The complete mitochondrial genome sequence of the little egret (Egretta garzetta)

Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3′ end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.     

The complete mitogenome of the snakehead Channa argus (Perciformes: Channoidei): genome characterization and phylogenetic implications

To better understand the phylogenetic status of the snakehead, Channa argus, we determined its complete mitogenome sequence using long-polymerase chain reaction and the direct sequencing method. The complete mitogenome sequence was 16,559?bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. This was the first report of the mitogenome sequence in suborder Channoidei. Phylogenetic relationships of 14 perciform suborders based on mitogenome sequences were reconstructed using Bayesian inference and maximum likelihood methods. The results strongly supported the monophyly of Perciformes and the snakehead, as a representative species of suborder Channoidei, formed the most basal branch having sister relationship with the clade containing all other analyzed perciform fishes. The further phylogenetic analyses of six channid species, based on cytochrome b gene, suggested that two channid genera constituted reciprocally monophyletic clades. In addition, the relaxed molecular clock method was used to estimate divergence dates among major suborders of Perciformes and major species in Channoidei.     

山鹧鸪属鸟类线粒体基因组的比较及系统发育研究

海南山鹧鸪(Arborophila ardens)对生境选择比较严格,种群数量稀少,属于濒危物种。为进一步研究山鹧鸪属的进化和系统发育关系,文章利用Illumina Hiseq2000高通量测序技术获得了海南山鹧鸪线粒体全基因组序列,从比较基因组学角度分析了4种山鹧鸪鸟类的线粒体基因组特征,并探讨了山鹧鸪属鸟类的系统发育地位。研究结果表明：(1) 海南山鹧鸪线粒体基因组长度为16 730 bp,编码13个蛋白质编码基因、2个核糖体RNA基因、22个转运RNA基因以及1个控制区;(2) 山鹧鸪属物种受到了纯化选择的作用,且在进化过程中积累了更多的非同义替换;(3) 山鹧鸪属位于雉科鸟类系统树的基部位置,其中白眉山鹧鸪与红喉山鹧鸪互为姐妹群,海南山鹧鸪位于山鹧鸪属的基部位置,与其他3种山鹧鸪鸟类的亲缘关系较远。     

A comparative analysis of the complete mitochondrial genome of the Eurasian otter <Emphasis Type="Italic">Lutra lutra</Emphasis> (Carnivora; Mustelidae)

Otter populations are declining throughout the world and most otter species are considered endangered. Molecular methods are suitable tools for population genetic research on endangered species. In the present study, we analyzed the complete mitochondrial genome (mitogenome) sequence of the Eurasian otter Lutra lutra. The mitochondrial DNA sequence of the Eurasian otter is 16,505 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (CR). The CR sequence of otters from Europe and Asia showed nearly identical numbers and nucleotide sequences of minisatellites. Phylogenetic analysis of Mustelidae mitogenomes, including individual genes, revealed that Lutrinae and Mustelinae form a clade, and that L. lutra and Enhydra lutris are sister taxa within the Lutrinae. Phylogenetic analyses revealed that of the 13 mitochondrial protein-coding genes, ND5 is the most reliable marker for analysis of phylogenetic relationships within the Mustelidae.     

Phylogenetic relationships of discoglossid frogs (Amphibia:Anura:Discoglossidae) based on complete mitochondrial genomes and nuclear genes

The complete nucleotide sequence of the mitochondrial (mt) genome was determined for three species of discoglossid frogs (Amphibia:Anura:Discoglossidae), representing three of the four recognized genera: Alytes obstetricans, Bombina orientalis, and Discoglossus galganoi. The organization and size of these newly determined mt genomes are similar to those previously reported for other vertebrates. Phylogenetic analyses (maximum likelihood, Bayesian inference, minimum evolution, and maximum parsimony) of mt protein-coding genes at the amino acid level were performed in combination with already published mt genome sequence data of three species of Neobatrachia, one of Pipoidea, and four of Caudata. Phylogenetic analyses based on the deduced amino acid sequences of all mt protein-coding genes arrived at the same topology. The monophyly of Discoglossidae is strongly supported. Within the Discoglossidae, Alytes is consistently recovered as sister group of Discoglossus, to the exclusion of Bombina. The three species representing Neobatrachia exhibited extremely long branches irrespective of the phylogenetic inference method used, and hence their relative position with respect to Discoglossidae and Xenopus may be artefactual due to a severe long branch attraction effect. To further investigate the phylogenetic intrarelationships of discoglossids, nucleotide sequences of four nuclear protein-coding genes (CXCR4, RAG1, RAG2, and Rhodopsin) with sequences available for the three discoglossid genera and Xenopus were retrieved from GenBank, and together with a concatenated nucleotide sequence data set containing all mt protein-coding genes except ND6 were subjected to separate and combined phylogenetic analyses. In all cases, a sister group relationship between Alytes and Discoglossus was recovered with high statistical support.     

Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae

Genome comparison has shed light on many fields of both basic and applied research, including the study of species phylogeny. Grass carp (Ctenopharyngodon idella) belongs to Cyprinidae, the largest freshwater fish family; but which subfamily it belongs to remains a controversial issue. In this study, the complete mitochondrial genome (mitogenome) sequence of grass carp was determined and phylogenetic analyses of all mitochondrial protein-coding genes and a nuclear gene (RAG 2) were conducted to explore the evolutionary relationship of grass carp with other cyprinid species. The mitogenome of grass carp is 16,609 bp in length. As with most other vertebrates, it contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one putative control region. Phylogenetic analyses using two different datasets (mitochondrial and nuclear) and three different computational algorithms (Bayesian, MP and ML) all revealed two distinct groups with high statistical support, indicating that Cyprininae and Leuciscinae are two separate, valid subfamilies. Importantly, our phylogenetic result provides strong molecular evidence in support of the placement of Ctenopharyngodon in Leuciscinae rather than in Cyprininae.     

Complete mitochondrial genome of a new vole Proedromys liangshanensis (Rodentia: Cricetidae) and phylogenetic analysis with related species: are there implications for the validity of the genus Proedromys?

AIM. The complete mitochondrial genome sequence of a newly discovered vole, Proedromys liangshanensis (Rodentia: Cricetidae: Arvicolinae), was determined. RESULTS. The mitogenome of P. liangshanensis is 16,296 bp in length. As with most other mammals, it contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one putative control region. The A+T content of the control region is 58.2%, the lowest proportion detected so far in Myomorpha. To confirm the phylogenetic position of P. liangshanensis, we carried out phylogenetic analyses based on complete mitochondrial genomic data using Bayesian, maximum parsimony, and maximum likelihood methods. CONCLUSION. All results revealed that P. liangshanenis is sister to Microtus. Although the results do not bear light on the validity of the genus Proedromys, based on the morphological characters, we suggest that Proedromys is an independent genus of equal rank to the genus Microtus.     

白纹方蟹线粒体基因组全序列测定及方蟹总科比较分析

为探讨该总科内部亲缘关系及其与线粒体基因排序之间的相关性,研究以方蟹科(Grapsidae)白纹方蟹(Grapsus albolineatus)为代表种,测定其线粒体基因组全序列。其全长为15577 bp,包含13个蛋白编码基因,22个tRNA基因, 2个rRNA基因和1个控制区。基因组碱基组成为33.4%A、12.0%G、20.6%C和34.0%T,具有明显的AT偏向性(67.4%)。除ATP8和ND1以GTG作为起始密码子外,其余蛋白编码基因均以ATN作为起始密码子;除COⅡ和Cyt b以T作为不完全终止密码子外,其余基因均以TAN作为终止密码子。亮氨酸(Leu)和半胱氨酸(Cys)分别是使用频率最高(15.28%)和最低(0.81%)的两种密码子。除tRNA-Ser1缺少DHU臂外,其余tRNA均能形成典型的三叶草结构。基于13个蛋白编码基因的核苷酸序列同时构建了方蟹总科的贝叶斯树(BI)和最大似然树(ML),两种方法构建的系统发育树扑拓结构一致,均显示所有方蟹科(Grapsidae)种类聚在一起,其中白纹方蟹与同属的细纹方蟹(G. tenuicrustatus)的亲缘关系最近;...     

Complete Mitochondrial Genome of Echinostoma hortense (Digenea: Echinostomatidae)

Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans.     

