position.

In this study, we obtained the complete mitochondrial genome sequence of Sphyraena jello and analyzed its phylogenetic position. The complete mitogenome of S. jello is 16 699 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Among the 37 genes, 28 were encoded on heavy strand, while 9 were encoded on light strand. The overall base composition was 28.97% for A, 16.14% for G, 29.64% for C, and 25.25% for T, with a higher A + T content (54.22%). The phylogenetic analysis based on 13 concatenated protein-coding genes suggested that S. jello is a sister species to Sphyraena barracuda in the family Sphyraenidae. This result should be useful for understanding the genetic structure, molecular evolution, and phylogeny of S. jello and related species.

The complete mitochondrial genome sequence of Thunnus alalunga (Bonnaterre, 1788).

Thunnus alalunga is an excellent food fish and is of great importance in recreational fisheries. In the study, the complete mitochondrial genome (mitogenome) of T. alalunga is sequenced and annotated, which is a circular DNA molecule with 16,527 bp in length. The overall nucleotide base composition of T. alalunga mitogenome is as follows: A, 28.37%; G, 16.69%; T, 25.46%; and C, 29.49%, with the A+T content of 53.83%, showing an obvious anti-G bias. The entire mitogenome encodes 37 genes in all, comprising 13 protein-coding genes (ATP6 and ATP8, COI-III, Cytb, ND1-6 and 4L), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. alalunga can provide useful information for the studies on molecular systematics, stock evaluation, and conservation genetics of teleost fishes.

Genetic structure of Scomber japonicus (Perciformes: Scombridae) along the coast of China revealed by complete mitochondrial cytochrome b sequences.

The phylogeography history and contemporary agents of selection for many marine fisheries, characterized by widespread species distributions in the face of significant harvest, remains poorly understood. Chub mackerel (Scomber japonicus) are a widespread species in the Indo-Pacific and represent one of the top five commercially fished species in the world, yet their phylogeographic history remains unknown. We characterized the genetic diversity, structure and demographic history of S. japonicus throughout adjacent Chinese seas (from the Yellow Sea to the South China Sea). Using 220 individuals from 11 sites, we inferred 55 distinct haplotypes from complete mitochondrial cytochrome b gene sequences. Haplotype diversity ranged from 0.505 to 0.967 and nucleotide diversity ranged from 0.00056 to 0.01042. Genetic differentiation (Fst) statistics suggested that the highest level of differentiation existed between the SanYa and SanSha localities (Fst = 0.86977), while the lowest levels of differentiation occurred between the DongGang and ShiDao localities (Fst ∼ 0). Kimura's genetic distances ranged from 0.001 to 0.011 within and from 0.001 to 0.018 between populations. Hierarchical analysis of molecular variance, Neighbor-joining and median-joining network analyses identified significant phylogeographic structure with two localities (SanYa, Hainan of the South China Sea and LianYunGang, Jiangsu of the East China Sea) explaining most of the genetic variation observed, while the remaining populations were poorly differentiated.

The complete mitochondrial genome sequence of Pampus chinensis (Perciformes: Stromateidae).

In this study, the complete mitochondrial genome of Pampus chinensis (Perciformes: Stromateidae) was determined. The mitogenome is 16,535 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall mtDNA nucleotide base composition of P. chinensis is A 29.72%, C 28.10%, G 15.34%, and T 26.84%, with an A + T content of 56.56%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of P. chinensis may be helpful to the studies on stock evaluation and conservation genetics of P. chinensis resource, as well as molecular phylogeny of Stromateidae.

The complete mitochondrial genome sequence of Pampus argenteus (Perciformes: Stromateidae).

In this study, we sequenced and annotated the complete mitochondrial genome of Pampus argenteus (Perciformes: Stromateidae). The mitogenome is 17,098 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall nucleotide base composition of P. argenteus mtDNA is A 30.35%, C 25.55%, G 15.28% and T 28.82%, with an A + T content of 59.17%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of P. argenteus may be helpful to the studies on conservation genetics and stock evaluation of P. argenteus resource, as well as molecular phylogeny and species identification of Stromateidae.

The sequence and organization of complete mitochondrial genome of the yellowfin tuna, Thunnus albacares (Bonnaterre, 1788).

Yellowfin tuna (Thunnus albacares) is one of the most important economic fishes around the world. In the present study, we determined the complete mitochondrial DNA sequence and organization of T. albacares. The entire mitochondrial genome is a circular-molecule of 16,528 bp in length, which encodes 37 genes in all. These genes comprise 13 protein-coding genes (ATP6 and 8, COI-III, Cytb, ND1-6 and 4 L), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. albacares can provide basic information for the studies on molecular taxonomy and conservation genetics of teleost fishes.

Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations.

