食线虫真菌洛斯里被毛孢线粒体基因组的再分析

【目的】鉴定洛斯里被毛孢OWVT-1菌株的线粒体基因组,验证公布的USA-87-5菌株线粒体基因组中的错误,对洛斯里被毛孢正确的线粒体基因组序列进行注释并开展不同被毛孢物种间的比较线粒体基因组学分析。【方法】借助DNA高通量测序数据并通过必要的Sanger测序组装OWVT-1的线粒体基因组。通过PCR验证OWVT-1与公布的USA-87-5线粒体基因组序列差异的真实性。利用多种生物信息方法分析和注释洛斯里被毛孢的线粒体基因组。【结果】公布的洛斯里被毛孢USA-87-5菌株的线粒体基因组存在几处序列错误,包括3处长片段的插入缺失和多处短片段的插入缺失。实际上,洛斯里被毛孢USA-87-5与OWVT-1菌株的线粒体基因组序列完全相同。该菌的线粒体基因组全长62949 bp,在7个基因中共插入13个内含子,部分内含子和基因间区显现出序列退化的特征。洛斯里被毛孢、明尼苏达被毛孢、线虫被毛孢的线粒体基因组具有较强的共线性关系。除一些独立的ORF外,核心蛋白编码基因、rRNA基因和tRNA基因的排列顺序非常保守。基因间区的长短是影响3种被毛孢线粒体基因组大小最主要的因素。【结论】公布的洛斯里被毛孢USA-87-5菌株线粒体基因组中存在序列错误。本文新报道了OWVT-1菌株的线粒体基因组,并进行注释和比较线粒体基因组学分析。     

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.     

Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences

Although adequate resolution of higher-level relationships of organisms apparently requires longer DNA sequences than those currently being analyzed, limitations of time and resources present difficulties in obtaining such sequences from many taxa. For fishes, these difficulties have been overcome by the development of a PCR-based approach for sequencing the complete mitochondrial genome (mitogenome), which employs a long PCR technique and many fish-versatile PCR primers. In addition, recent studies have demonstrated that such mitogenomic data are useful and decisive in resolving persistent controversies over higher-level relationships of teleosts. As a first step toward resolution of higher teleostean relationships, which have been described as the "(unresolved) bush at the top of the tree," we investigated relationships using mitogenomic data from 48 purposefully chosen teleosts, of which those from 38 were newly determined during the present study (a total of 632,315 bp), using the above method. Maximum-parsimony and maximum-likelihood analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and third codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) from the 48 species. The resultant two trees from the two methods were well resolved and largely congruent, with many internal branches supported by high statistical values. The tree topologies themselves, however, exhibited considerable variation from the previous morphology-based cladistic hypotheses, with most of the latter being confidently rejected by the mitogenomic data. Such incongruence resulted largely from the phylogenetic positions or limits of long-standing problematic taxa, which were quite unexpected from previous morphological and molecular analyses. We concluded that the present study provided a basis of and guidelines for future investigations of teleostean evolutionary mitogenomics and that purposeful higher-density taxonomic sampling, subsequent sequencing efforts, and phylogenetic analyses of their mitogenomes may be decisive in resolving persistent controversies over higher-level relationships of teleosts, the most diversified group of all vertebrates, comprising over 23,500 extant species.     

Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus)

The Indian wild pig is a sub-species (Sus scrofa cristatus) which is different from the other pig breeds and is protected under Schedule-III of the Indian Wildlife (Protection) Act, 1972. In this study, complete mitogenome of two Indian wild pigs was sequenced and characterized by shotgun sequencing and de novo assembly, which revealed sequence size of 16,738 and 16,251?bp, respectively, (Accession no. MG725630 and MG725631). The mitogenome sequence in this study displayed 98% homology with previously reported mitogenome of pigs from different parts of the world. Mitogenome analysis by MITOS Web server revealed similarity of gene organization with the other vertebrates (13 protein-coding, 22 tRNAs, 2 rRNAs genes, and a control region). The mitogenomic sequences of Indian wild pig maintained a separate clade in the phylogenetic tree constructed by using 62 whole mitogenome sequences across the world. The phylogeny derived from mitogenomic sequences revealed distinct separate European–American and Asiatic pig clades. It was concluded that whole mitogenome sequencing using NGS without designing mitogenome-specific primer for amplification, is possible thereby reducing the cost and labor. This study is the first report of complete sequence of mitogenome of Indian wild pig.     