社鼠（Niviventer confucianus）线粒体基因组全序列分析

社鼠（Niviventer confucianus）属于啮齿目（Rodentia）、鼠科（Muridae）、白腹鼠属（Niviventer）,关于该物种的分子系统学研究极少。为获取社鼠线粒体基因组全序列,提取其基因组总DNA,参照近缘物种线粒体基因组全序列设计34对特异性引物,利用PCR扩增全部片段后进行测序,之后对其基因组组成及结构特点进行了初步分析。结果表明,社鼠线粒体基因组全序列长16 281 bp（GenBank收录号：KJ152220）,包含22个tRNA基因、13个蛋白质编码基因、2个rRNA基因和1个非编码控制区;基因组核苷酸组成为34.0%A、28.6%T、24.9%C、12.5%G。将所得序列与社鼠近缘物种（川西白腹鼠、小家鼠、褐家鼠）的线粒体全基因组进行比较,结果显示,四个物种的线粒体基因组虽然在基因组大小、部分tRNA二级结构、部分蛋白质编码基因的起始或终止密码子及控制区长度和碱基组成上有差异,但基因组结构和序列特征方面都具有较高的相似性。四个物种线粒体全基因组间的遗传距离显示,社鼠与川西白腹鼠距离最近,而与小家鼠距离最远。该研究为利用线粒体全基因组信息进行啮齿类分子系统学研究提供了有价值的资料。     

The complete mitochondrial genome of Microtus fortis calamorum (Arvicolinae, Rodentia) and its phylogenetic analysis

Microtus fortis is a special resource of rodent in China. It is a promising experimental animal model for the study on the mechanism of Schistosome japonicum resistance. The first complete mitochondrial genome sequence for Microtus fortis calamorum, a subspecies of M. fortis (Arvicolinae, Rodentia), was reported in this study. The mitochondrial genome sequence of M. f. calamorum (Genbank: JF261175) showed a typical vertebrate pattern with 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs and one major noncoding region (CR region).The extended termination associated sequences (ETAS-1 and ETAS-2) and conserved sequence block 1 (CSB-1) were found in the CR region. The putative origin of replication for the light strand (O(L)) of M. f. calamorum was 35bp long and showed high conservation in stem and adjacent sequences, but the difference existed in the loop region among three species of genus Microtus. In order to investigate the phylogenetic position of M. f. calamorum, the phylogenetic trees (Maximum likelihood and Bayesian methods) were constructed based on 12 protein-coding genes (except for ND6 gene) on H strand from 16 rodent species. M. f. calamorum was classified into genus Microtus, Arvcicolinae for the highly phylogenetic relationship with Microtus kikuchii (Taiwan vole). Further phylogenetic analysis results based on the cytochrome b gene ranged from M. f. calamorum to one of the subspecies of M. fortis, which formed a sister group of Microtus middendorfii in the genus Microtus.     

Complete mitochondrial genome of Neochauliodes parasparsus (Megaloptera: Corydalidae) with phylogenetic consideration

We sequenced the complete mitochondrial genome (mitogenome) of Neochauliodes parasparsus. The 15,995-bp mitogenome contained the standard set of 13 protein-coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a putative control region, with a gene arrangement that was identical to that reported for most other megalopteran species. We also predicted the secondary structure of all the RNA genes and analysed the preferred codon usage of the protein-coding genes. The putative 1265-bp control region contained two tandem repeated regions and several microsatellite-like elements. The phylogenetic analysis of available neuropteridan mitogenomes, based on the 13 protein-coding genes, appeared to support the current view of the neuropteridan phylogeny, and among the Neochauliodes spp., N. parasparsus was the most closely related to N. punctatolosus.     

The complete mitochondrial genome sequence of the world's largest fish,the whale shark (Rhincodon typus), and its comparison with those of related shark species

The whale shark (Rhincodon typus) is the largest extant species of fish, belonging to the order Orectolobiformes. It is listed as a “vulnerable” species on the International Union for Conservation of Nature (IUCN)'s Red List of Threatened Species, which makes it an important species for conservation efforts. We report here the first complete sequence of the mitochondrial genome (mitogenome) of the whale shark obtained by next-generation sequencing methods. The assembled mitogenome is a 16,875 bp circle, comprising of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. We also performed comparative analysis of the whale shark mitogenome to the available mitogenome sequences of 17 other shark species, four from the order Orectolobiformes, five from Lamniformes and eight from Carcharhiniformes. The nucleotide composition, number and arrangement of the genes in whale shark mitogenome are the same as found in the mitogenomes of the other members of the order Orectolobiformes and its closest orders Lamniformes and Carcharhiniformes, although the whale shark mitogenome had a slightly longer control region. The availability of mitogenome sequence of whale shark will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this species.     

