Complete mitochondrial genome of the Korean stumpy bullhead Pseudobagrus brevicorpus (Siluriformes, Bagridae)

We describe the complete mitochondrial genome sequence of the Korean stumpy bullhead Pseudobagrus brevicorpus, which is an endangered species in Korea. The circle genome (16,526?bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.     

Complete mitochondrial genome of a forensically important muscid, Hydrotaea chalcogaster (Diptera: Muscidae), with notes on its phylogenetic position

Muscidae are a dipteran family which is important for forensic investigations. However, it has received limited attention in forensic entomological experiments as a reason of identification issues. It is hard to identify specimens by morphological methods, especially in developmental stages. Therefore, complete mitochondrial genome sequences can be important tool in forensic entomology for identifying species. In this study we sequenced and analyzed the first complete mitochondrial genome from a forensically important Muscidae species Hydrotaea (=Ophyra) chalcogaster by next-generation sequencing. The mitochondrial genome of the sequenced species is circular molecules of 17,076?bp which have the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes and a control region. Rearrangements of gene positions are identical with the ancestral insect genome. Furthermore, phylogenetic relationships of the family Muscidae were evaluated in regard to mitochondrial protein coding genes. The inferred trees indicate that the Muscidae is a paraphyletic family. These data provide additional information for molecular identification of muscid species.     

两种毛蚜线粒体基因组比较分析

【目的】线粒体基因组分析已被应用于昆虫系统发育研究。本研究以蚜科Aphididae重要类群毛蚜亚科物种为代表,测定并比较分析了该类蚜虫的线粒体基因组特征,探讨了基于线粒体基因组信息的蚜虫系统发育关系重建。【方法】以毛蚜亚科三角枫多态毛蚜Periphyllus acerihabitans Zhang和针茅小毛蚜Chaetosiphella stipae Hille Ris Lambers,1947为研究对象,利用长短PCR相结合的方法测定线粒体基因组的序列,分析了基因组的基本特征;基于在线t RNAscan-SE Search Server搜索方法预测了t RNA的二级结构;基于12个物种(本研究获得的2个物种和10个Gen Bank上下载的物种数据)的蛋白编码基因(PCGs)序列,利用最大似然法和贝叶斯法重建了蚜科的系统发育关系。【结果】两种毛蚜均获得了约94%的线粒体基因组数据,P.acerihabitans获得了14 908 bp,控制区为1 205 bp;C.stipae获得了13 893 bp,控制区为609 bp。两种毛蚜同时获得33个基因,包含接近完整的13个蛋白编码基因(PCGs)(nad5不完整),18个tRNA,2个rRNA基因;ka/ks值表明,C.stipae的进化速率更快。从基因组组成、基因排列顺序、核苷酸组成分析、密码子使用情况、t RNA二级结构等特征来分析,两种蚜虫线粒体基因组基本特征相似。系统发育重建结果表明毛蚜亚科、蚜亚科的单系性得到了支持,毛蚜亚科位于蚜科的基部位置。【结论】两种毛蚜线粒体基因组的基本特征相似,符合蚜虫线粒体基因组的一般特征,两种线粒体基因组的长度差异主要来自控制区长度的不同;系统发育重建支持毛蚜亚科与蚜亚科的单系性,毛蚜亚科位于蚜科较为基部的位置。研究结果为蚜虫类系统发育重建提供了参考。     

The complete mitochondrial genome of the Sichuan taimen (Hucho bleekeri): repetitive sequences in the control region and phylogenetic implications for Salmonidae

The complete mitochondrial DNA genome of the Sichuan taimen (Hucho bleekeri) was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequence method. The entire mitochondrial genome of this species is 16,997 bp in length, making it the longest among the completely sequenced Salmonidae mitochondrial genomes. It consists of two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one control region (CR). The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar to those of other teleosts. A T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region, which were almost identical among the three H. bleekeri individuals examined. Both phylogenetic analyses based on 12 concatenated protein-coding genes of the heavy strand and on just the control region show that H. bleekeri is a basal species in Salmoninae. In addition, Salmo, Salvelinus and Oncorhynchus all represent monophyletic groups, respectively. All freshwater species occupied basal phylogenetic positions, and also possessed various tandem repeats in their mitochondrial control regions. These results support established phylogenetic relationships among genera in Salmonidae based on morphological and molecular analyses, and are consistent with the hypothesis that Salmonidae evolved from freshwater species.     

