昆虫线粒体基因组重排的研究进展

动物线粒体基因组通常组成稳定,基因排列也相对保守,极少发生重组。但是昆虫的线粒体基因组具有重排的可能性,而且这些重排事件可能为系统发育研究提供重要的信息。因此,深入研究昆虫线粒体基因组的重排可能有助于解决具有争议的系统发生关系。本文对昆虫线粒体基因组的重排类型、重排机理和重排在昆虫系统发育分析中的应用等方面的研究进展进行了介绍。     

昆虫比较线粒体基因组学研究进展

动物线粒体基因组因其基因组成稳定、基因排列相对保守、普遍为母系遗传、极少发生重组等而被广泛应用于进化与系统发育等研究。目前,昆虫中已有356个线粒体基因组序列被测定,代表了33个目中的28个目。大量比较基因组学研究使得我们对昆虫线粒体基因组的特征与进化方式有了较为清晰的认识。本文对昆虫线粒体基因组的测序进展、基因组的结构特征、碱基组成、控制区的特征、基因重排及其机理、进化速率及其在昆虫系统发育研究中的应用等方面的研究进展进行介绍。     

半翅目昆虫线粒体基因组学研究进展

线粒体基因组广泛应用于昆虫系统发育、分子进化、种群遗传学及谱系地理学等众多研究领域.半翅目是昆虫纲外翅部中最大的一个目,具有重要的经济意义.目前,已对100种半翅目昆虫进行了线粒体基因组测序,其中81种在中国完成测序.本文综述了半翅目昆虫线粒体基因学研究的已有成果,比较分析了半翅目昆虫线粒体基因组的基本特征,包括基因组大小、基因含量、基因重排、碱基组成、密码子使用、蛋白质编码基因的进化模式、RNA基因及非编码区,并系统总结了线粒体基因组数据在半翅目昆虫系统进化研究中的应用现状.最后,针对线粒体基因组的获得、注释和应用过程中存在的问题进行了讨论,并提出了今后半翅目昆虫线粒体基因组学的研究重点.     

传粉和非传粉榕小蜂线粒体基因组进化差异(英文)

【目的】目前关于榕小蜂类群的线粒体基因组报道很少,本研究旨在探讨传粉和非传粉榕小蜂两个群体的线粒体基因组的进化差异。【方法】以15种榕小蜂的线粒体基因组(其中11种的线粒体基因组为新测定)数据为基础,采用比较线粒体基因组学方法,分析榕小蜂的线粒体基因组序列和进化特征。【结果】本研究新测定的11个榕小蜂物种的近全长线粒体基因组的长度范围为12 768~17 060 bp,AT含量均大于80%,除了非传粉榕小蜂Philotrypesis tridentata外,其余物种的AT偏斜为负,GC偏斜为正。榕小蜂线粒体基因重排事件很丰富,并且重排情况可能会对该类群的系统发育分析具有重要的价值。进一步的选择压力分析显示,榕小蜂线粒体基因组中的蛋白质编码基因的ω值均远远小于1,表明这些基因经历了纯化选择,传粉榕小蜂线粒体基因组中的大部分基因比非传粉榕小蜂积累了更多的非同义突变。此外与非传粉榕小蜂相比,传粉榕小蜂的线粒体基因组还具有更丰富的基因重排、更高的核苷酸多态性和更高的氨基酸替换率。【结论】传粉榕小蜂比非传粉榕小蜂的线粒体基因组进化更快,这可能与两个群体显著不同的生活方式或进化史有关。     

尼罗鳄线粒体基因组全序列分析及鳄类系统发生关系的探讨

大多数脊椎动物的线粒体基因组（约16—18kb）的组成是相对较稳定的,但在不同类群中,线粒体基因组在基因结构和基因排列方式等方面均显示了极大的多样性,这种多样性可能反映了真核细胞不同的进化路线（Saccone et al．,1999）。就目前的研究而言,线粒体基因组是惟一一个能够从基因组水平上来分析动物系统发生的分子标记,可以从线粒体基因组序列信息、基因组成及基因排列方式等进行多方位的分子进化研究,因而线粒体基因组全序列将成为动物分子系统发生最有力的证据（Saccone et al．,1999）。     

