Topological conflicts in phylogenetic analysis of different regions of the sable ( Martes zibellina L.) mitochondrial genome

Phylogenetic analysis of different regions of the mitochondrial genome of the sable showed the presence of several topologies of phylogenetic trees, but the most statistically significant topology is A-BC, which was obtained as a result of the analysis of the mitochondrial genome as a whole, as well as of the individual CO1, ND4, and ND5 genes. Analysis of the intergroup divergence of the mtDNA haplotypes (D xy) indicated that the maximum D xy values between A and BC groups were accompanied by minimum differences between B and C groups only for six genes showing the A-BC topology (12S rRNA, CO1, CO2, ND4, ND5, and CYTB). It is assumed that the topological conflicts observed in the analysis of individual sable mtDNA genes are associated with the uneven distribution of mutations along the mitochondrial genome and the mitochondrial tree. This may be due to random causes, as well as the nonuniform effect of selection.     

Genetic relationships among species of Contracaecum Railliet & Henry, 1912 and Phocascaris Höst, 1932 (Nematoda: Anisakidae) from pinnipeds inferred from mitochondrial cox2 sequences, and congruence with allozyme data

The genetic relationships among 11 taxa, belonging to the genus Contracaecum (C. osculatum A, C. osculatum B, C. osculatum (s.s.), C. osculatum D, C. osculatum E, C. osculatum baicalensis, C. mirounga, C. radiatum, C. ogmorhini (s.s.), C. margolisi) and Phocascoris (Phocoscris cystophorae), parasites as adults of seals, were inferred from sequence analysis 1519 bp) of the mitochondrial cytochrome c oxidase subunit II (mtDNA cox2) gene. Phylogenetic analyses obtained from Parsimony (MP) and Neighbour-Joining (NJ) K2P distance values generated similar topologies, each well supported at major nodes. All analyses delineated two main clades: the first encompassing the parasites of the phocid seals, i.e. the C. osculatum species complex, C. osculatum boicolensis, C. mirounga and C. radiatum, with the latter two species forming a separate subclade; the second including the parasites of otarids, i.e. C. ogmorhini (s.s.) and C. margolisi. An overall high congruence between mtDNA inferred tree topologies and those produced from nuclear data sets (20 allozyme loci) was observed. Comparison of the phylogenetic hypothesis here produced for Controcaecum spp. plus Phocascaris with those currently available for their definitive hosts (pinnipeds) suggests parallelism between hosts and parasite phylogenetic tree topologies.     

大豆蚜线粒体基因组序列测定与分析

采用LongPCR和引物步移法测得大豆蚜Aphis glycines Matsumura线粒体基因组约90%的序列,并与蚜总科Aphidoidea已报道的3种蚜虫进行了比较。结果表明:已测得的序列长度为13696bp,AT含量为83.3%;蛋白质编码基因起始密码子都为ATN,COI、ND4、CYTB、ND2使用不完整终止密码子T,其余都使用常见终止密码子TAA;15个tRNA基因除tRNA-W外都能折叠成典型的三叶草二级结构。比较大豆蚜、豌豆蚜Acyrthosiphon pisum(Harris)、麦二叉蚜Schizaphis graminum(Rondani)和葡萄根瘤蚜Daktulosphaira vitifoliae(Fitch)的线粒体基因组,结果表明4个种均具有后生动物线粒体基因组中常见的基因,基因顺序与假想昆虫祖先的排列方式相同,但豌豆蚜包含3个tRNA-M;蛋白质编码基因的起始密码子都为ATN,除葡萄根瘤蚜外,其他3种蚜虫的COⅠ、ND4使用不完整终止密码子T;tRNA-W的二级结构中都存在TψC臂中"茎"的结构缺失,只有环的结构;而蛋白质编码基因使用最频繁的氨基酸略有不同,大豆蚜为Leu,豌豆蚜和麦二叉蚜为Ile;大豆蚜和麦二叉蚜的ND4/ND4L都存在7bp的重叠序列,而豌豆蚜和葡萄根瘤蚜没有发现此现象。     

Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae).