北京鸭线粒体基因组全序列测定和分析

线粒体DNA作为遗传标记,已在家鸡(Gallus gallus)和家鹅(Anser anser)的研究中取得了重大进展,而对家鸭(Anas platyrhychos domesticus)的研究却很少.本研究参照近源物种线粒体基因组序列设计15对引物,通过PCR扩增、测序、拼接,获得北京鸭(A.platyrhychos)线粒体基因组全序列,初步分析其特点和各基因的定位.结果显示,北京鸭线粒体基因组全长16 604 bp,碱基组成为29.19%A、22.20%T、15.80%G、32.81%C,包含13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个非编码控制区(D-loop),基因组成及排列顺序与其他鸟类相似.基于线粒体D-loop区全序列,用N-J法构建了7种雁形目鸟类系统进化树,结果表明,北京鸭与绿头鸭(A.platyrhychos)系统进化关系较近.     

Complete mitochondrial genome of blackchin tilapia Sarotherodon melanotheron (Perciformes, Cichlidae)

Blackchin tilapia, Sarotherodon melanotheron, is a highly salt-tolerant species in tilapias. In this paper, the complete mitochondrial genome of S. melanotheron was determined first. The mitogenome (16,627 bp) had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding, 22 tRNA, 2 rRNA genes, and 1 putative control region. It shared 95.1%, 93.2%, and 92.2% mitogenome sequence with Oreochromis aureus, Oreochromis niloticus, and Oreochromis mossambicus, respectively.     

入侵害虫甘薯凹胫跳甲的鉴定及线粒体基因组分析

【目的】基于形态学鉴定和分子生物学技术确认甘薯凹胫跳甲Chaetocnema confinis是否入侵中国大陆,测定甘薯凹胫跳甲线粒体基因组序列,分析基因组结构及其系统发育关系。【方法】应用显微镜观察从广东不同地点采集的甘薯凹胫跳甲成虫的形态特征,并扩增cox1基因DNA序列进行分子鉴定;利用Illumina MiSeq测序平台对甘薯凹胫跳甲线粒体基因组进行测序、拼装、注释和特征分析;基于亲缘关系相近种属的线粒体基因组序列进行共线性分析和构建系统发育树,分析基因重排和系统发育关系。【结果】形态和分子鉴定结果表明大陆甘薯上发现的跳甲为甘薯凹胫跳甲。甘薯凹胫跳甲线粒体基因组序列大小为15 685 bp,包括有13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个非编码控制区;这37个基因之间排列紧凑,间隔总长度101 bp,排列顺序与模式昆虫Drosophila yakuba线粒体基因排列顺序相同。甘薯凹胫跳甲线粒体基因组A+T含量为77.3%,具有明显的AT偏向性。13个蛋白质编码基因的起始密码子均为ATN。在22个tRNA基因中除trnS1的DHU臂缺失,trnD, trnG, trnN和trnT的二级结构中缺少TψC环外,其余17个都能形成典型的三叶草式二级结构,另trnK的反密码子突变为UUU,trnS1的反密码子突变为UCU。甘薯凹胫跳甲的控制区片段长度仅有60 bp,是目前已报道的昆虫线粒体基因组中最短的控制区。基于线粒体基因组的系统发育分析表明,甘薯凹胫跳甲与跳甲亚科(Alticinae)黄曲条跳甲Phyllotreta striolata亲缘关系最近。【结论】甘薯凹胫跳甲已经入侵到中国大陆。本研究获得了甘薯凹胫跳甲的线粒体基因组序列,为防控甘薯凹胫跳甲和分析叶甲科(Chrysomelidae)各种属间的系统发育关系奠定了基础。     

Complete mitochondrial genome of the groundhopper Alulatettix yunnanensis (Insecta: Orthoptera: Tetrigoidea)

In this work, we sequenced the first complete mitochondrial genome of Tetrigoidea species, Alulatettix yunnanensis. The circle genome (15,104 bp) consists of 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes, and an A+T-rich region. It has the typical invertebrate mitochondrial gene arrangement.     

Complete mitochondrial genome sequence of the dragonet Callionymus curvicornis (Perciformes: Callionymoidei: Callionymidae)

We determined the complete mitochondrial genome (mitogenome) sequence of the dragonet Callionymus curvicornis. The total length of C. curvicornis mitogenome is 16,406 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. This is the first report of a complete mitochondrial genome in the fish suborder Callionymoidei.     

The mitochondrial genome structure of the clouded leopard (Neofelis nebulosa).

The complete 16 844 bp mitochondrial genome of Neofelis nebulosa has been sequenced and compared with the complete mitochondrial genomes of Felis catus and the Acinonyx jubatus. The base composition of the mitochondrial genome of N. nebulosa is as follows: A, 5343 bp (31.7%); C, 4441 bp (26.4%); G, 2491 bp (14.8%); T, 4569 bp (27.1%). The genome complement and the gene order of this mitochondrial genome was found to be typical of those reported for other mammals. Several unusual features of this genome, however, were found. First, in protein-coding regions, AT bias in the genome was not prevalent in the third position of codons, as it is in most other mammals, but was found in the second position of codons. Second, in tRNA regions, tRNASer (AGY), which lacked the "DHU" arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, no repetitive sequences (RS)-2 were found. However, RS-2 repetitive motifs usually occurr in the control regions of most great cats. In addition, 4 variable sites were found in CSB-3 of the control region. Fourth, AT content in the control region of the mtDNA from the clouded leopard was lower than it is in other regions.     

