赤狐线粒体全基因组及系统发育分析

测定了赤狐的线粒体基因组全序列,总长度为16 723 bp,碱基组成为：31.3% A、26.1% C、14.8% G、27.8% T。和大多数哺乳动物一样,赤狐的线粒体全基因组包含13个蛋白质编码基因、2个核糖体RNA基因、22个转运RNA基因和1个控制区。除ND3基因起始密码子为不常见的ATT外,赤狐与北极狐、狼、家犬、郊狼的线粒体蛋白质编码遵循相同模式。在控制区的保守序列区段1和2之间发现一段较长的富含AC的随机重复序列。为了验证赤狐与其他犬科动物的系统发育关系,利用12个重链蛋白质编码基因,分别通过邻接法和最大简约法构建了系统发育树。结果表明：赤狐与北极狐是姐妹群,它们在犬科中都属于赤狐型分支,而灰狼、家犬和郊狼则属于狼型分支,与现有的系统进化研究结果一致。     

The complete mitochondrial genome of a threatened loach (<Emphasis Type="Italic">Sinibotia reevesae</Emphasis>) and its phylogeny

In present study, the complete mitochondrial genome of Sinibotia reevesae was first sequenced using the next-generation sequencing technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,572 bp in length, and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 displacement loop locus. It presents a typical gene organization and order for completely sequenced cypriniformes mitogenomes. The control region could be divided into three parts included the extended termination associated sequence domain, the central conserved domain and the conserved sequence block. Interestingly, two stem-loop domains were found in control region and O_L region, respectively. Furthermore, phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Maximum likelihood and Bayesian analysis) both highly supported the close relationship of S. reevesae and Sinibotia superciliaris, which was in line with the previous classifications based on morphological and molecular studies. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.     

Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications

To understand the systematic status of Bahaba taipingensis within Sciaenidae, the complete mitochondrial genome (mitogenome) sequence of Chinese bahaba has recently been determined by long PCR and primer walking methods. The complete mitochondrial genome is 16500 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. Within the control region, we identified the extended termination associated sequence domain (ETAS), the central conserved sequence block domain (CSB-D, SCB-E and CSB-F) and the conserved sequence block domain (CSB-1, CSB-2 and CSB-3). Phylogenetic analyses revealed that Bahaba taipingensis is more closely related to Pseudosciaeniae than Argyrosominae and Sciaeninae. Additionally, Bahaba taipingensis is the sister taxon of Miichthys miiuy, and those two are sister to Collichthys plus Larimichthys.     

Complete mitochondrial genome of Coelomactra antiquata (Mollusca: Bivalvia): The first representative from the family Mactridae with novel gene order and unusual tandem repeats

The complete mitochondrial genome plays an important role in the accurate inference of phylogenetic relationships among metazoans. Mactridae, also known as trough shells or duck clams, is an important family of marine bivalve clams in the order Veneroida. Here we present the complete mitochondrial genome sequence of the Xishishe Coelomactra antiquata (Mollusca: Bivalvia), which is the first representative from the family Mactridae. The mitochondrial genome of C. antiquata is of 17,384 bp in length, and encodes 35 genes, including 12 protein-coding, 21 transfer RNA, and 2 ribosomal RNA genes. Compared with the typical gene content of animal mitochondrial genomes, atp8 and tRNAS₂ are missing. Gene order of the mitochondrial genome of C. antiquata is unique compared with others from Veneroida. In the mitochondrial genome of the C. antiquata, a total of 2189 bp of non-coding nucleotides are scattered among 26 non-coding regions. The largest non-coding region contains one section of tandem repeats (99 bp × 11), which is the second largest tandem repeats found in the mitochondrial genomes from Veneroida. The phylogenetic trees based on mitochondrial genomes support the monophyly of Veneridae and Lucinidae, and the relationship at the family level: ((Veneridae + Mactridae) + (Cardiidae + Solecurtidae)) + Lucinidae. The phylogenetic result is consistent with the morphological classification. Meanwhile, bootstrap values are very high (BP = 94–100), suggesting that the evolutionary relationship based on mitochondrial genomes is very reliable.     

Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration

The complete sequence of the 16,493 nucleotide mitochondrial genome from the single species of the family Sciaenidae, the miiuy croaker, Miichthys miiuy, was determined. The nucleotide sequences of M. miiuy mitochondrial DNA have been compared with those of three other Sciaenidae fishes. The contents of the M. miiuy mitochondrial genome are 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and two non-coding regions (L-strand replication origin and control region), the gene order of which is identical to that observed in most vertebrates. The L-strand replication origin of M. miiuy is not pyrimidine-rich compared to those of most bony fishes. Within the control region, we identified the extended termination associated sequence domain, the central conserved sequence block domain and the conserved sequence block domain, while the typical central conserved blocks CSB-D, -E and -F could not be detected in the three other Sciaenidae species. In the ML phylogenetic analyses, the monophyly of Pseudosciaeniae was not supported, which is against with the morphological results. Collichthys niveatus is most closely related to Larimichthys polyactis, and Collichthys and Larimichthys may be merged into one genus, based on the current datasets.     

Structure,DNA sequence variation and phylogenetic implications of the mitochondrial control region in horseshoe bats

There have been few studies of the structural and evolutionary characteristics of the mitochondrial control region (CR) in rhinolophids, yet this could have important consequences for the interpretation of phylogenetic relationships within this group. Here we sequenced and analyzed the CR of 37 individuals from 12 Rhinolophus species, including 2 species from GenBank. The length of the CR ranged from 1335 to 1514 bp, and the base composition was very similar among species. The CR of horseshoe bats, like that of other mammals, could be subdivided into a central conserved domain (CD) and two flanking variable domains, extended termination associated sequences (ETAS), and conserved sequence blocks (CSB). Besides the common conserved blocks (ETAS1, ETAS2, F-B boxes, CSB1, CSB2 and CSB3) found in 3 domains, an ETAS2-like and a CSB1-like element were also detected in the ETAS and CSB domains, respectively, in all individuals. Notwithstanding a short tandem repeat (11 or 13 bp) between CSB1 and CSB2 in all specimens, the base composition, copy number and arrays are all variable. A long tandem repeat (79 bp) was only identified in the ETAS domain in one individual of R. pusillus. Phylogenetic reconstructions based on the CR sequences indicated that the molecular phylogenetic relationships among some Rhinolophus species were inconsistent with the results of phenetic analyses, but similar to phylogenetic constructions using cytochrome b. An unidentified species R. sp and 3 species from the philippinensis-group that were clearly morphologically different comprised a monophyletic group, which could have resulted from morphological independent evolution.     

The complete mitochondrial genome of bighead croaker, <Emphasis Type="Italic">Collichthys niveatus</Emphasis> (Perciformes,Sciaenidae): structure of control region and phylogenetic considerations

Sciaenidae is a diverse, commercially important family. To understand the phylogenetic position of Collichthys niveatus in this family, we present its complete mitochondrial genome sequence. The genome is 16469 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes. Further sequencing for the complete control region was performed on Collichthys lucida. Although the conserved sequence domains such as extend termination associated sequence (ETAS) and conserved sequence block domains (CSB-1, CSB-2 and CSB-3) are recognized in the control region of the two congeneric species, the typical central conserved blocks (CSB-F, CSB-E and CSB-D) could not be detected, while they are found in Miichthys miiuy and Cynoscion acoupa of Sciaenidae and other Percoidei fishes. Phylogenetic analyses do not support the monophyly of Pseudosciaeniae, which is against with the morphological results. C. niveatus is most closely related to Larimichthys polyactis, and Collichthys and Larimichthys may be merged into one genus, based on the current datasets.     

Complete mitochondrial genome of Odontobutis haifengensis (Perciformes,Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis

Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016 bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.     

