Genome, Mitochondrial

基因组, 线粒体
  • 文章类型: Journal Article
    我们旨在区分Synodontiseupterus和Synodontispolli。我们对其线粒体基因组进行了测序和生物信息学分析,并基于14种Mochokidae物种的蛋白质编码基因(PCG)序列,使用最大似然和贝叶斯方法构建了Mochokidae鱼的系统发育树。Eupterus线粒体基因组的总长度为16,579bp,包括13个(PCG),22个tRNA基因,两个rRNA基因,和一个D循环,具有AT偏倚的核苷酸组成(56.0%)。S.polli线粒体基因组的总长度为16,544bp,包括13个PCG,22个tRNA基因,两个rRNA基因,和一个D循环,具有AT偏倚的核苷酸组成(55.0%)。在这两个物种中,除了COI,PCGs使用ATG作为起始密码子,绝大多数使用TAG或TAA作为结束密码子,和一些使用不完整的密码子(T-或TA-)作为结束密码子。系统发育分析表明,eupterus和Synodontisclaras汇聚成一个分支,S.Poli和SynodontisPetricola汇聚成一个分支,Mochokiellapaynei,Mochokusbrevis,Synodontis属的9种汇聚成一个分支,和M.paynei聚集在Synodontis属。该研究为重建更清晰的Mochokidae鱼类分类系统奠定了基础。
    We aimed to distinguish Synodontis eupterus and Synodontis polli. We performed sequencing and bioinformatic analysis of their mitochondrial genomes and constructed a phylogenetic tree of Mochokidae fish using maximum likelihood and Bayesian methods based on protein-coding gene (PCG) sequences of 14 Mochokidae species. The total length of the S. eupterus mitochondrial genome was 16,579 bp, including 13 (PCGs), 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (56.0%). The total length of the S. polli mitochondrial genome was 16,544 bp, including 13 PCGs, 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (55.0%). In both species, except for COI, PCGs use ATG as the starting codon, the vast majority use TAG or TAA as the ending codon, and a few use incomplete codons (T - or TA -) as the ending codon. Phylogenetic analysis showed that S. eupterus and Synodontis clarias converged into one branch, S. polli and Synodontis petricola converged into one branch, Mochokiella paynei, Mochokus brevis, and nine species of the genus Synodontis converged into one branch, and M. paynei clustered with the genus Synodontis. This study lays a foundation for rebuilding a clearer Mochokidae fish classification system.
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  • 文章类型: Journal Article
    背景:香附是沿海生态系统中的重要物种,具有经济和生态价值。为了阐明结构特征,变异,以及梭菌细胞器基因组的进化,我们测序了,组装,并比较了它的线粒体和叶绿体基因组。
    结果:我们组装了梭菌的线粒体和叶绿体基因组。线粒体基因组(mtDNA)的总长度为927,413bp,GC含量为40.59%。它由两个圆形DNA组成,包括37个蛋白质编码基因(PCGs),22个tRNA,和五个rRNA。叶绿体基因组(cpDNA)的长度为186,204bp,包含93个PCG,40个tRNA,和8个rRNA。mtDNA和cpDNA包含81和129个串联重复,分别,和346和1,170个分散的重复,分别,两者都有270个简单的序列重复。细胞器基因组中第三个高频密码子(RSCU>1)倾向于A或U结束,而低频密码子(RSCU<1)倾向于在G或C结束。PCGs的RNA编辑位点相对较少,在mtDNA和cpDNA中只有9个和23个位点,分别。mtDNA中共有28个线粒体质体DNA(MTPT)来源于cpDNA,包括三个完整的trnT-GGU,trnH-GUG,和trnS-GCU.系统发育和共线性表明,蛇床子和圆周子之间的关系最密切。线粒体rns基因表现出最大的核苷酸变异性,而核苷酸变异性最大的叶绿体基因是infA。细胞器基因组中的大多数PCGs是负选择的,并且在进化上高度保守。只有6个线粒体基因和2个叶绿体基因显示Ka/Ks>1;atp9,atp6和rps7可能已经经历了潜在的正选择。
    结论:我们组装并验证了C.stoloniferus的mtDNA,它包含一个15,034bp的反向互补序列。梭菌的细胞器基因组序列为物种鉴定提供了宝贵的基因组资源,进化,和莎草科的比较基因组研究。
    BACKGROUND: Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes.
