木通红喀木虱线粒体基因组的测定与序列分析

为保护木通等药用植物资源,了解其生物学性质,寻找其生理生化特性,以木通红喀木虱Cacopsylla coccinea为研究对象,测定了该研究对象的线粒体基因组并分析了其序列特征。采用PCR扩增、基因克隆等技术成功测得木通红喀木虱全线粒体基因组,全长为14 832 bp,共编码37个基因,包括13个蛋白质编码基因、22个转运RNA基因,2个核糖体RNA基因和一个富含AT的非编码区。以木通红喀木虱、枸杞木虱和脉斑银木虱三种昆虫为材料,采用比较基因组学和生物信息学方法,分析木虱科线粒体基因组的分子组成特征。主要组成特征:(1)三种昆虫基因组大小相似;(2)木通红喀木虱线粒体trnV基因发生重排;(3)脉斑银木虱间隔区最长,而枸杞木虱重叠区为最大;(4)三种昆虫AT含量基本相似,均约为70%;(5)三种昆虫存在碱基不对称,其中H-链和L-链上的第3个密码子位点AT的含量远高于其它位点;(6)三种昆虫线粒体基因组中nad5、nad6和cob基因的碱基置换率均小于1,说明它们受到负选择作用。     

黑斑蛙重盘吸虫的线粒体基因组特征及其系统发育研究

重盘科Diplodiscidae Cohn, 1904复殖吸虫是两栖动物最为常见的寄生虫,形态多样,目前未见基于线粒体基因组的遗传多样性研究。本研究记述并分析了寄生于滇蛙Dianrana pleuraden肠道的重盘科重盘属Diplodiscus Diesing, 1836黑斑蛙重盘吸虫D.nigromaculati的线粒体全基因组序列,为后续开展此类吸虫的遗传结构及遗传多样性研究提供了新的数据。黑斑蛙重盘吸虫线粒体基因组全长14 697 bp(GenBank登录号：MW698822),由22个tRNA基因、12个蛋白编码基因、2个rRNA基因和1个非编码区组成;AT含量(60%)高于GC含量(40%),但AT含量为目前已报道同盘总科Paramphistomoidea Fischoeder, 1901中最低;trnG基因和trnE基因的互换成为同盘总科吸虫线粒体基因组遗传结构的重要特征。基于12个蛋白编码基因的系统发育树支持重盘属隶属于重盘科。本研究中,滇蛙为黑斑蛙重盘吸虫的宿主新记录。     

Progress in the complete mitochondrial genomes of the Acari

蜱螨亚纲包括蜱类和螨类,是节肢动物中物种多样性最高的类群之一.本文综述了当前已测序的28种蜱螨线粒体基因组的研究成果.概括起来,蜱螨线粒体基因组具有以下特点:(1)大小变异显著,其中柑橘全爪螨Panonychus citri线粒体基因组在目前已测节肢动物中最小(13077 bp);(2)一般碱基组成偏向A和T,但6种蜱螨具有相反的GC-偏斜(正值);(3)基因组的碱基组成及A+T富集区的位置、长度和拷贝数等变异显著,其中4种叶螨的A+T含量最高,其A+T富集区在目前已测节肢动物中最短(44 -57 bp);(4)基因高度重排,特别是真螨总目的种类,但重排与高分类阶元无相关性;(5)真螨总目部分螨类的tRNA基因极度缩短,不能形成经典的三叶草二级结构.作者建议要进一步测定更多蜱螨的线粒体基因组,验证蜱螨非典型tRNA基因的生物学功能性,分析蜱螨线粒体基因组的分子进化机制,开展蜱螨线粒体转录组研究等.     