The age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint differences, genes in different functional categories might show dissimilar retention patterns after duplication. It is known that genes in some functional categories are highly duplicated in the early stage of vertebrate evolution. However, the correlations of the age distribution pattern of gene duplication between the different functional categories are still unknown. To investigate this issue, we developed a robust pipeline to date the gene duplication events in the human genome. We successfully estimated about three-quarters of the duplication events within the human genome, along with the age distribution pattern in each Gene Ontology (GO) slim category. We found that some GO slim categories show different distribution patterns when compared to the whole genome. Further hierarchical clustering of the GO slim functional categories enabled grouping into two main clusters. We found that human genes located in the duplicated copy number variant regions, whose duplicate genes have not been fixed in the human population, were mainly enriched in the groups with a high proportion of recently duplicated genes. Moreover, we used a phylogenetic tree-based method to date the age of duplications in three signaling-related gene superfamilies: transcription factors, protein kinases and G-protein coupled receptors. These superfamilies were expressed in different subcellular localizations. They showed a similar age distribution as the signaling-related GO slim categories. We also compared the differences between the age distributions of gene duplications in multiple subcellular localizations. We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome.

Characterization of the complete mitochondrial genome of Gymnocypris namensis (Cypriniformes: Cyprinidae).

The complete mitochondrial DNA sequence of Gymnocypris namensis was determined and analyzed. The mitogenome of G. namensis is 16,674 bp long, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and two non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The gene order of G. namensis mitogenome is identical to that observed in most other vertebrates. The complete mitogenome sequence information of G. namensis can provide useful data for further studies on molecular systematics, taxonomic status, stock evaluation and conservation genetics.

Complete mitochondrial genome sequence of Gymnocypris dobula (Cypriniformes: Cyprinidae).

Gymnocypris dobula is listed as Vulnerable (VU) status in the IUCN's Red List of Threatened Species. In this paper, complete mitochondrial DNA sequence of G. dobula was determined. The complete mitogenome is 16,720 bp in length, and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of G. dobula is conducive to futher studies on molecular systematics, stock evaluation and conservation genetics.

Sequence and organization of the complete mitochondrial genome of Schizopygopsis thermalis (Cypriniformes: Cyprinidae).

In this study, we determined the complete mitogenome sequence of Schizopygopsis thermalis. The complete mitogenome of S. thermalis is 16,676 bp in length, which contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mtDNA sequence of S. thermalis provides useful genetic markers for the studies on molecular systematic, population genetics and phylogeography.

Complete mitochondrial genome of Pelteobagrus fulvidraco (Siluriformes: Bagridae): genome description and related phylogenetic analyses.

Pelteobagrus fulvidraco (yellow catfish) is a small-sized species in the family Bagridae, order Siluriformes. In this study, we determined the complete mitogenome sequence of P. fulvidraco and performed phylogenetic analysis with closely related species. The complete mitochondrial genome of P. fulvidraco was 16,527 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and the origin of light-strand replication. We inferred that five markers in mitogenome, i.e. D-loop, ND5, 16SrRNA, COXI and ND1, may be suitable markers for studies on population genetics, phylogeny, conservation genetics and evolutionary adaptation mechanisms.

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

In this study, we sequenced and annotated the complete mitochondrial genome of Schizothorax waltoni (Cypriniformes:Cyprinidae). The mitogenome is 16,587 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (O(L)) and control region (D-loop). The overall nucleotide base composition of S. waltoni mtDNA is A 29.96%, C 27.07%, G 17.58%, and T 25.39%, with an A + T content of 55.35%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of S. waltoni can contribute to the studies on conservation genetics and stock evaluation of S. waltoni resource, as well as molecular phylogeny and species identification of Cyprinidae.

The complete mitochondrial genome sequence of Ancherythroculter nigrocauda (Cypriniformes:Cyprinidae).

Ancherythroculter nigrocauda is a fish endemic to the upper reaches of the Yangtze River in China. In this study, we determined and analyzed the complete mitochondrial DNA (mtDNA) sequence of this species. The mitogenome is 16,623 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (O(L)) and control region (D-loop). This mitogenome sequence data can contribute to elucidate the evolutionary mechanisms, molecular systematics, and biogeography of Ancherythroculter and is useful to conservation genetics and stock evaluation for A. nigrocauda.

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

Schizothorax oconnori is mainly distributed in the Yarlung Zangbo River drainage in Tibet, China. S. oconnori is assessed as least concern species in International Union for Conservation of Nature Red List. In this paper, we determined the complete mitochondrial DNA (mtDNA) sequence of S. oconnori. The mitogenome is 16,590 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: origin of light-strand replication (O(L)) and control region (D-loop). The complete mitogenome sequence information of S. oconnori can be used in the studies on molecular systematics, stock evaluation and conservation genetics and will be helpful in the development of rational management strategies and sustainable utilization for S. oconnori resource.

The complete mitochondrial genome sequence of Schizopygopsis younghusbandi (Cypriniformes: Cyprinidae).

In this paper, we determined complete mitochondrial DNA sequence of Schizopygopsis younghusbandi. The mitogenome is 16,674 bp in length, which includes 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence of S. younghusbandi is useful to the studies on taxonomic status, molecular systematics, stock evaluation, and conservation genetics.