    RESULTS: We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection.
    CONCLUSIONS: We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.
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  • 文章类型: Journal Article
    背景:Austroplea属的Lymnaeid蜗牛是肝吸虫(肝片)的重要载体,造成澳大利亚和新西兰的畜牧业生产损失。然而,由于严重依赖形态分析和相对缺乏遗传数据,因此Austroplea中的物种状况不明确。这项研究旨在表征A.cf的线粒体基因组。brazieri,维多利亚东部肝吸虫的中间宿主。
    方法:从第二代和第三代测序数据的组合中组装和注释线粒体基因组。出于比较目的,我们对线粒体蛋白质编码基因的串联核苷酸序列进行了系统发育分析,细胞色素c氧化酶亚基1和16S基因。
    结果:组装的mt基因组为13,757个碱基对,包含37个基因,包括13个蛋白质编码基因,22个转移RNA基因和2个核糖体RNA基因。mt基因组长度,基因顺序和核苷酸组成与相关的lymnaeids物种相似。置于A的mt核苷酸序列的系统发育分析。brazieri与Orientogalbaolula处于同一进化枝,具有强大的统计支持。由于这些代表lymnaeid分类群的序列广泛可用,因此构建了cox1和16Smt序列的系统发育。正如预期的那样,在这两个系统发育中,A.参见。brazieri与其他Austropeplea序列聚集在一起,但是节点支撑很低。
    结论:A.cf.brazieri应该为未来的分子提供有用的资源,这种社会经济上重要的lymnaeid物种的流行病学和寄生虫学研究。
    BACKGROUND: Lymnaeid snails of the genus Austropeplea are an important vector of the liver fluke (Fasciola hepatica), contributing to livestock production losses in Australia and New Zealand. However, the species status within Austropeplea is ambiguous due to heavy reliance on morphological analysis and a relative lack of genetic data. This study aimed to characterise the mitochondrial genome of A. cf. brazieri, an intermediate host of liver fluke in eastern Victoria.
    METHODS: The mitochondrial genome was assembled and annotated from a combination of second- and third-generation sequencing data. For comparative purposes, we performed phylogenetic analyses of the concatenated nucleotide sequences of the mitochondrial protein-coding genes, cytochrome c oxidase subunit 1 and 16S genes.
    RESULTS: The assembled mt genome was 13,757 base pairs and comprised 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The mt genome length, gene order and nucleotide compositions were similar to related species of lymnaeids. Phylogenetic analyses of the mt nucleotide sequences placed A. cf. brazieri within the same clade as Orientogalba ollula with strong statistical supports. Phylogenies of the cox1 and 16S mt sequences were constructed due to the wide availability of these sequences representing the lymnaeid taxa. As expected in both these phylogenies, A. cf. brazieri clustered with other Austropeplea sequences, but the nodal supports were low.
    CONCLUSIONS: The representative mt genome of A. cf. brazieri should provide a useful resource for future molecular, epidemiology and parasitological studies of this socio-economically important lymnaeid species.