Complete mitochondrial genome of the Seoul frog Rana chosenica (Amphibia, Ranidae): comparison of R. chosenica and R. plancyi

Here, we have sequenced the complete mitochondrial genome of the Seoul frog Rana chosenica (Amphibia, Ranidae), which is known as a Korean endemic species. It is listed as a vulnerable species by IUCN Red List and also an endangered species in South Korea. The complete mitochondrial genome of R. chosenica consists of 18,357?bp. Its gene arrangement pattern was identical with those of other Rana frogs. We compared the mitochondrial genome of R. chosenica with that of the Peking frog Rana plancyi that has been known closely related to R. chosenica. Nucleotide sequence similarity between the two whole mitochondrial genomes was 95.7%, and the relatively low similarity seems to indicate that the two species are distinctly separated on the species level. The information of mitochondrial genome comparison of the two species was discussed in detail.     

暗纹东方鲀线粒体基因组核苷酸全序列测定与分析

以暗纹东方鲀(Takifugu fasciatus)肝的线粒体DNA为模板,参照红鳍东方鲀(T.rubripes)等近源鱼类的线粒体基因组DNA序列,设计合成14对特异引物,进行PCR扩增并测序,首次获得了暗纹东方鲀线粒体基因组全序列。结果表明,暗纹东方鲀线粒体基因组序列全长16 444 bp(GenBank登录号为GQ409967),A+T含量为55.8%,其mtDNA结构与其他脊椎动物相似,由22个tRNA基因、2个rRNA基因、13个蛋白质编码基因和1段819 bp非编码的控制区(D-loop)所组成。蛋白质基因除COⅠ和ND6的起始密码子为GTG、CCT以外,均为典型的起始密码子ATG。ND1、ATPase8、COⅢ、ND4L、ND5、Cyt b使用典型的终止密码子TAA,其他的使用不完全终止密码子。除ND6和tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer、tRNAGlu、tRNAPro在L-链上编码之外,其余基因均在H-链编码。基因排列顺序与已测定的鲀类一致,这显示了鲀类线粒体基因排列顺序上的保守性。tRNA基因核苷酸长度为64～73nt,预测了22个tRNA基因的二级结构,均呈较为典型的三叶草状。基于19种鲀类mtDNA全序列构建的进化树表明,暗纹东方鲀与红鳍东方鲀、中华东方鲀(T.chinensis)聚成一个姊妹群。结果还支持东方鲀属鱼类为一单系类群。     

Complete mitochondrial genome of the Bewick's swan Cygnus columbianus bewickii (Aves, Anseriformes, Anatidae)

The mitochondrial genome of Bewick's swan Cygnus columbianus bewickii was completely sequenced and then the resultant data were compared with those of the whistling swan Cygnus columbianus columbianus. The complete mitochondrial genome sequence of C. c. bewickii was 16,727?bp in length and its gene arrangement pattern, gene content, and genome organization were identical to those of Cygnus species. The similarities of nucleotide and amino acid sequences between the two swans were 99.1% and 99.6%, respectively. Out of the 13 protein-coding genes and 2 rRNA genes, COIII showed the lowest nucleotide sequence similarity with 98.0%. On the other hand, in amino acid sequence similarities, both COII and ATP6 showed the lowest with 98.7% in common. The control region has the 97.8% nucleotide sequence similarity.     

Complete mitochondrial genome of the Baikal teal Anas formosa (Aves, Anseriformes, Anatidae)

The Baikal teal Anas formosa (Aves, Anseriformes, Anatidae) is classified as "Vulnerable" on the IUCN Red List. Here, whole mitochondrial genome of A. formosa was amplified and sequenced. The total length of the Baikal teal mitochondrial genome is 16,594?bp, which consists of 13 protein-coding, 2 rRNA, 22 tRNA genes and 1 control region. The characteristics of the mitochondrial genomes were analyzed and discussed in detail.     

