Mitogenomes provide new insights into the evolutionary history of Prodiamesinae (Diptera: Chironomidae)

Evolutionary analysis of Prodiamesinae has long been impeded by lack of information, and its phylogenetic relationship with Orthocladiinae remains questionable. Here, ten complete mitochondrial genomes (mitogenomes) of Orthocladiinae sensu lato were newly sequenced, including three Prodiamesinae species and seven Orthocladiinae species. Coupled with published mitogenomes, a total of 12 mitogenomes of Orthocladiinae sensu lato were selected for a comparative mitogenomic analysis and phylogenetic reconstruction. Mitogenomes of Orthocladiinae sensu lato are conserved in structure, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, and the control region displayed the highest A + T content. All protein-coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the mitogenomes of Orthocladiinae sensu lato are highly conserved, and they are practically useful for phylogenetic inference, suggesting a re-classification of Orthocladiinae by sinking Prodiamesinae as a subgroup of Orthocladiinae.     

重伞灵芝线粒体基因组在灵芝种间鉴定中的应用

线粒体是“动力工厂”,能够进行氧化代谢实现能量的转化,参与三羧酸循环形成ATP。随着分子生物学和生物信息学技术的发展,担子菌灵芝属中已有几种灵芝的线粒体基因组被相继报道,但尚未有对重伞灵芝线粒体基因组的报道。本研究通过对重伞灵芝YX线粒体基因组进行组装注释,比较分析了与其他灵芝属物种的差异,根据差异序列构建分子标记对重伞灵芝菌株快速鉴定。结果显示重伞灵芝线粒体基因组大小为67 340bp的闭合环形结构,含有15个普通蛋白编码基因,28个tRNA基因,以及rRNA的大小亚基基因。共5个基因含有12个内含子,主要为IB型,部分为ID型,包含LAGLIDADG_1 superfamily、GIY-YIG_Cterm superfamily保守结构域。根据重伞灵芝线粒体cox2基因设计的特异性引物扩增结果显示：4株重伞灵芝的cox2基因片段均可准确扩增,且扩增不出其他灵芝物种的cox2基因片段。基于各灵芝菌株线粒体cox2基因序列构建系统进化树,可以将4株重伞灵芝归在同一分支上,并且同源性为98%,与ITS鉴定结果一致。可见,基于线粒体基因cox2特异性引物可以快速地对重伞灵芝进行鉴定,且只需通过观察扩增条带的有无,无需测序,省时省力。     

The enigmatic Crimean green lizard (Lacerta viridis magnifica) is extinct but not valid: Mitogenomics of a 120-year-old museum specimen reveals historical introduction

It has been proposed that Lacerta viridis magnifica Sobolevssky, 1930 represents an extinct species or subspecies of green lizard endemic to the southern Crimea. Using NGS protocols optimized for heavily degraded DNA, we sequenced the complete mitogenome of one of the originally formalin-preserved specimens collected in the late 19th century. A comparison with sequence data of other green lizards revealed that L. v. magnifica is a junior synonym of the northern subspecies of the western green lizard (L. b. bilineata Daudin, 1802), which occurs at least 1,500 km away, beyond the distribution ranges of other green lizards. In medieval times, a Genoese colony existed in the Crimean region where the extinct green lizards occurred. Until the early 20th century, close ties to Italy persisted, and locals of Genoese descent sent their children for education to Italy, where L. b. bilineata occurs. This suggests that the extinct Crimean green lizards have been introduced accidentally or intentionally from Italy. Our study exemplifies the value of historical formalin-preserved museum specimens for clarifying the status of questionable rare or extinct taxa.     

基于线粒体基因组的华蝉族系统发育地位研究(半翅目: 蝉科)(英文)

【目的】本研究旨在明确无鼓膜发音器的华蝉族(Sinosenini)昆虫在蝉总科(Cicadoidea)的系统发育地位。【方法】依据在陕西宁陕采集的合哑蝉Karenia caelatata成虫标本,对华蝉族的合哑蝉K. caelatata线粒体基因组进行测序、注释和生物信息学分析;并与蝉总科其他类群的线粒体基因组进行了比较,然后利用最大似然法(ML)和贝叶斯法(BI)分别构建了蝉总科分子系统发育树。【结果】合哑蝉线粒体基因组长14 960 bp (GenBank登录号: MN922304),其基因组成、蛋白编码基因的核苷酸组成和密码子使用等,与蝉总科其他类群具相似特征。核苷酸多样性分析表明,atp8, nad6和nad2为易变基因,而cox1比较保守。非同义替换率和同义替换率比表明,蝉总科昆虫线粒体基因组进化处于高水平的纯化选择下。系统发育分析结果支持蝉次目(Cicadomorpha)的单系性,该次目3个总科的关系为：角蝉总科Membraciodea+(蝉总科Cicadoidea+沫蝉总科Cercopodidea)。无鼓膜发音器的哑蝉属与蝉亚科(Cicadinae)的蜩蝉族(Dundubiini)相关类群聚在一起,且与寒蝉属Meimuna关系最近;黑蝉族(Cicadatrini)的草蝉属Mogannia和音蝉属Vagitanus则与姬蝉亚科(Cicadettinae)相关类群聚在一起;日宁蝉属Yezoterpnosia并非一个单系群。【结论】华蝉族应从姬蝉亚科转移至蝉亚科并与蜩蝉族(Dundubiini)合并,而黑蝉族应从蝉亚科转移至姬蝉亚科。研究结果为进一步解析具有不同发声机制的蝉科昆虫系统演化提供了新信息。     