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  • 文章类型: Journal Article
    背景:真核细胞含有具有自身基因组的称为线粒体的细胞器。大多数细胞含有数千个复制的线粒体,即使在非分裂细胞中,通过相对容易出错的过程导致其基因组中的体细胞突变。因为与核基因组相比突变率更高,线粒体突变已经被用来追踪细胞谱系,特别是使用单细胞测序来测量单个细胞中的线粒体突变。然而,从线粒体突变推断细胞谱系树的现有方法不能建立“异质体”模型,“这是存在多个线粒体克隆,在单个细胞中具有不同的突变集。因此,单细胞测序数据提供了单个细胞中线粒体克隆的混合物,与线粒体克隆树描述的这些克隆之间的祖先关系。虽然在癌症肿瘤样本批量测序的背景下,已经广泛研究了来自进化相关基因组混合物的体细胞突变的反卷积,线粒体去卷积的问题有一个额外的限制,即线粒体克隆树必须与细胞谱系树一致。
    结果:我们将从单细胞测序数据中推断线粒体克隆树和细胞谱系树的一致对的问题形式化为嵌套完美系统发育混合物(NPPM)问题。我们推导了NPPM问题解的组合表征,制定一个算法,梅林,用混合整数线性规划来解决这个问题。我们在模拟数据上显示,MERLIN优于现有方法,这些方法既不模拟线粒体异质体,也不模拟线粒体克隆树与细胞谱系树之间的一致性。我们使用MERLIN分析胃癌细胞系的5220个细胞的单细胞全基因组测序数据,并显示MERLIN与现有方法相比推断了更生物学上合理的细胞谱系树和线粒体克隆树。
    方法:https://github.com/raphael-group/MERLIN。
    BACKGROUND: Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even in nondividing cells, by means of a relatively error-prone process resulting in somatic mutations in their genome. Because of the higher mutation rate compared to the nuclear genome, mitochondrial mutations have been used to track cellular lineage, particularly using single-cell sequencing that measures mitochondrial mutations in individual cells. However, existing methods to infer the cell lineage tree from mitochondrial mutations do not model \"heteroplasmy,\" which is the presence of multiple mitochondrial clones with distinct sets of mutations in an individual cell. Single-cell sequencing data thus provide a mixture of the mitochondrial clones in individual cells, with the ancestral relationships between these clones described by a mitochondrial clone tree. While deconvolution of somatic mutations from a mixture of evolutionarily related genomes has been extensively studied in the context of bulk sequencing of cancer tumor samples, the problem of mitochondrial deconvolution has the additional constraint that the mitochondrial clone tree must be concordant with the cell lineage tree.
    RESULTS: We formalize the problem of inferring a concordant pair of a mitochondrial clone tree and a cell lineage tree from single-cell sequencing data as the Nested Perfect Phylogeny Mixture (NPPM) problem. We derive a combinatorial characterization of the solutions to the NPPM problem, and formulate an algorithm, MERLIN, to solve this problem exactly using a mixed integer linear program. We show on simulated data that MERLIN outperforms existing methods that do not model mitochondrial heteroplasmy nor the concordance between the mitochondrial clone tree and the cell lineage tree. We use MERLIN to analyze single-cell whole-genome sequencing data of 5220 cells of a gastric cancer cell line and show that MERLIN infers a more biologically plausible cell lineage tree and mitochondrial clone tree compared to existing methods.
    METHODS: https://github.com/raphael-group/MERLIN.
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  • 文章类型: Journal Article
    背景:心裂,一组热带树木(约20spp.)在樟科中,有两栖-太平洋分离分布:10种分布在东南亚,而南美的热带雨林则限制了8种。以前,使用两个核标记的系统发育分析解决了拉丁美洲五个物种之间的关系。然而,亚洲物种之间的系统发育关系仍然鲜为人知。
    结果:这里,我们首先确定了完整的线粒体基因组(有丝分裂基因组),质体,和C.henryi的核核糖体顺反子(nrDNA)序列,长度为1,168,029bp,154,938个基点,6495bp,分别。我们在C.henryi的有丝分裂基因组中发现了2233个重复序列和368个潜在的SSR,在其有丝分裂基因组和质体之间发现了50个同源DNA片段。基因合成分析显示,木兰的有丝分裂基因组中有大量重排,HernandiaNymphaeifolia,和C.henryi,其中只有六个保守的成簇基因。为了重建亚洲十种Caryodaphnopsis物种的关系,我们创建了三个数据集:一个是有丝分裂基因组(编码基因和十个基因间区域),另一个是质体(全基因组),另一个是核核糖体顺反子。所有的22个Caryodaphnopsis个体被分为四个,五,和基于有丝分裂基因组的六个不同的进化枝,质体,和nrDNA数据集,分别。
    结论:该研究显示了Caryodaphnopsis物种的核和细胞器基因组数据内部和之间的系统发育冲突。中国河口和麻栗坡的同胞石竹物种可能与不完整的谱系分类有关,叶绿体捕获,和/或杂交,将该物种作为进化史上的一个复合体混合在一起。
    BACKGROUND: Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.
    RESULTS: Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.
    CONCLUSIONS: The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.
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  • 文章类型: Journal Article
    这项研究分析了石虎窑墓葬出土的马遗骸中的古代DNA。这些发现可追溯到新疆汉唐时期(大约2200至1100年前)。获得两个高质量的线粒体基因组并使用下一代测序进行分析。基因组被分成两个母体单倍群,B和D,根据一项包括欧亚大陆古代和当代样本的研究。根据原始马单倍型G1,唐代马与Akhal-Teke马之间观察到了紧密的遗传亲和力。历史证据表明,古代丝绸之路在其传播中起着至关重要的作用。此外,获得了Akhal-Teke马的母系历史,并表明该品种的早期驯化是出于军事目的。
    This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.