鱼类线粒体DNA重排研究进展

一般认为鱼类线粒体基因组在结构上具有高度的保守性,但是通过分析NCBI数据库中的1 255种鱼类线粒体基因组全序列(截至2013年11月3日),发现~52种鱼线粒体基因组发生了重排。进一步的分析发现这些重排具有3种类型:滑移(shuffling)、移位(translocation)和倒置(inversion),并多发生于WANCY基因簇、IQM基因簇、ND6基因、控制区(D-loop)及其邻接基因等区域。该文根据已报道的4种常见的解释重排的模型:复制随机丢失(duplication-random loss)、复制非随机丢失(duplication-nonrandom loss)、线粒体内的重组(intramitochondrial recombination)以及由tRNA基因错误起始引起的复制(tRNAmiss-priming model)解释了鱼类重排产生的可能机制,并探讨了重排现象在鱼类系统发生研究中的应用,以期为鱼类线粒体的进化研究提供科学依据。     

植绥螨科线粒体基因组研究进展

植绥螨科属于囊螨总科,大部分植绥螨为害螨、害虫的重要天敌,在农业生产上具有重要的应用价值。其线粒体基因组具有独特特征,引起了生物学家的广泛关注。本文就植绥螨科线粒体基因组的结构、非编码区、碱基组成、基因重排和tRNA的特征进行综述,其特征有:(1)植绥螨科中发现了螯肢动物最大的线粒体基因组;(2)植绥螨科线粒体基因组非编码区的AT含量差异大,编码区的AT含量差异小;(3)植绥螨科线粒体基因组均发生了不同程度的的基因重排;(4)已测定的植绥螨科部分物种tRNA基因二级结构出现了截短和碱基错配的现象,部分物种的线粒体基因组出现反密码子突变的情况。在今后的研究中应进一步测定植绥螨科关键类群的线粒体基因组,深入分析植绥螨科出现大量基因重排的原因,以期能反映植绥螨科的真实进化历程。     

动物线粒体基因组研究进展

对动物线粒体分子生物学的最新研究进展进行了较详细的阐述.从线粒体基因组(mtDNA)的研究背景出发,重点介绍了动物线粒体基因组的组成和结构特点,以及目前动物mtDNA与核基因组的关系、线粒体基因的遗传、起源和进化研究中的热点问题.     

啮总目昆虫的线粒体基因组多样性及系统发育研究进展

啮总目包括啮虫目（皮虱和书虱）和虱目（羽虱和吸虱）,是农业和医学等领域具有重要经济意义和研究价值的类群,目前已鉴定和描述的物种超过10 000个。啮总目昆虫线粒体基因组的变异性在昆虫各类群中最为剧烈,这些变异包括基因组的结构、基因排序、基因含量和链上分布等诸多方面。本文全面分析和总结了啮总目昆虫裂化线粒体基因组的进化属性,并结合两侧对称动物线粒体基因组的裂化特征重构了线粒体基因组环裂化的过程。引入“线粒体基因组核型”的概念来描述动物线粒体基因组丰富的变异程度。动物线粒体的染色体有减小的趋势,而线粒体基因组的裂化正是体现这种趋势的一种重要策略。同时,总结和探讨了目前具有争议的啮总目主要类群间的系统发育关系。本综述为啮总目昆虫线粒体基因组学、啮总目系统发生关系以及两侧对称动物线粒体基因组进化模式的研究提供一个新的视角。     