池蝶蚌线粒体基因组全序列分析简

采用普通PCR扩增、SHOT-GUN测序、软件拼接首次获得了池蝶蚌(Hyriopsis schlegelii)线粒体基因组全序列。线粒体基因组全长为15939 bp,由13个蛋白质编码基因、22个tRNA基因、2个SrRNA基因和28个长度为1—393 bp的非编码区组成;除ND3-ND5、ND4L、ATP6、ATP8、COX1-COX3、tRNA-D、tRNA-H之外,其他大多数基因在L链编码。池蝶蚌线粒体全基因组序列、蛋白编码基因、tRNA基因、rRNA基因及非编码区的A+T含量分别为60.36%、59.84%、61.7%、60.23%及62.5%,与其他淡水蚌类一致,均表现出A+T偏好性,淡水蚌类线粒体基因组长度的差异主要表现在非编码区长度的差异。池蝶蚌mtDNA的COX2-12SrRNA区域基因排列存在差异,是ND3、tRNAHis、tRNAAla、tRNASer1、tRNASer2、tRNAGlu、ND2、tRNAMet 8个基因发生重组造成。22个tRNA基因都具有典型的三叶草二级结构,tRNA-E与tRNA-W间的非编码区含有一个ORF区,而控制区并未发现。从GenBank上下载的14种双壳纲贝类的mtDNA序列构建的系统进化树,显示池蝶蚌与三角帆蚌亲缘关系最近。研究结果为淡水珍珠蚌线粒体基因重排及进化特征提供理论依据。     

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。     

池蝶蚌线粒体基因组全序列分析

采用普通PCR扩增、SHOT-GUN测序、软件拼接首次获得了池蝶蚌（Hyriopsis schlegelii）线粒体基因组全序列。线粒体基因组全长为15939 bp,由13个蛋白质编码基因、22个tRNA基因、2个SrRNA基因和28个长度为1393 bp的非编码区组成;除ND3-ND5、ND4L、ATP6、ATP8、COX1-COX3、tRNA-D、tRNA-H之外,其他大多数基因在L链编码。池蝶蚌线粒体全基因组序列、蛋白编码基因、tRNA基因、rRNA基因及非编码区的A+T含量分别为60.36%、59.84%、61.7%、60.23%及62.5%,与其他淡水蚌类一致,均表现出A+T偏好性,淡水蚌类线粒体基因组长度的差异主要表现在非编码区长度的差异。池蝶蚌mtDNA的COX2-12SrRNA区域基因排列存在差异,是ND3、tRNAHis、tRNAAla、tRNASer1、tRNASer2、tRNAGlu、ND2、tRNAMet 8个基因发生重组造成。22个tRNA基因都具有典型的三叶草二级结构,tRNA-E与 tRNA-W间的非编码区含有一个ORF区,而控制区并未发现。从GenBank上下载的14种双壳纲贝类的mtDNA序列构建的系统进化树,显示池蝶蚌与三角帆蚌亲缘关系最近。研究结果为淡水珍珠蚌线粒体基因重排及进化特征提供理论依据。       

斐豹蛱蝶线粒体基因组全序列的测定和分析(英文)

该研究对斐豹蛱蝶(Argyreus hyperbius)(鳞翅目:蛱蝶科)线粒体基因组全序列进行了测定和初步分析。结果表明:斐豹蛱蝶线粒体基因全序列全长为15156bp,包含13个蛋白质编码基因、22个tRNA和2个rRNA基因以及1个非编码的A+T富集区,基因排列顺序与其它鳞翅目种类一致;线粒体全序列核苷酸组成和密码子使用显示出明显的A+T偏好(80.8%)和轻微的AT偏移(AT skew,?0.019)。基因组中共存在11个2～52bp不等的基因间隔区,总长96bp;以及14个1～8bp不等的基因重叠区,总长34bp。除COI以CGA作为起始密码子外,13个蛋白质编码基因中的其余12个基因是以ATN作为起始密码子。除COI和COII基因是以单独的一个T为终止密码子,其余11个蛋白质编码基因都是以TAA结尾的。除了缺少DHU臂的tRNASer(AGN),其余的tRNA基因都显示典型的三叶草结构。tRNA(AGN)和ND1之间的基因间隔区包含一个ATACTAA结构域,这个结构域在鳞翅目中是保守的。A+T富集区没有较大的多拷贝重复序列,但是包含一些微小重复结构:ATAGA结构域下游的20bp poly-T结构,ATTTA结构域后的(AT)9重复,以及位于tRNAMet上游的5bp poly-A结构等。这项研究所揭示的斐豹蛱蝶的线粒体基因组特征,不仅为认识蛱蝶科的遗传多样性贡献数据,而且对于该物种的保护生物学、群体遗传学、谱系地理及演化研究等具有重要意义。     