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  • 文章类型: Journal Article
    托尔图拉·阿特维伦斯(Sm。)林德。是生物土壤结皮的重要组成部分,对旱地栖息地的干燥具有非凡的耐受性。然而,仍然缺乏这种耐干燥(DT)苔藓的细胞器基因组的知识。这里,我们组装了第一个报告的Tortula细胞器基因组,并在Pottiaceae家族中进行了全面分析。T.atrovirens在Pottiaceae中表现出第二大叶绿体基因组(129,646bp),与其他陆地植物相比,其有丝分裂基因组(105,877bp)和其他苔藓的大小较小。T.atrovirens的叶绿体和线粒体基因组的特征在于IR边界的扩展和不存在大重复序列介导的同源重组。通过作图RNA-seq数据检测到总共57个RNA编辑位点。此外,该基因的含量和顺序在Pottiaceae细胞器基因组中高度保守。系统发育分析表明苔藓植物是共生的,他们的三个血统(角,苔藓,和苔藓)和维管植物形成连续的姐妹进化枝。Timmiellaanomala显然与单系pottiaceae分开,和T.atrovirens与Pottioideae内的丝状体紧密相关。此外,我们检测到四个候选分子标记的高变区。我们的发现为T.atrovirens的细胞器基因组和Pottiaceae家族中的进化关系提供了有价值的见解,促进未来从苔藓植物中发现DT遗传资源。
    Tortula atrovirens (Sm.) Lindb. is an important component of biological soil crusts and possesses an extraordinary tolerance against desiccation in dryland habitats. However, knowledge of the organelle genome of this desiccation-tolerant (DT) moss is still lacking. Here, we assembled the first reported Tortula organelle genome and conducted a comprehensive analysis within the Pottiaceae family. T. atrovirens exhibited the second largest chloroplast genome (129,646 bp) within the Pottiaceae, whereas its mitogenome (105,877 bp) and those of other mosses were smaller in size compared to other land plants. The chloroplast and mitochondrial genomes of T. atrovirens were characterized by the expansion of IR boundaries and the absence of homologous recombination-mediated by large repeats. A total of 57 RNA editing sites were detected through mapping RNA-seq data. Moreover, the gene content and order were highly conserved among the Pottiaceae organelle genomes. Phylogenetic analysis showed that bryophytes are paraphyletic, with their three lineages (hornworts, mosses, and liverworts) and vascular plants forming successive sister clades. Timmiella anomala is clearly separated from the monophyletic Pottiaceae, and T. atrovirens is closely related to Syntrichia filaris within the Pottioideae. In addition, we detected four hypervariable regions for candidate-molecular markers. Our findings provide valuable insights into the organelle genomes of T. atrovirens and the evolutionary relationships within the Pottiaceae family, facilitating future discovery of DT genetic resources from bryophytes.
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  • 文章类型: Journal Article
    旧世界的鹌鹑,Coturnixcoturnix(普通鹌鹑)和Coturnixjaponica(日本鹌鹑),形态相似,但占据不同的地理范围。这项研究旨在通过对其线粒体基因组的全面分析来阐明其进化轨迹和祖先分布模式。有丝分裂基因组分析显示高度结构保守,相同的翻译机制,两个物种的进化压力相似。选择分析显示,由于进化史上的环境变化和适应要求,在Coturnix谱系中对nad4基因树进行了积极选择的重要证据。发散时间估计意味着Coturnix物种之间的多样化发生在上世纪中期(13.89Ma),它们目前的分布主要是由分散而不是全球替代事件形成的。系统发育分析表明,coturnix和粳稻之间有着密切的关系,在更新世时期,发散估计为2.25Ma。祖先范围重建表明,Coturnix进化枝的祖先分布在东方地区。C.coturnix随后分散到欧亚大陆和非洲,和C.japonica到东亚。我们假设C.coturnix和C.japonica的当前地理分布来自其独特的扩散策略,发展到逃避种间地域性,并受到青藏高原地理限制的影响。这项研究促进了我们对导致C.coturnix和C.japonica多样化的生物地理和进化过程的理解,为该属的进一步研究奠定了重要基础。
    The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau\'s geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.