The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences

In a previous study based on 100 whole mitochondrial genome (mitogenome) sequences, we sought to provide a new perspective on the ordinal relationships of higher ray-finned fish (Actinopterygii). The study left unexplored the phylogenetic position of toadfishes (order Batrachoidiformes), as data were unavailable owing to technical difficulties. In the present study, we successfully determined mitogenomic sequences for two toadfish species ( Batrachomoeus trispinosus and Porichthys myriaster ) and found that the difficulties resulted from unusual gene arrangements and associated repetitive non-coding sequences. Unambiguously aligned, concatenated mitogenomic sequences (13 461 bp) from 102 higher actinopterygians (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd and 3rd codon positions of the protein-coding genes, tRNA genes and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenies strongly suggest that the toadfishes are not members of relatively primitive higher actinopterygians (Paracanthopterygii), but belong to a crown group of actinopterygians (Percomorpha), as was demonstrated for ophidiiform eels (Ophidiiformes) and anglerfishes (Lophiiformes) in the previous study. We propose revised limits of major unranked categories for higher actinopterygians and a new name (Berycomorpha) for a clade comprising two reciprocally paraphyletic orders (Beryciformes and Stephanoberyciformes) based on the present mitogenomic phylogenies.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 289–306.     

Characterisation of the complete mitochondrial genome of the black-footed abalone Haliotis iris

The complete mitogenome of Haliotis iris, an economically important shellfish endemic to New Zealand, was sequenced for the first time. The mitogenome was 17,131?base pairs (bp) in length and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a control region. All 13 genes were initiated by the start codon ATG, except for nad5 (ATA). Two typical stop codons, TAA and TAG, were present. All of the tRNAs could be folded into typical cloverleaf secondary structures except tRNA^Ser1 and tRNA^Lys, which lacked a DHU stem and complete amino acid acceptor stem, respectively. The control region was 1132?bp in length and contained six AT tandem repeats. According to the gene order of the mitogenome, the 30 analysed Vetigastropoda species could be classified into three types—type I: over half of the studied species were very similar to the gastropod ancestral gene order, and the rearrangements occurred in five tRNAs; type II: eight species were found to be missing several tRNA genes; type III: Fissurellidae, Lepetodrilidae showed a large inverted fragment.     

访花昆虫野蚜蝇线粒体基因组结构分析

野蚜蝇Syrphus torvus(Osten-Sacken)成虫具访花习性,是重要的传粉昆虫;幼虫捕食蚜虫,是蚜虫重要天敌之一.本研究通过高通量测序、组装拼接获得了完整的野蚜蝇线粒体基因组全序列(GenBank登录号:MW074962),其序列全长为16 444 bp,包含13个蛋白编码基因(PCGs)、22个tRNAs、2个rRNAs和D-loop区.野蚜蝇线粒体全序列A+T含量为80.6％,G+C含量为19.4％,表现出明显的A+T偏斜.除了 COXI、ATP8、ATP6和ND1的起始密码子为TTG,其它9个PCGs以ATN为起始密码子;COXI的终止密码子为不完整的T--,ATP6为TAG,其余11个PCGs的终止子为TAA.22个tRNAs的二级结构均为典型的三叶草结构,并预测了野蚜蝇rRNAs的二级结构.野蚜蝇D-loop区存在重复序列和茎环结构,22种蚜蝇科基因间隔区与重叠区具有6个保守区域.基于24个物种(22个蚜蝇科和2个缟蝇科)的PCGs序列,通过贝叶斯法(BI)和最大似然法(ML)构建系统发育树,结果显示,野蚜蝇和黑足蚜蝇Syrphus vitripennis互为姊妹种,支持了蚜蝇亚科Syrphinae的单系性,两种拓扑结构中管蚜蝇亚科Eristalinae均没有聚为一支.该研究结果丰富了蚜蝇科线粒体基因组学基本数据,为进一步深化蚜蝇科系统发育关系讨论提供了参考.     

Sundasalanx(Sundasalangidae) is a progenetic clupeiform, not a closely‐related group of salangids (Osmeriformes): mitogenomic evidence

Partitioned Bayesian analysis of whole mitochondrial genome sequences from 30 basal teleosts confidently placed Sundasalanx (Sundasalangidae) within the Clupeiformes, not Osmeriformes as originally thought. This study represents the first demonstration of the phylogenetic position of Sundasalanx on a phylogenetic tree.