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 the Stonefly Kamimuria wangi (Plecoptera: Perlidae) and Phylogenetic Position of Plecoptera Based on Mitogenomes

This study determined the mitochondrial genome sequence of the stonefly, Kamimuria wangi. In order to investigate the relatedness of stonefly to other members of Neoptera, a phylogenetic analysis was undertaken based on 13 protein-coding genes of mitochondrial genomes in 13 representative insects. The mitochondrial genome of the stonefly is a circular molecule consisting of 16,179 nucleotides and contains the 37 genes typically found in other insects. A 10-bp poly-T stretch was observed in the A+T-rich region of the K. wangi mitochondrial genome. Downstream of the poly-T stretch, two regions were located with potential ability to form stem-loop structures; these were designated stem-loop 1 (positions 15848–15651) and stem-loop 2 (15965–15998). The arrangement of genes and nucleotide composition of the K. wangi mitogenome are similar to those in Pteronarcys princeps, suggesting a conserved genome evolution within the Plecoptera. Phylogenetic analysis using maximum likelihood and Bayesian inference of 13 protein-coding genes supported a novel relationship between the Plecoptera and Ephemeroptera. The results contradict the existence of a monophyletic Plectoptera and Plecoptera as sister taxa to Embiidina, and thus requires further analyses with additional mitogenome sampling at the base of the Neoptera.     

The complete mitochondrial genome of Eterusia aedea (Lepidoptera,Zygaenidae) and comparison with other zygaenid moths

Zygaenidae comprises >1036 species, including many folivorous pests in agriculture. In the present study, the complete mitochondrial genome (mitogenome) of a major pest of tea trees, Eterusia aedea was determined. The 15,196-bp circular genome contained the common set of 37 mitochondrial genes (including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and exhibited the similar genomic features to reported Zygaenidae mitogenome. Comparative analyses of Zygaenidae mitogenomes showed a typical evolutionary trend of lepidopteran mitogenomes. In addition, we also investigated the gene order of lepidopteran mitogenomes and proposed that the novel gene order trnA-trnR-trnN-trnE-trnS-trnF from Zygaenidae and Gelechiidae and most other gene rearrangements of this tRNA cluster evolved independently. Finally, the mitogenomic phylogeny of Lepidoptera was reconstructed based on multiple mitochondrial datasets. And all the phylogenetic results revealed the sister relationships of Cossoidea and Zygaenoidea with both BI and ML methods, which is the first stable mitogenomic evidence for this clade.     

Mitochondrial genome of <Emphasis Type="Italic">Pteronotus personatus</Emphasis> (Chiroptera: Mormoopidae): comparison with selected bats and phylogenetic considerations

We described the complete mitochondrial genome (mitogenome) of the Wagner’s mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes. The order of protein-coding and rRNA genes was highly conserved in all mitogenomes. All protein-coding genes started with an ATG codon, except for ND2, ND3, and ND5, which initiated with ATA, and terminated with the typical stop codon TAA/TAG or the codon AGA. Phylogenetic trees constructed using Maximum Parsimony, Maximum Likelihood, and Bayesian inference methods showed an identical topology and indicated the monophyly of different families of bats (Mormoopidae, Phyllostomidae, Vespertilionidae, Rhinolophidae, and Pteropopidae) and the existence of two major clades corresponding to the suborders Yangochiroptera and Yinpterochiroptera. The mitogenome sequence provided here will be useful for further phylogenetic analyses and population genetic studies in mormoopid bats.     

Complete mitogenome sequence of black carp (<Emphasis Type="Italic">Mylopharyngodon piceus</Emphasis>) and its use for molecular phylogeny of leuciscine fishes

The black carp Mylopharyngodon piceus (Cyprinidae), native to eastern Asian, is a large, commercially important fish, and has been introduced to many other countries for variable reasons. In this study, the complete mitochondrial genome sequences from three specimens of black carp were first determined and were used to evaluate the sister relationship between black carp and grass carp (Ctenopharyngodon idellus). Two individuals had a mitogenome of 16,609 bp, while the other was 16,611 bp in length. Similar to most vertebrates, the black carp contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analyses using three different computational algorithms (Maximum Parsimony, Maximum Likelihood, and Bayesian analysis) revealed two distinct clades in subfamily Leuciscinae. However, the sister taxonomic relationship of black carp and grass carp was not observed using sequences of nearly complete mitochondrial genomes, which suggests more nuclear gene markers are needed to resolve the phylogenetic relationship between black carp and grass carp.     

Complete mitochondrial genome of Oxuderces dentatus (Perciformes, Gobioidei)

The complete mitochondrial genome (mitogenome) of Oxuderces dentatus was determined first. The genome was 17,116?bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand was T 27.9%, C 26.8%, A 30.2%, and G 15.1%, with a slight A+T bias of 58.1%. In addition to the discrete and conserved sequence blocks, unusual long tandem repeat unit (three 150-bp tandem repeat units and an incomplete copy of 146?bp) was also detected within CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.