动物与植物线粒体基因组结构的差异—两种进化途径

从进化的角度分析和综合多细胞动物、高等植物、原生动物、藻类和真菌的线粒体基因组的大小和各自的结构特点,并根据作者提出的重复序更与基因结构的起源和进货的模式与途径,得出线粒体通过内共生起源,也是从原始的线粒体基因组向小基因组和大基因组两种方向发展,并有着两种与核基因组的可比较的进货途径的结论。这两种进化途径能很好地说明不同类型的真核生理的线本基因组的结构差异和特点。本文还提出了一个关于重复序列、断列     

线粒体基因组:结构特点和基因含量进化

线粒体具有其自身的遗传系统——一个来自内共生的α-变形细菌祖先的基因组。线粒体基因组的生物学功能非常保守,仅涉及与线粒体有关的5个方面的过程:呼吸和氧化磷酸化、翻译、转录、RNA成熟和蛋白运输。真核生物线粒体基因含量的变化异常显著,在包括被子植物在内的各种真核生物相对频繁地发生线粒体基因丢失的同时,动物和某些植物类群的线粒体基因含量相对来说则比较稳定。tRNA基因含量的变化反映了线粒体对来自核的tRNA在使用上的差异,而蛋白基因含量的变化主要是由于功能性的基因转移到核所造成的。对线粒体基因组学领域中有关基因组起源、结构和基因含量进化方面的研究进行综述。     

Insect mitochondrial genomics 2: The complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements.

Mitochondrial (mt) genome sequences of insects are receiving renewed attention in molecular phylogentic studies, studies of mt-genome rearrangement, and other unusual molecular phenomena, such as translational frameshifting. At present, the basal neopteran lineages are poorly represented by mt-genome sequences. Complete mt-genome sequences are available in the databases for only the Orthoptera and Blatteria; 9 orders are unrepresented. Here, we present the complete mt-genome sequence of a giant stonefly, Pteronarcys princeps (Plecoptera; Pteronarcyidae). The 16,004 bp genome is typical in its genome content, gene organisation, and nucleotide composition. The genome shows evidence of strand-specific mutational biases, correlated with the time between the initiation of leading and the initiation of lagging strand replication. Comparisons with other insects reveal that this trend is seen in other insect groups, but is not universally consistent among sampled mt-genomes. The A+T region is compared with that of 2 stoneflies in the family Peltoperlidae. Conserved stem-loop structures and sequence blocks are noted between these distantly related families.     

Neuroactive substances specifically modulate rhythmic body contractions in the nerveless metazoon Tethya wilhelma (Demospongiae, Porifera)

Background

Mitochondrial (mt) gene arrangement is highly variable among molluscs and especially among bivalves. Of the 30 complete molluscan mt-genomes published to date, only one is of a heterodont bivalve, although this is the most diverse taxon in terms of species numbers. We determined the complete sequence of the mitochondrial genomes of Acanthocardia tuberculata and Hiatella arctica, (Mollusca, Bivalvia, Heterodonta) and describe their gene contents and genome organisations to assess the variability of these features among the Bivalvia and their value for phylogenetic inference.

Results

The size of the mt-genome in Acanthocardia tuberculata is 16.104 basepairs (bp), and in Hiatella arctica 18.244 bp. The Acanthocardia mt-genome contains 12 of the typical protein coding genes, lacking the Atpase subunit 8 (atp8) gene, as all published marine bivalves. In contrast, a complete atp8 gene is present in Hiatella arctica. In addition, we found a putative truncated atp8 gene when re-annotating the mt-genome of Venerupis philippinarum. Both mt-genomes reported here encode all genes on the same strand and have an additional trnM. In Acanthocardia several large non-coding regions are present. One of these contains 3.5 nearly identical copies of a 167 bp motive. In Hiatella, the 3' end of the NADH dehydrogenase subunit (nad)6 gene is duplicated together with the adjacent non-coding region. The gene arrangement of Hiatella is markedly different from all other known molluscan mt-genomes, that of Acanthocardia shows few identities with the Venerupis philippinarum. Phylogenetic analyses on amino acid and nucleotide levels robustly support the Heterodonta and the sister group relationship of Acanthocardia and Venerupis. Monophyletic Bivalvia are resolved only by a Bayesian inference of the nucleotide data set. In all other analyses the two unionid species, being to only ones with genes located on both strands, do not group with the remaining bivalves.