Complete mitochondrial genome of the <Emphasis Type="Italic">Pleuronichthys lighti</Emphasis> (Pleuronectiformes,Pleuronectidae) with phylogenetic consideration

Mitochondrial genome has been used to shed light on many fields of both basic and applied research, including the study of molecular evolution. The complete mitochondrial genome sequence of 17368 bp nucleotides from the Pleuronichthys lighti was determined. It was a circular double-stranded DNA molecule with identical set of 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes as well as a non-coding control region. Stand asymmetry in the nucleotide composition was reflected in the codon usage of genes oriented in opposite directions. In the control region, we identified the extended termination associated sequence domain, the central conserved sequence block domain and the conserved sequence block domain, and two complete repeat region. They were “TTACAATA” and “TGTTGTAA”, respectively. All known 12 mitochondrial genomes of Pleuronectinae fishes were downloaded and analyzed; there were 5570 variable sites in the consensus sequences of 15241 base pairs, calculation of total sites were 35.5%. The highest sequence divergence was 50% (ATP8) and the Kimura-2-parameter genetic distance was 0.235 (ND6), whereas the COIII had the lowest sequence divergence (28.8%) and genetic distance (0.128); the protein coding genes were mainly acted by purifying selection which was detected by selection tests. Analysis of confidence and the information content for per nucleotide revealed ND5, ATP6, COI and ND4 genes were suitable molecular markers for phylogenetic study of Pleuronectinae fishes. Phylogenetic analysis using Bayesian computational algorithms based on COI genes provided support for the taxonomic status of P. lighti, which was consistent with the traditional taxonomy.     

Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs

The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359 bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The genome composition is highly A + T biased 68.42%, and exhibits a negative AT–skew (? 0.036) and GC–skew (? 0.269) among Brachyura crabs. Gene rearrangements were detected, as was tandem duplication followed by random loss, which explains the translocation of mitochondrial genes. Phylogenetic analysis showed that H. wuana and H. tientsinensis clustered on one branch with high nodal support values. These results confirm that the placement of H. wuana within the Varunidae family of Thoracotrematan crabs. This study will provided a better understanding for gene rearrangements and crab evolution in the further.     

Complete mitochondrial genome of Membranipora grandicella (Bryozoa: Cheilostomatida) determined with next-generation sequencing: The first representative of the suborder Malacostegina

Next-generation sequencing (NGS) has proven a valuable platform for fast and easy obtaining of large numbers of sequences at relatively low cost. In this study we use shot-gun sequencing method on Illumina HiSeq 2000, to obtain enough sequences for the assembly of the bryozoan Membranipora grandicella (Bryozoa: Cheilostomatida) mitochondrial genome, which is the first representative of the suborder Malacostegina. The complete mitochondrial genome is 15,861 bp in length, which is relatively larger than other studied bryozoans. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs and 20 transfer RNAs. To investigate the phylogenetic position and the inner relationships of the phylum Bryozoa, phylogenetic trees were constructed with amino acid sequences of 11 PCGs from 30 metazoans. Two superclades of protostomes, namely Lophotrochozoa and Ecdysozoa, are recovered as monophyletic with strong support in both ML and Bayesian analyses. Somewhat to surprise, Bryozoa appears as the sister group of Chaetognatha with moderate or high support. The relationship among five bryozoans is Tubulipora flabellaris + (M. grandicella + (Flustrellidra hispida + (Bugula neritina + Watersipora subtorquata))), which supports for the view that Cheilostomatida is not a natural, monophyletic clade. NGS proved to be a quick and easy method for sequencing a complete mitochondrial genome.     

The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration

The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA^His differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.     

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3′ end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA^Glu and tRNA^Phe genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned.     

The first complete mitochondrial genome from Bostrychus genus (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotridae fish phylogeny

To understand the phylogenetic position of Bostrychus sinensis in Eleotridae and the phylogenetic relationships of the family, we determined the nucleotide sequence of the mitochondrial (mt) genome of Bostrychus sinensis. It is the first complete mitochondrial genome sequence of Bostrychus genus. The entire mtDNA sequence was 16508 bp in length with a standard set of 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a noncoding control region. The mitochondrial genome of B. sinensis had common features with those of other bony fishes with respect to gene arrangement, base composition, and tRNA structures. Phylogenetic hypotheses within Eleotridae fish have been controversial at the genus level. We used the mitochondrial cytochrome b (cytb) gene sequence to examine phylogenetic relationships of Eleotridae by using partitioned Bayesian method. When the specific models and parameter estimates were presumed for partitioning the total data, the harmonic mean –lnL was improved. The phylogenetic analysis supported the monophyly of Hypseleotris and Gobiomorphs. In addition, the Bostrychus were most closely related to Ophiocara, and the Philypnodon is also the sister to Microphlypnus, based on the current datasets. Further, extensive taxonomic sampling and more molecular information are needed to confirm the phylogenetic relationships in Eleotridae.     