瓦氏黄颡鱼线粒体全基因组序列分析及系统进化

鲿科鱼类种类繁多, 外形相似, 形态学分类较为困难。为了给鲿科鱼类乃至鲇形目鱼类的系统进化研究积累基础资料, 文章采用参照近缘物种线粒体基因组设计覆盖全基因组引物的方法, 利用16对引物对瓦氏黄颡鱼(Pelteobagrus vachelli)线粒体全基因组进行扩增, PCR产物转化到质粒后测序, 最终获得线粒体基因组全序列, 其全长为16 527 bp, 包括2个rRNA基因、22个tRNA基因、13个编码蛋白质基因和一个非编码控制区。瓦氏黄颡鱼(P. vachelli)线粒体基因组结构和基因排列顺序与现已公布的鲇形目鱼类完全一致, 序列分析表明, 与鲇形目其他种属间具有较高的同源性, 与拟鲿属的同源性最高(91%)。利用鲇形目共4科6属9种及3个外群的线粒体全基因组序列, 从线粒体基因组水平探讨了鲿科鱼类及其在鲇形目的系统进化地位, 结果表明: 鲿科鱼类的瓦氏黄颡鱼(P. vachelli)、黄颡鱼(Pelteobagrus fulvidraco)、光泽黄颡鱼(Pelteobagrus nitidus)及越南拟鲿(Pseudobagrus tokiensis)构成一单系群; 拟鲿属与黄颡鱼属的关系较近; 黄颡鱼属中瓦氏黄颡鱼(P. vachelli)与光泽黄颡鱼(P.nitidus)的关系近于黄颡鱼(P. fulvidraco)。     

Complete mitochondrial genome of the longtooth grouper Epinephelus bruneus (Perciformes, Serranidae)

We determined the complete nucleotide sequence of the mitochondrial (mt) genome for the longtooth grouper, Epinephelus bruneus (Perciformes, Serranidae). This mt genome, consisting of 16,686 base pairs (bp), encoded genes for 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region as those found in other vertebrates, with the gene order identical to that of typical vertebrates. A major noncoding region between the trnP and trnF genes (991 bp) was considered to be the control region (D-loop). Within this sequence, 22 copies of a 17-bp tandem repeat element, 5'-TGATATTACATATATGC-3', were identified in the control region unlike previous reported Epinephelus species.     

Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae)

The Walking goby Scartelaos histophorus (Perciformes, Gobiidae) is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of S. histophorus was first determined. The genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. The overall base composition of S. histophorus is 27.5% for T, 28.0% for C, 28.3% for A, and 16.1% for G, with a slight A+T bias of 55.8%. It has the typical vertebrate mitochondrial gene arrangement.     

A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.)

ABSTRACT: BACKGROUND: Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF) created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138. RESULTS: Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3kb, similarity >99.9%). It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region. Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences. CONCLUSIONS: Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats. The rearrangement has produced four unique regions in Ogura-type mitochondrial genome, and most of the unique regions are composed of known Brassicaceae mitochondrial sequences. This suggests that the regions unique to the Ogura-type genome were generated by integration and shuffling of pre-existing mitochondrial sequences during the evolution of Brassicaceae, and novel genes such as orf138 could have been created by the shuffling process of mitochondrial genome.     

Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera

Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~ 1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes.     

萧氏松茎象线粒体基因组全序列测定与分析

象甲是鞘翅目中物种最丰富的类群, 目前关于其线粒体基因组全序列的研究还未见报道。本研究利用长距PCR和引物步移法对萧氏松茎象Hylobitelus xiaoi Zhang线粒体基因组全序列进行了测定。结果显示： 萧氏松茎象线粒体基因组序列全长16 123 bp（GenBank登录号为JX847496）, 共编码37个基因和1个非编码的控制区, 基因次序与典型的六足动物线粒体基因排列一致, 未发现基因重排现象。在基因组中两个值得注意的发现分别是： 1）N链上存在1个额外的trnV-like序列, 反密码子为GAC, 长度为69 bp, 其中65 bp与J链上的trnD重叠; 2）trnS^UCN和nad1之间存在1个长度为232 bp的基因间隔区。全部13个蛋白质编码基因的起始密码子均为ATN, 9个蛋白质编码基因的终止密码子为TAA, 其余4个蛋白质编码基因中, nad1和cox2的终止密码子为TAG, nad4和nad5则以不完整的终止密码子T作为终止信号。除trnS^AGN外, 其余的tRNAs均可形成典型的三叶草结构。而trnS^AGN的反密码子由TCT替代GCT, 反密码子臂延长形成9 bp（中间含1个碱基突起）, TΨC臂由正常的5 bp变为6 bp, DHU臂缩短仅1 bp, 各个臂之间没有连接碱基。线粒体控制区中包括10处长度不少于5 bp的poly-T（最长poly-T长度为14 bp）和2处微卫星样重复序列 (TA)₆和(TA)₉。本研究结果为探讨象甲总科在鞘翅目中的系统学地位及其与其他总科间的系统发生关系等问题提供了重要的分子生物学数据。