We determined the complete nucleotide sequence of the mitochondrial genome for the rabbitfish Siganus fuscescens (Perciformes, Siganidae). This mitochondrial genome, consisting of 16,491 base pairs (bp), included 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region similar those found in other vertebrates; the gene order was identical to that of typical vertebrates. Most of the genes of S. fuscescens were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser [UCN], Glu, and Pro) genes were encoded on the L-strand. The reading frames of ATPase 8 and 6 and those of ND4L and ND4 overlapped by ten and seven nucleotides, respectively. All mitochondrial protein-coding genes began with an ATG start codon, except for CO1, which started with GTG. Open reading frames of S. fuscescens ended with TAA (ND1, CO1, ATPase 8, ND4L, ND5 and ND6), and the remainder had incomplete stop codons, either TA (ATPase 6 and CO3) or T (ND2, CO2, ND3, ND4, and Cytb). The origin of L-strand replication in S. fuscescens was located in a cluster of five tRNA genes (WANCY) and was 34 nucleotides in length. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (828 bp) was considered to be the control region (D-loop). Within this sequence, we identified a conserved sequence block characteristic of this region. The rabbitfish was grouped with Siganus canaliculatus in most parsimony analyses, which showed 100% bootstrap support for their divergence. These findings are useful for inferring phylogenetic relationships and identification within the suborder Acanthuroidei.     

基于线粒体基因分析蓝孔雀与绿孔雀的遗传差异

种间的遗传差异是物种分类和确定保护管理单元的基础,本研究利用DNA条形码技术对未知样本进行鉴定,通过NCBI进行BLAST得到结果是:与绿孔雀的同源性为96%。近一步通过对蓝孔雀(Pavo cristatus)和绿孔雀(Pavo muticus)线粒体细胞色素C氧化酶Ⅰ(cytochrome coxidaseⅠ,COⅠ)基因及线粒体基因组的比较分析,结果表明两物种间的COⅠ基因在碱基组成、核苷酸多样性等各项指标上均具有明显差异。遗传距离分析结果表明蓝孔雀与绿孔雀种内遗传距离为分别0和0.012,种间遗传距离为0.045,表明种间仍具有明显的遗传差异。通过对两物种线粒体基因组各基因的比较分析,发现ND1基因变异位点所占比例相对较高,考虑作为绿孔雀和蓝孔雀种群遗传学研究的最优分子标记。本研究将为分析孔雀类群间的系统发育及制定绿孔雀的保护措施提供了更多科学依据。     

Intraspecific mitochondrial genome comparison identified CYTB as a high-resolution population marker in a new pest Athetis lepigone

A new outbreak pest, Athetis lepigone (Möschler) (Lepidoptera: Noctuidae), has caused severe economic loss in maize crops in China. In order to conduct population genetics study with a more polymorphic and scientific mitochondrial marker, we sequenced the complete mitochondrial genomes of 13 different A. lepigone individuals. Intraspecific comparison of all PCGs showed that the NADH dehydrogenase and cytochrome b genes had the highest nucleotide diversity. We also found evidence of episodic positive selection on two amino acids, which are encoded by NADH dehydrogenase genes (ND3 and ND4L), against a background of widespread neutral selection of all other mitochondrial PCGs. The genetic divergence observed in this study indicated that the cytochrome b gene (CYTB) is better than COI at recovering population structure. The preliminary population genetic analysis illustrated strong gene flow among A. lepigone populations in China. Our study provides basic information for further research on population genetics of A. lepigone.     

Morphological and genetic analyses of xeniid soft coral diversity (Octocorallia; Alcyonacea)

Studies on the biodiversity and evolution of octocorals are hindered by the incomplete knowledge of their taxonomy, which is due to few reliable morphological characters. Therefore, assessment of true species diversity within abundant and ecologically important families such as Xeniidae is difficult. Mitochondrial genes provide a reliable solution to this problem for a wide range of taxa. However, low mutation rates of the mitochondrial DNA in octocorals result in insufficient variability for species discrimination. We compared the variation of a fragment of the Signal Recognition Particle 54 gene (SRP54, proposed for octocorals) and the mitochondrial ND6/ND3 marker among members of the xeniid genera Ovabunda, Xenia, Heteroxenia and Bayerxenia. The mean uncorrected pairwise sequence divergence was 39 % for SRP54 compared to 2 % for ND6/ND3. Morphological assignments were not always supported by genetics: Species diversity was underestimated (one case) or overestimated, probably reflecting intraspecific polymorphisms or hinting at recent speciations. ND6/ND3 is informative for some species-level assignments, whereas SRP54 shows the variability needed for species delimitations within this understudied taxon. Our results on both genes show their potential for evolutionary and biodiversity studies in Xeniidae.     

Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation

The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome.     

A redescription of the pinniped parasite Contracaecum ogmorhini (Nematoda, Ascaridoidea), with an assessment of its antiboreal circumpolar distribution

The otariid seal parasite Contracaecum ogmorhini Johnston & Mawson, 1941 is redescribed based upon new material and the type specimens. The geographical records of this species indicate that it has an antiboreal circumpolar distribution with an isolated population on the south-west coast of North America. The species is considered to be morphologically more similar to Contracaecum spp. from birds than to those from phocid seals: its possible evolution is commented upon. The material identified as C. osculatum (Rudolphi) by Flores-Barroeta et al . is considered conspecific with C. ogmorhini , thus suggesting that it is this species, and not C. osculatum , which is responsible for abnormal tissue migration and brain damage in pinnipeds.     

A low rate of replacement substitutions in two major Ovis aries mitochondrial genomes

Two mitochondrial DNA molecules which represent major Ovis aries mtDNA haplogroups were cloned and comparatively sequenced to assess the degree of intraspecific variation. A total of 9623 bp that correspond to 58% of both mitochondrial genomes were determined. The control region, the Cyt b , ND2, ND3, ND4L, COIII and 12 tRNA genes, including the origin of L-strand replication, were completely characterized. Partial sequence information was obtained from the 12S and 16S rRNA and an additional six protein coding and six tRNA genes. The control regions of the two mtDNAs showed a nucleotide divergence of 4·34% while coding regions differed by 0·44%. The number of sheep coding region substitutions was similar to values observed in intraspecific comparisons of mitochondrial DNAs that represent remote points in genealogical trees of mice and humans. However, replacement substitutions were only observed at ∼30% of the rate in mice and ∼20% of the rate in humans. Nucleotide substitutions with a potential for phenotypic effects were found in the 12S and 16S rRNA and in the ND1 and COIII genes.     

华北地区中华蒙潮虫(甲壳动物亚门:等足目)种群遗传多样性研究

中华蒙潮虫Mongoloniscus sinensis(Dollfus,1901)隶属于甲壳动物亚门Crustacea等足目Isopoda潮虫亚目Oniscidea,中国特有种。为了探究中华蒙潮虫的种群遗传分化和系统进化关系,采用PCR对采自华北地区10个地理种群89只个体线粒体2个基因COⅠ和ND5进行联合分析。结果表明:1)中华蒙潮虫COⅠ部分基因长604 bp,ND5部分基因长615 bp,拼接序列长1 219 bp,T、C、A和G含量分别为41.0%、11.2%、30.8%和17.0%,具有显著的A+T偏倚;变异位点503个(占总核苷酸序列的41.3%),序列间的转换/颠换比值为2.8。2)89只个体共45种单倍型,单倍型多样性0.964,核苷酸多样性0.005 6,整体遗传多样性水平中等;单倍型H1、H15、H16、H21、H41为2～3个种群共享单倍型。3)联合基因(COⅠ+ND5)系统发育树表明,最早出现的是华北以北地区(山西大同、河北石家庄),最晚分化出的是华北以南地区(山西临汾、陕西西安未央区、河南新乡),演化路线为从北向南,个别种群单倍型未按地理来源形成明显的簇群。4)平均遗传分化指数为0.513,基因流为0.24;分子变异分析结果表明,种群的变异与分化主要来自种群内部,错配分布呈多峰,结合中性检验(Tajima's D=-1.429;Fu's F_s=6.499),发现中华蒙潮虫近期未经历扩张,但种群内部分化显著,增长平稳。本研究首次基于线粒体多基因联合分析了中华蒙潮虫种群遗传多样性。     

