比较基因组学揭示了 Ludwigia(Onagraceae, Myrtales)质体进化的新见解。

IF 2.6 4区 综合性期刊 Q2 MULTIDISCIPLINARY SCIENCES Science Progress Pub Date : 2024-07-01 DOI:10.1177/00368504241272741
Hoang Danh Nguyen, Hoang Dang Khoa Do, Minh Thiet Vu
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引用次数: 0

摘要

报春花柳属(Ludwigia L.)是一种定义明确的大戟科属植物,共有 87 个种,广泛分布于世界各地。在这项研究中,我们对该属的三个物种,包括 Ludwigia adscendens、Ludwigia hyssopifolia 和 Ludwigia prostrata 的完整叶绿体(cp)基因组进行了测序和鉴定。三个Ludwigia cp基因组的大小从158,354到159,592 bp不等,每个基因组包含113个基因,包括79个独特的蛋白质编码基因(PCGs)、4个rRNA基因和30个tRNA基因。对路德维格 cp 基因组进行比较后发现,它们在基因组成、基因方向和 GC 含量方面高度保守。此外,我们还比较了 cp 基因组的结构,并重建了与大戟科相关物种的系统发育关系。在倒位重复区(IR)的收缩/扩张方面,在Oenothera属、Chamaenerion属和Epilobium属中发现了两种扩张的IR区结构,在Ludwigia属和Circeae属中发现了原始的IR区结构。clpP、ycf2和ycf1基因区域在Onagraceae科所有可获得的cp基因组中具有高度差异的核苷酸。利用 39 个 Onagraceae cp 基因组中的 79 个 PCGs 进行系统发育重建,推断 Ludwigia(包括 L. adscendens、L. hyssopifolia、L. prostrata 和 Ludwigia octovalvis)支系为单系,并得到引导值和后验概率值的良好支持。本研究提供了三个Ludwigia物种的参考cp基因组,可用于Ludwigia和Onagraceae类群的物种鉴定和系统发育重建。
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Comparative genomics revealed new insights into the plastome evolution of Ludwigia (Onagraceae, Myrtales).

The primrose-willow (Ludwigia L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including Ludwigia adscendens, Ludwigia hyssopifolia, and Ludwigia prostrata. Three Ludwigia cp genomes ranged from 158,354 to 159,592 bp in size, and each contained 113 genes, including 79 unique protein-coding genes (PCGs), four rRNA genes, and 30 tRNA genes. A comparison of the Ludwigia cp genomes revealed that they were highly conserved in gene composition, gene orientation, and GC content. Moreover, we compared the structure of cp genomes and reconstructed phylogenetic relationships with related species in the Onagraceae family. Regarding contraction/expansion of inverted repeat (IR) region, two kinds of expansion IR region structures were found in Oenothera, Chamaenerion, and Epilobium genera, with primitive IR structures in Ludwigia and Circeae genera. The regions clpP, ycf2, and ycf1 genes possessed highly divergent nucleotides among all available cp genomes of the Onagraceae family. The phylogenetic reconstruction using 79 PCGs from 39 Onagraceae cp genomes inferred that Ludwigia (including L. adscendens, L. hyssopifolia, L. prostrata, and Ludwigia octovalvis) clade was monophyletic and well-supported by the bootstrap and posterior probability values. This study provides the reference cp genomes of three Ludwigia species, which can be used for species identification and phylogenetic reconstruction of Ludwigia and Onagraceae taxa.

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来源期刊
Science Progress
Science Progress Multidisciplinary-Multidisciplinary
CiteScore
3.80
自引率
0.00%
发文量
119
期刊介绍: Science Progress has for over 100 years been a highly regarded review publication in science, technology and medicine. Its objective is to excite the readers'' interest in areas with which they may not be fully familiar but which could facilitate their interest, or even activity, in a cognate field.
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