Complete Mitochondrial Genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura,Arthropoda) and Implications for Chelicerate Phylogenetic Studies

Horseshoe crabs (order Xiphosura) are often referred to as an ancient order of marine chelicerates and have been considered as keystone taxa for the understanding of chelicerate evolution. However, the mitochondrial genome of this order is only available from a single species, Limulus polyphemus. In the present study, we analyzed the complete mitochondrial genomes from two Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus tridentatus to offer novel data for the evolutionary relationship within Xiphosura and their position in the chelicerate phylogeny. The mitochondrial genomes of C. rotundicauda (15,033 bp) and T. tridentatus (15,006 bp) encode 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Overall sequences and genome structure of two Asian species were highly similar to that of Limulus polyphemus, though clear differences among three were found in the stem-loop structure of the putative control region. In the phylogenetic analysis with complete mitochondrial genomes of 43 chelicerate species, C. rotundicauda and T. tridentatus were recovered as a monophyly, while L. polyphemus solely formed an independent clade. Xiphosuran species were placed at the basal root of the tree, and major other chelicerate taxa were clustered in a single monophyly, clearly confirming that horseshoe crabs composed an ancestral taxon among chelicerates. By contrast, the phylogenetic tree without the information of Asian horseshoe crabs did not support monophyletic clustering of other chelicerates. In conclusion, our analyses may provide more robust and reliable perspective on the study of evolutionary history for chelicerates than earlier analyses with a single Atlantic species.     

Structure of the Mitochondrial DNA Control Region of the Sinipercine Fishes and Their Phylogenetic Relationship

The mitochondrial DNA control region of Siniperca chuatsi, S. kneri, S. scherzeri, S. obscura, S. undulata, Coreosiniperca roulei and Coreoperca whiteheadi were amplified by PCR amplification and directly sequenced. The mtDNA control region of the sinipercine fishes could be separated into three domains, namely, the terminal associated sequence domain, the central conserved sequence domain and the conserved sequence block domain. The extended terminal associated sequence (ETAS), three conserved sequence blocks (CSB-F, CSB-E, CSB-D) in the central conserved sequence domain and three conserved sequence blocks (CSB1, CSB2, CSB3) in the conserved sequence block domain were also identified. The phylogenetic relationships among these sinipercine fishes were constructed through neighbor-joining and maximum parsimony methods using Percidae and Serranidae as outgroups. Results showed that sinipercine fishes were a monophyletic group, with Siniperca forming one group, and Coreoperca forming another group. Coreosiniperca roulei did not form an independent group but was merged into the genus Siniperca. Thus it should be renamed as Siniperca roulei.     

Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: An ultra-large metazoan mitochondrial genome

The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8–10 length variants. The motifs of the HTR arrays are about 353–362 bp and the number of repeats ranges from 1 to 11.     

The first mitochondrial genome for Brahmin moths (Brahmaeidae) and implications for the higher phylogeny of Bombycoidea

Bombycoidea comprises 10 families and 4723 species, and the phylogenetic relationships among families are still in debate. In this study, we have determined the complete mitochondrial genome (mitogenome) of Brahmaea porphyria. The 15,429-bp mitogenome contains a common set of 37 mitochondrial genes including 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an inferred control region, and shares the conserved gene rearrangement (trnM-trnI-trnQ) in most ditrysian mitogenomes. Moreover, we analysed the secondary structure for all the tRNA genes of B. porphyria and the preference of codon usage in the PCGs of B. porphyria. The putative 373-bp control region (CR) possesses three types of conserved elements, including ATAGA, Ploy-T stretch, and microsatellite-like elements. A phylogenetic analysis among available Bombycoidea mitogenomes using the concatenated 37 mitochondrial genes appears to support the hypothesis of (Sphingidae+Bombycidae)+Saturniidae and the relatively basal phylogenetic position of Brahmaeidae within Bombycoidea.