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  • 文章类型: Dataset
    梅果蛾Grapholitafunebrana(Tortricidae,鳞翅目)是玫瑰科中许多野生和栽培核果和其他植物的重要害虫。这里,我们用Illumina组装了它的核和线粒体基因组,纳米孔,和Hi-C测序技术。核基因组大小为570.9Mb,重复率为51.28%,BUCSO完整性为97.7%。男性的核型为2n=56。我们确定了17,979个蛋白质编码基因,5,643tRNA,和94个rRNA。我们还确定了该物种的线粒体基因组,并注释了13个蛋白质编码基因,22个tRNA,和2个rRNA。这些基因组提供了理解遗传学的资源,生态学,和蠕虫蛾的基因组进化。
    The plum fruit moth Grapholita funebrana (Tortricidae, Lepidoptera) is an important pest of many wild and cultivated stone fruits and other plants in the family Rosaceae. Here, we assembled its nuclear and mitochondrial genomes using Illumina, Nanopore, and Hi-C sequencing technologies. The nuclear genome size is 570.9 Mb, with a repeat rate of 51.28%, and a BUCSO completeness of 97.7%. The karyotype for males is 2n = 56. We identified 17,979 protein-coding genes, 5,643 tRNAs, and 94 rRNAs. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomes provide resources to understand the genetics, ecology, and genome evolution of the tortricid moths.
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  • 文章类型: Journal Article
    结论:我们首次报道了樟树的线粒体基因组,揭示木木兰线粒体基因组非编码区中频繁的重排事件。作为木兰科樟科的代表种之一,樟树具有重要的经济和生态价值。在这项研究中,使用PacBioHiFi测序完整组装并注释了C.camphora的线粒体基因组(有丝分裂基因组)。樟树有丝分裂体的特点是分支结构,跨度900,894bp,包含43个蛋白质编码基因(PCGs),24个tRNA,和3个rRNA。这些PCGs中的大多数都在纯化选择中,只有两个(ccmFc和rps7)表现出阳性选择的迹象。樟树有丝分裂基因组包含许多重复序列和细胞内基因转移,共有36个线粒体质体DNA,总计23,816bp的合并长度。比较分析表明,木兰有丝分裂基因组的非编码区在进化过程中经历了频繁的重排,但编码序列仍然高度保守(蛋白质编码序列的相似性超过98%)。此外,基于来自23个植物有丝分裂基因组的25个PCGs,重建了最大似然系统发育树。该分析支持了樟树和切家菜之间最密切的关系,与APGIV分类系统一致。本研究阐明了樟树有丝分裂体的独特进化特征,这将为樟科的遗传学和进化研究提供有价值的见解。
    CONCLUSIONS: We reported the mitochondrial genome of Cinnamomum camphora for the first time, revealing frequent rearrangement events in the non-coding regions of Magnoliids mitochondrial genomes. As one of the representative species in the Lauraceae family of Magnoliids, Cinnamomum camphora holds significant economic and ecological value. In this study, the mitochondrial genome (mitogenome) of C. camphora was complete assembled and annotated using PacBio HiFi sequencing. The C. camphora mitogenome is characterized by a branch structure, spans 900,894 bp, and contains 43 protein-coding genes (PCGs), 24 tRNAs, and 3 rRNAs. Most of these PCGs are under purifying selection, with only two (ccmFc and rps7) exhibiting signs of positive selection. The C. camphora mitogenome contains numerous repetitive sequences and intracellular gene transfers, with a total of 36 mitochondrial plastid DNAs, amounting to a combined length of 23,816 bp. Comparative analysis revealed that the non-coding regions of Magnoliids mitogenomes have undergone frequent rearrangements during evolution, but the coding sequences remain highly conserved (more than 98% similarity for protein-coding sequences). Furthermore, a maximum-likelihood phylogenetic tree was reconstructed based on 25 PCGs from 23 plant mitogenomes. The analysis supports the closest relationship between C. camphora and C. chekiangense, consistent with the APG IV classification system. This study elucidates the unique evolutionary features of the C. camphora mitogenome, which will provide valuable insights into the study of genetics and evolution of the family Lauraceae.
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