The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes)

The Chinese rare minnow, Gobiocypris rarus, which is endemic to China, is an attractive aquatic laboratory animal in China. In the present study, the complete mitogenome sequence of G. rarus has been determined using long polymerase chain reaction (PCR) method. It was 16,601 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, the gene composition and order of which are similar to most other vertebrates. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand is 29.5% A, 27.6% T, 25.7% C, and 17.2% G, with a slight AT bias of 57.1%. There are 10 regions of gene overlap totaling 27 bp and 13 intergenic spacer regions totaling 63 bp. The mitogenome sequence of G. rarus could contribute to a better solution of its phylogenetic position within cyprinid fishes based on the whole mitogenomic data.     

Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: An avian case study

Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate heterogeneity, without discarding data, by applying separate evolutionary models to differing portions of the mitogenome. To facilitate use of complete mitogenomic sequences in phylogenetics, we (1) suggest a set of categories for dividing mitogenomic datasets into subsets, (2) explore differences in evolutionary dynamics among those subsets, and (3) apply a method for combining data subsets with similar properties to produce effective and efficient partitioning schemes. We demonstrate these procedures with a case study, using the mitogenomes of species in the grackles and allies clade of New World blackbirds (Icteridae). We found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that we tested. As hoped, we found that analyses using whole mitogenomic sequences yielded much better-resolved and more strongly-supported hypotheses of the phylogenetic history of that locus than did a conventional 2-kilobase sample (i.e. sequences of the cytochrome b and ND2 genes). Mitogenomes have much untapped potential for phylogenetics, especially of birds, a taxon for which they have been little exploited except in investigations of ordinal-level relationships.     

FisOmics: A portal of fish genomic resources

An online portal, accessible at URL: http://mail.nbfgr.res.in/FisOmics/, was developed that features different genomic databases and tools. The portal, named as FisOmics, acts as a platform for sharing fish genomic sequences and related information in addition to facilitating the access of high-performance computational resources for genome and proteome data analyses. It provides the ability for quarrying, analysing and visualizing genomic sequences and related information. The featured databases in FisOmics are in the World Wide Web domain already. The aim to develop portal was to provide a nodal point to access the featured databases and work conveniently. Presently, FisOmics includes databases on barcode sequences, microsatellite markers, mitogenome sequences, hypoxia-responsive genes and karyology of fishes. Besides, it has a link to other molecular resources and reports on the on-going activities and research achievements.     

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis

Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.     

Three New Ranidae Mitogenomes and the Evolution of Mitochondrial Gene Rearrangements among Ranidae Species

Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae.In this study,we determined the complete mitogenome sequence of three Rana frogs.By combining the available mitogenomic data sets from Gen Bank,we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae.The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement.Except for the genus Babina,the monophyly of each genus was well supported.The genus Amnirana occupied the most basal position among the Ranidae.The[Lithobates+Rana]was the closest sister group of Odorrana.The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high,with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types.Some taxa owned their unique gene rearrangement characteristics,which had significant implication for their phylogeny analysis.All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.     

The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.     

The complete mitogenome of the snakehead Channa argus (Perciformes: Channoidei): genome characterization and phylogenetic implications

To better understand the phylogenetic status of the snakehead, Channa argus, we determined its complete mitogenome sequence using long-polymerase chain reaction and the direct sequencing method. The complete mitogenome sequence was 16,559?bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. This was the first report of the mitogenome sequence in suborder Channoidei. Phylogenetic relationships of 14 perciform suborders based on mitogenome sequences were reconstructed using Bayesian inference and maximum likelihood methods. The results strongly supported the monophyly of Perciformes and the snakehead, as a representative species of suborder Channoidei, formed the most basal branch having sister relationship with the clade containing all other analyzed perciform fishes. The further phylogenetic analyses of six channid species, based on cytochrome b gene, suggested that two channid genera constituted reciprocally monophyletic clades. In addition, the relaxed molecular clock method was used to estimate divergence dates among major suborders of Perciformes and major species in Channoidei.     

Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences

Recent mitogenomic studies suggest a new position for the deep-sea fishes of the order Alepocephaliformes, placing them within the Otocephala in contrast to their traditional placement within the Euteleostei. However, these studies included only two alepocephaliform taxa and left several questions unsolved about their systematics. Here we use whole mitogenome sequences to reconstruct phylogenetic relationships for 11 alepocephaliform taxa, sampled from all five nominal families, and a large selection of non-alepocephaliform teleosts, to address the following three questions: (1) is the Alepocephaliformes monophyletic, (2) what is its phylogenetic position within the Teleostei and (3) what are the relationships among the alepocephaliform families? Our character sets, including unambiguously aligned, concatenated mitogenome sequences that we have divided into four (first and second codon positions, tRNA genes, and rRNA genes) or five partitions (same as before plus the transversions at third codon positions, using "RY" coding), were analyzed by the partitioned maximum likelihood and Bayesian methods. Our result strongly supported the monophyly of the Alepocephaliformes and its close relationship to the Clupeiformes and Ostariophysi. Altogether, these three groups comprise the Otocephala. Statistical comparison using likelihood-based SH test confidently rejected the monophyly of the Euteleostei when including the Alepocephaliformes. However, increasing the taxonomic sampling within the Alepocephaliformes did not resolve its position relative to the Clupeiformes and Ostariophysi. Within the Alepocephaliformes, our results strongly supported the monophyly of the platytroctid genera but not that of the remaining taxa. From one analysis to other, platytroctids were either the sister group of the remaining taxa or nested within the alepocephalids. Inferred relationships among alepocephaliform taxa were not congruent with any of the previously published phylogenetic hypotheses based on morphological characters.     

Revealing hidden plant diversity in arid environments

Estimating total plant diversity in extreme or hyperarid environments can be challenging, as adaptations to pronounced climate variability include evading prolonged stress periods through seeds or specialized underground organs. Short‐term surveys of these ecosystems are thus likely poor estimators of actual diversity. Here we develop a multimethod strategy to obtain a more complete understanding of plant diversity from a community in the Atacama Desert. We explicitly test environmental DNA‐based techniques (eDNA) to see if they can reveal the observed and ‘hidden' (dormant or locally rare) species. To estimate total plant diversity, we performed long‐term traditional surveys during eight consecutive years, including El Niño and La Niña events, we then analyzed eDNA from soil samples using high‐throughput sequencing. We further used soil pollen analysis and soil seed bank germination assays to identify ‘hidden' species. Each approach offers different subsets of current biodiversity at different taxonomic, spatial and temporal resolution, with a total of 92 taxa identified along the transect. Traditional field surveys identified 77 plant species over eight consecutive years. Observed community composition greatly varies interannually, with only 22 species seen every year. eDNA analysis revealed 37 taxa, eight of which were ‘hidden' in our field surveys. Soil samples contain a viable seed bank of 21 taxa. Soil pollen (27 taxa) and eDNA analysis show affinities with vegetation at the landscape scale but a weak relationship to local plot diversity. Multimethod approaches (including eDNA) in deserts are valuable tools that add to a comprehensive assessment of biodiversity in such extreme environments, where using a single method or observations over a few years is insufficient. Our results can also explain the resilience of Atacama plant communities as ‘hidden' taxa may have been active in the recent past or could even emerge in the future as accelerated global environmental change continues unabated.     

PCR-Based Approach for Sequencing Mitochondrial Genomes of Decapod Crustaceans,with a Practical Example from Kuruma Prawn (<Emphasis Type="Italic">Marsupenaeus japonicus</Emphasis>)

An approach for sequencing the entire mitochondrial genomes (mitogenomes) of decapod crustaceans using 79 newly designed and 7 published polymerase chain reaction (PCR) primers is described. The approach comprises the following steps: (1) the entire mitogenome is amplified in 2 or 3 long PCRs; (2) the 86 primers are used in different combinations to amplify contiguous, overlapping short segments of the entire mitogenome with the diluted long PCR products as templates; (3) direct cycle sequencing is conducted using the short PCR products. This strategy allows a more rapid determination of decapod mitogenomic sequences than a traditional method using cloned mitochondrial DNA and primer walking strategy. As a practical example, the mitogenomic sequence for a kuruma prawn Marsupenaeus japonicus (Crustacea: Decapoda), was determined using the PCR-based approach.     