Conclusion

The two mt-genomes reported here add to and underline the high variability of gene order and presence of duplications in bivalve and molluscan taxa. Some genomic traits like the loss of the atp8 gene or the encoding of all genes on the same strand are homoplastic among the Bivalvia. These characters, gene order, and the nucleotide sequence data show considerable potential of resolving phylogenetic patterns at lower taxonomic levels.     

Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome

Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum--Ctenophora--has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we Polymerase Chain Reaction (PCR) amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10 kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, likely to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies.     

The complete mitochondrial genome sequence of Sogatella furcifera (Horváth) and a comparative mitogenomic analysis of three predominant rice planthoppers

The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the most destructive pests of rice crops in many Asian countries. Using long-PCR and shotgun library methods, we sequenced the entire mitochondrial genomes (mt-genomes) of two WBPH individuals. Total lengths of the mt-genome of the two WBPH individuals were 16,612 bp and 16,654 bp with an identical AT content of 76.19%. Among the 13 protein coding genes (PCGs), only nad5 used an atypical initiation codon GTG. Most of the tRNA genes had the typical cloverleaf secondary structure except that the dihydrouridine (DHU) arms in two trnS genes and the TΨC arm of trnG gene did not form a stable stem-loop structure. Similar to the brown planthopper (BPH), Nilaparvata lugens (Stål), and the small brown planthopper (SBPH), Laodelphax striatellus (Fallén), some extraordinary features were observed in the WBPH mt-genome. These include similar gene rearrangement pattern, unusually short length of the atp8 gene and variable numbers of tandem repeat (VNTR) structure in control region. Interestingly, the same tandem repeat unit with stable secondary structure appeared in two different planthoppers, WBPH and SBPH, which belong to two different genera of the Delphacidae. This peculiar feature provides a direct evidence for the close relationship between the two planthoppers and updates our understanding of the evolutionary characteristics of mitochondrial control region. Comparison with two other predominant rice planthoppers (BPH and SBPH) revealed that different PCGs of mitochondria exhibit different evolutionary patterns.     

Complete mitochondrial genome sequence of D. littoralis (Diptera: Drosophilidae). Comparative analysis of mitochondrial genomes in the Drosophila virilis group

An analysis of the complete sequence of the mitochondrial genome (mt-genome) of D. littoralis is presented. Its basic characteristics, such as size, nucleotide composition, gene order, and the degree of purifying selection pressure on different parts of the genome are given. The details of the structure of proteinencoding genes and tRNA genes are discussed. The structure of nonencoding regions (control region and intergenic spacers) of mtDNA of the virilis group is given. Fragments of the mt-genes atp6 and cox3 were found in the nuclear genome of D. virilis. The evolutionary history of the mitochondrial and nuclear sequences of these genes indicates that the process of formation of mt-pseudogenes is currently taking place and is associated with the activity of retrotransposons.     

Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia)

Cnidarians are early-diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re-evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt-genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt-genomes of members of eight of nine zoantharian families. Although all examined mt-genomes had the same gene order arrangement, there were variations among mt-genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt-DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt-genome protein-coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An “early” transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher-level phylogeny and taxonomy of Zoantharia.     

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 genetic localization of presumptive mitochondrial messenger RNAs on rat-liver mitochondrial DNA.

High molecular weight mitochondrial (mt) RNAs were isolated from rat liver mitochondria and hybridized in the presence of excess competitor mt rRNA and/or mt tRNA to restriction fragments of mtDNA. The data reveals that there are a few areas of the mt-genome on which the complementary of these presumptive messenger RNAs is most pronounced. These areas are away from the parts of the genome which are coding for the mt rRNA or containing the D-loop.