甜果螨全线粒体基因组测序与分析

【目的】测定和分析甜果螨Carpoglyphus lactis线粒体基因组全序列,并在线粒体基因组水平探讨其在真螨总目(Acariformes)中的系统发育地位,为真螨总目分类及果螨科线粒体基因组研究提供科学依据。【方法】挑取实验室饲养的甜果螨成螨,用传统的酚氯仿抽提法和试剂盒提取法提取甜果螨基因组DNA。然后采用节肢动物或螨类线粒体基因的通用引物PCR扩增出甜果螨线粒体基因cox1,cob,rrnS和nad4-nad5的部分序列;再设计种特异性引物进行Long-PCR扩增和步移法测序,测出甜果螨线粒体基因组全序列。应用SeqMan, SEQUIN 9.0和tRNAscan等生物信息学软件,对甜果螨线粒体基因组的基因结构等进行生物信息学分析。最后基于17种真螨总目螨类的蛋白质编码基因,采用最大似然法构建系统发育树。【结果】甜果螨线粒体全基因组总长为14 060 bp(GenBank登录号:MN073839),为典型的闭合双链DNA分子,共由37个基因组成,包括13个蛋白质编码基因(PCGs)、22个tRNA基因和2个rRNA基因;甜果螨线粒体基因组还包括1个大的非编码区(large non-coding region, LNR)。系统发育分析结果显示,甜果螨Carpoglyphus lactis属于无气门亚目粉螨总科(Acaroidae),与椭圆食粉螨Aleuroglyphus ovatus构成一支。粉螨总科(Acaroidae)和薄口螨总科(Histiostomatoidae)聚成一簇,与痒螨股(Psoroptidia)构成姐妹群。【结论】本研究首次获得并分析了甜果螨线粒体基因组全序列。甜果螨与椭圆食粉螨的亲缘关系较近。     

蜱螨线粒体基因组研究进展

蜱螨亚纲包括蜱类和螨类, 是节肢动物中物种多样性最高的类群之一。本文综述了当前已测序的28种蜱螨线粒体基因组的研究成果。概括起来, 蜱螨线粒体基因组具有以下特点： （1）大小变异显著, 其中柑橘全爪螨Panonychus citri线粒体基因组在目前已测节肢动物中最小（13 077 bp）; （2）一般碱基组成偏向A和T, 但6种蜱螨具有相反的GC-偏斜（正值）; （3）基因组的碱基组成及A+T富集区的位置、 长度和拷贝数等变异显著, 其中4种叶螨的A+T含量最高, 其A+T富集区在目前已测节肢动物中最短（44~57 bp）; （4）基因高度重排, 特别是真螨总目的种类, 但重排与高分类阶元无相关性; （5）真螨总目部分螨类的tRNA基因极度缩短, 不能形成经典的三叶草二级结构。作者建议要进一步测定更多蜱螨的线粒体基因组, 验证蜱螨非典型tRNA基因的生物学功能性, 分析蜱螨线粒体基因组的分子进化机制, 开展蜱螨线粒体转录组研究等。     

后生动物线粒体基因组:起源、大小和基因排列进化

由于受到强烈的进化约束,后生动物线粒体基因组在大小和基因含量上一直保持稳定,相比之下核基因组则发生了巨大的改变。后生动物线粒体基因组结构的可塑性在一定程度上归功于可能由tRNA基因介导的基因重排事件,虽然亲缘关系密切的物种间也可能出现基因重排,但同门内的线粒体基因组仍趋向于具有类似的结构特征。我们对后生动物线粒体基因组的起源、大小和基因排列进化方面的特点进行了介绍。     

Mitochondrial genome reorganization characterizes various lineages of mesostigmatid mites (Acari: Parasitiformes)