Mitochondrial genome sequences of the striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis

We determined the complete mitochondrial (mt) genome sequences of the striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis. The mt genomes of A. a. coreae and A. a. chejuensis are 16,260 and 16,261 base pairs in length, respectively. The general features of the 13 protein-coding genes of the two species are similar to those of other rodents. The TAG termination codon for NADH dehydrogenase subunit (ND) 3 is unique to Apodemus in the Muroidea. The L-strand replication origin has the potential to form a stable stem-loop structure. Within the control region, a termination-associated sequence and several conserved sequence blocks were observed. The diversity of the 13 protein-coding genes, 2 rRNAs, and 1 control region between the two species ranged between 0.005 (ATP8) and 0.027 (ND4L).     

Complete mitochondrial genome of the boreal digging frog Kaloula borealis (Anura, Microhylidae)

We sequenced the complete mitochondrial genome from the boreal digging frog Kaloula borealis. The genome sequence was 17,173 bp in size, and the gene order and contents were identical to those of previously reported amphibian mitochondrial genomes. Of 13 protein-coding genes (PCGs), 5 genes (CO2, ATPase 6, CO3, ND3, and ND4) had incomplete stop codons. Also ND1 gene used GTG as a start codon, while CO1 and ND5 genes used AGG as a stop codon. The base composition of K. borealis mitogenome showed a strong anti-G bias (6.11%) on the 3rd position of PCGs.     

Structure and expression of the overlapping ND4L and ND5 genes of Neurospora crassa mitochondria

Summary Genes homologous to the mammalian mitochondrial NADH dehydrogenase subunit genes ND4L and ND5 were identified in the mitochondrial genome of the filamentous fungus Neurospora crassa, and the structure and expression of these genes was examined. The ND4L gene (interrupted by one intervening sequence) potentially encodes an 89 residue long hydrophobic protein that shares about 26% homology (or 41% homology if conservative amino acid substitutions are allowed) with the analogous human mitochondrial protein. The ND5 gene (which contains two introns) encodes a 715 residue polypeptide that shares 23% homology with the human analogue; a 300 amino acid long region is highly conserved (50% homology) in the two ND5 proteins. The stop codon of the ND4L gene overlaps the initiation codon of the downstream ND5 gene, and the two genes are contranscribed and probably cotranslated. A presumed mature dicistronic (ND4L plus ND5) RNA was detected. The postulated mRNA (about 3.2 kb) contains 5 and 3 non-coding regions of about 86 and 730 nucleotides, respectively; this species is generated from very large precursor RNAs by a complex processing pathway. The ND4L and ND5 introns are all stable after their excision from the precursor species.Abbreviations bp base pairs - rRNA ribosomal RNA - ND NADH dehydrogenase - URF unidentified reading frame - kDal kilodaltons; a.a., amino acid     

Maxicircle (mitochondrial) genome sequence (partial) of Leishmania major: gene content, arrangement and composition compared with Leishmania tarentolae

We report 8420 bp of DNA sequence data from the maxicircle (mitochondrial) genome of Leishmania major (MHOM/SU/73/5ASKH), a much larger portion of this genome than has been reported previously from any Leishmania species infecting humans. This region contains 10 partial and complete genes: 5 protein-encoding genes (COII, COIII, ND1, ND7 and Cyt b); two ribosomal RNA subunits (12S and 9S) and three unidentified open reading frames (MURF1, MURF4 (ATPase6) and MURF5), as in the lizard-infecting species L. tarentolae. The genes from L. major exhibit 85-87% identity with those of L. tarentolae at the nucleotide level and 71-94% identity at the amino acid level. Most differences between sequences from the two species are transversions. The gene order and arrangement within the maxicircle of L. major are similar to those in L. tarentolae, but base composition and codon usage differ between the species. Codons assigned for initiation for protein-coding genes available for comparison are similar in five genes in the two species. Pre-editing was identified in some of the protein-coding genes. Short intergenic non-coding regions are also present in L. major as they are in L. tarentolae. Intergenic regions between 9S rRNA and MURF5, MURF1 and ND1 genes are G+C rich and considered to be extensive RNA editing regions. The RNA editing process is likely to be conserved in similar pattern in L. major as in L. tarentolae.     

Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed

The mitochondrial DNA (mtDNA) from the salmon louse, Lepeophtheirus salmonis, is 15445 bp. It includes the genes coding for cytochrome B (Cyt B), ATPase subunit 6 and 8 (A6 and A8), NADH dehydrogenase subunits 1-6 and 4L (ND1, ND2, ND3, ND4, ND4L, ND5 and ND6), cytochrome c oxidase subunits I-III (COI, COII and COIII), two rRNA genes (12S rRNA and 16S rRNA) and 22 tRNAs. Two copies of tRNA-Lys are present in the mtDNA of L. salmonis, while tRNA-Cys was not identified. Both DNA strands contain coding regions in the salmon louse, in contrast to the other copepod characterized Tigriopus japonicus, but only a few genes overlap. In vertebrates, ND4 and ND4L are transcribed as one bicistronic mRNA, and are therefore localized together. The same organization is also found in crustaceans, with the exceptions of T. japonicus, Neocalanus cristatus and L. salmonis that deviate from this pattern. Another exception of the L. salmonis mtDNA is that A6 and A8 do not overlap, but are separated by several genes. The protein-coding genes have a bias towards AT-rich codons. The mitochondrial gene order in L. salmonis differs significantly from the copepods T. japonicus, Eucalanus bungii, N. cristatus and the other 13 crustaceans previously characterized. Furthermore, the mitochondrial rRNA genes are encoded on opposite strands in L. salmonis. This has not been found in any other arthropods, but has been reported in two starfish species. In a phylogenetic analysis, using an alignment of mitochondrial protein sequences, L. salmonis groups together with T. japonicus, being distant relatives to the other crustaceans.     

地中海实蝇幼虫分子鉴定

通过对从秘鲁进口的葡萄中截获实蝇类幼虫进行ITS区和线粒体COⅠ,COⅡ,COⅢ、ND5基因序列的扩增和测序,并与GenBank中对应的序列进行比对,结果表明,截获样品ITS区序列和地中海实蝇Ceratitis capitata(Wiedemann)同源性为95·16%(其中ITS1为99·52%,ITS2为86·2%),线粒体COⅠ,COⅡ,COⅢ,ND5基因序列和地中海实蝇C.capitata同源性为100%,99·9%,99·5%,99·8%;基于COⅠ序列构建的系统发育树中,幼虫样品和地中海实蝇最为接近。根据序列分析和系统发育关系分析的结果,将截获的实蝇类幼虫鉴定为地中海实蝇C.capitata。     

赤麂线粒体全基因组的序列和结构

提取赤麂细胞株总DNA,参照我们实验室已测定的同属动物小麂线粒体全基因组序列设计引物,PCR扩增、测序、拼接,获得赤麂线粒体全基因组序列并进行生物信息学分析。赤麂线粒体全基因组序列全长16354bp。定位了22个tRNA基因、2个rRNA基因、13个蛋白编码基因和1个D-loop区。赤麂与小麂及其它哺乳动物线粒体的基因组结构相同,它们的序列同源性都较高。     

Genetic divergence of Connecticut Melanoplus femurrubrum populations

We surveyed Melanoplus femurrubrum populations within the state of Connecticut for genetic diversity at multiple genetic markers, including three mitochondrial [cytochrome oxidase subunit 1 (COI), reduced form of nicotinamide adenine dinucleotide dehydrogenase subunit 2 (ND2), and AT rich] and one nuclear [internal transcribed spacers of the ribosomal DNA cluster (ITS1)] gene regions. All markers were variable, and the AT-rich gene showed the highest sequence divergence. Analysis of molecular variance (AMOVA), fixation index (Fst) analysis, and phylogeographic patterns showed little divergence between northern and southern regions. Estimates of genetic diversity (pi) showed higher mitochondrial diversity in the northern region but nearly equal diversity for the ITS1 gene. This study shows for the first time in Melanoplus genetic variation for the ND2, AT rich, and ITS genes within a small geographic area. Our methods and results should be useful for other researchers interested in conducting population-level studies on closely related species.