Complete mitochondrial genome sequence of Catla catla and its phylogenetic consideration

Complete nucleotide sequence of mitochondrial genome (mitogenome) of the Catla catla (Ostariophysi: Cypriniformes: Cyprinidae) was determined in the present study. Its length is 16,594 bp and contains 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs and one non-coding control region. Most of the genes 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 two pair of genes overlapped: ATPase 8 with 6 and ND4L with ND4 by seven nucleotides each. The main non-coding region was 929 bp, with three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and an unusual simple sequence repeat, (TA)₇. Phylogenetic analyses based on complete mitochondrial genome sequences were in favor of the traditional taxonomy of family Cyprinidae. In conclusion present mitogenome of Catla catla adds more information to our understanding of diversity and evolution of mitogenome in fishes.     

丝带凤蝶线粒体基因组全序列及其系统学意义(英文)

锯凤蝶类与凤蝶科其他类群的系统发生关系及其分类学地位一直存在争议。本研究采用PCR和long PCR技术测定了属于锯凤蝶类的丝带凤蝶Sericinus montelus线粒体基因组全序列; 结合已有的其他凤蝶科物种的相应序列数据, 基于13个蛋白质编码基因重建了凤蝶科主要类群的系统发生树, 探讨了它们之间的系统发生关系。基因组分析结果表明： 丝带凤蝶线粒体基因组全长15 242 bp, 包括13个编码蛋白基因(ATP6, ATP8, COⅠ-Ⅲ, ND1-6, ND4L和Cytb)、 22个tRNA基因、 16S和12S rRNA基因以及非编码的控制区; 基因组A, T, G和C含量分别为40.1%, 40.8%, 7.4%和11.7%, 表现出明显的AT偏倚。所有的蛋白质编码基因都使用标准的起始密码子(ATN); 除ND4 和 ND4L基因使用单个的T作为终止密码子外, 其余蛋白编码基因都使用了标准的终止密码子(TAA)。除丝氨酸 tRNA的二氢尿苷突环缺失外, 所有tRNA基因都形成典型的三叶草型结构。基因组中共存在12个大小介于2~65 bp之间的基因间隔区以及15个大小介于1~8 bp之间的基因重叠区, 其中, 存在于COⅡ和tRNA^Lys之间的24 bp的间隔区在其他鳞翅目昆虫中未曾见到。以邻接法和最大简约法并基于13个蛋白质编码基因序列对凤蝶科进行了系统发生分析。结果显示, 丝带凤蝶和中华虎凤蝶Luehdorfia chinensis先构成一个支系, 再和冰清绢蝶Parnassius bremeri构成姊妹群; 表明锯凤蝶类应作为族级分类单元归于凤蝶科下的绢蝶亚科。     

The mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements

The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein‐coding genes, two rRNA genes, and 22 tRNA genes. We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein‐coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co‐occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro‐ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution.     

肺囊康定产生菌Glarea lozoyensis线粒体基因组序列的再分析

[目的] Glarea lozoyensis是抗真菌药物卡泊芬净的产生菌,其突变菌株ATCC 74030的线粒体基因组已被报道。我们此前的研究发现诱变剂能引起该菌某些细胞核基因的突变,但诱变剂是否也能引起线粒体DNA序列的改变并不清楚。[方法] 组装野生型菌株ATCC 20868的线粒体基因组,并与发表的突变型菌株ATCC 74030的线粒体基因组进行比较。通过PCR验证野生和突变菌株线粒体基因组间表现差异之处,并利用正确的线粒体基因组序列进行新的分析。[结果] 我们成功组装出野生型菌株ATCC 20868的线粒体基因组,通过比较其与发表的ATCC 74030的线粒体基因组序列,发现存在6处单核苷酸变异位点和2处具有长度差异的区域。然而,随后的PCR验证和序列比较并没有发现2个菌株间存在这些差异。最初观察到的碱基差异是因为发表的ATCC 74030线粒体基因组存在序列错误。有趣的是,在Glarea lozoyensis的线粒体基因组中,我们发现存在3个具有内含子的tRNA基因和1个rnpB基因。同时,该菌线粒体基因组中存在多种重复序列,在其线粒体和细胞核基因组间也存在明显的DNA片段重复事件。[结论] 诱变剂没有引起G. lozoyensis线粒体DNA的任何改变;发表的ATCC 74030的线粒体基因组存在序列错误。我们报道G. lozoyensis正确的线粒体基因组序列,并且发现该菌线粒体和细胞核基因组间频繁的基因交流。     

Ancient mitogenomics

The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.