Mesostigmata is an extremely diverse group of mites with more than 11,000 described species in 109 families. The complete mitochondrial (mt) genomes of five species of mesostigmatid mites from three families (Varroidae, Ologamasidae, Phytoseiidae) have been reported previously; all of them are rearranged or highly rearranged in gene order. However, it is unclear when mt genome reorganization occurred and how common it is in mesostigmatid mites. We sequenced the mt genomes of ten species of mesostigmatid mites from five more families (Blattisociidae, Diplogyniidae, Laelapidae, Macrochelidae, Parasitidae). We found that species in the families Diplogyniidae and Parasitidae have retained the ancestral mt genome organization of arthropods, which is in stark contrast to the highly rearranged mt genomes in the Phytoseiidae species. As in the Varroidae and Ologamasidae species, the mt genomes of the Blattisociidae, Macrochelidae and Laelapidae species are also rearranged but are less rearranged than in the Phytoseiidae species. Each of the six mesostigmatid families that have rearranged mt genomes is characterized by unique gene order not seen in other mesostigmatid families. Furthermore, the mt genome organization also differs among three genera of the Phytoseiidae, between two genera of the Laelapidae, and among three Macrocheles species of the Macrochelidae. Our results indicate that: (a) the most recent common ancestor of mesostigmatid mites likely retained the ancestral mt genome organization of arthropods; and (b) mt genome organization characterizes various lineages of mesostigmatid mites and provides a valuable source of information for understanding their phylogeny and evolution.     

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.     

Two ancient bacterial endosymbionts have coevolved with the planthoppers (Insecta: Hemiptera: Fulgoroidea)

Background

Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.

Results

We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.

Conclusion

The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.     

The complete mitochondrial genome of Pseudochauhanea macrorchis (Monogenea: Chauhaneidae) revealed a highly repetitive region and a gene rearrangement hot spot in Polyopisthocotylea

The complete mitochondrial genome of Pseudochauhanea macrorchis was determined and compared with other monogenean mitochondrial genomes from GenBank. The circular genome was 15,031 bp in length and encoded 36 genes (12 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) typically found in flatworms. Structures of the mitochondrial genome were mostly concordant with that known for Microcotyle sebastis and Polylabris halichoeres, but also contained two noted features-a gene rearrangement hot spot and the highly repetitive region (HRR) in major non-coding region (NCR). The gene rearrangement hot spot located between the cox3 and nad5 genes, including a cluster of tRNA genes, nad6 gene and one major NCR. The HRR seemed to be a unique feature of the polyopisthocotylean mitochondrial genomes. In conclusion, the present study provided new molecular data for future studies of the comparative mitochondrial genomics and also served as a resource of markers for the studies of species populations and monogenean phylogenetics.     

双翅目昆虫线粒体基因组结构特点及其测序通用引物的设计和应用

研究双翅目昆虫线粒体基因组的结构特点, 并设计其测序的通用引物, 为今后双翅目昆虫线粒体基因组的研究提供参考和依据。利用比较基因组学和生物信息学方法, 分析了已经完全测序的26个双翅目昆虫线粒体基因组的结构特点、 碱基组成和保守区, 并据此设计了双翅目昆虫基因组测序的通用引物。结果表明： 双翅目昆虫线粒体基因组长14 503~19 517 bp, 其结构保守, 含有37个编码基因, 包括13个蛋白质编码基因, 22个tRNA编码基因和2个rRNA编码基因, 此外还包含一段长度差异很大的非编码区(AT富含区)。基因组内基因排列次序稳定, 除个别基因外, 其余都与黑腹果蝇Drosophila melanogaster基因排列次序一致。基因组的碱基组成不均衡, AT含量在72.59%~85.15%之间, 碱基使用存在偏向性, 偏好使用AC碱基。全基因组的核苷酸和氨基酸序列保守, 共鉴定了11个保守区。在保守区内共设计了26对双翅目线粒体基因组测序通用引物, 扩增的目标片段都在1 200 bp以内。将该套通用引物用于葱蝇Delia antiqua线粒体全基因组测序, 结果证明其高效、 合用。     

Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light-strand replication and the nearby tRNA genes or the regions flanking the origin of heavy-strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.     

The Mitochondrial Genome of Soybean Reveals Complex Genome Structures and Gene Evolution at Intercellular and Phylogenetic Levels

Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.