苦豆种叶绿体基因组的比较:属内可变DNA标记的鉴定和系统发育关系。

IF 4.8 2区 生物学 Q1 PLANT SCIENCES
Na Duan, Dafu Ru, Bingbing Liu
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引用次数: 0

摘要

背景:苦槐属是凤蝶科(蚕豆科)中具有重要药用价值的属,因其药用、生态和经济重要性而闻名。然而,由于有限的遗传数据和缺乏有效的分子标记,该属在分类和系统发育上仍然存在不确定性,特别是在中国。本研究旨在通过对中国特有的6种苦豆子的叶绿体基因组进行测序和分析,从而为今后的研究提供丰富的遗传资源。结果:利用Illumina HiSeq平台,对来自中国的苦豆子(苦豆子、苦豆子、苦豆子、tonkinensis、Sophora velutina和Sophora velutina var. cavaleriei)的6个叶绿体基因组进行了测序。将这些新生成的cp.基因组与先前发表的苦豆子cp.基因组进行比较分析,发现苦豆子cp.基因组的大小范围为151,270 ~ 154,378 bp(不包括S. japonica和S. xanthantha)。我们观察到,在一些物种中,倒置重复序列(IR)区域的扩增导致rpl2易位到大单拷贝(LSC)区域,ycf1的假原化,以及trnH的缺失。比较基因组分析显示,在该属中,trnC-GCA和trnF-GAA之间存在约24kb的反转,这一现象首次被观察到涉及至少三次重排。此外,我们还鉴定了三个有价值的分子标记(trnT-UGU - trnL-UAA, psbE - petL和rps11 - rpl36),这些标记适合于槐树的系统发育推断。结论:基于叶绿体基因组的系统发育分析有力地支持了假槐属植物的单系性。重要的是,我们的系统发育结果表明,粳稻和黄原花不应该被归为苦豆子属。这些发现对丰富苦豆子叶绿体基因组数据具有重要意义,为解决分类歧义提供了宝贵的遗传资源和分子标记,为今后苦豆子的系统发育、进化和分类研究提供了参考。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Comparative chloroplast genomes of Sophora species: identification of variable DNA markers and phylogenetic relationships within the genus.

Backgroud: Sophora L. is a medicinally significant genus within Papilionoideae (Fabaceae), renowned for its medicinal, ecological, and economic importance. However, taxonomic and phylogenetic uncertainties persist within this genus, especially in China, due to limited genetic data and the lack of effective molecular markers. This study aimed to address these limitations by sequencing and analyzing chloroplast (cp.) genomes from six Sophora species endemic to China, thereby enriching genetic resources for future research.

Result: Here, we reported and characterized six chloroplast (cp.) genomes of Sophora species (Sophora xanthantha, Sophora davidii, Sophora moocroftiana, Sophora tonkinensis, Sophora velutina, and Sophora velutina var. cavaleriei) from China, sequenced using the Illumina HiSeq platform. Comparative analyses of these newly generated cp. genomes, alongside previously published Sophora cp. genomes, revealed that the Sophora cp. genomes exhibited a size range of 151,270 - 154,378 bp (excluding S. japonica and S. xanthantha). We observed expansions of the inverted repeat (IR) regions in Sophora, leading to the translocation of rpl2 into the large single-copy (LSC) region, pseudogenization of ycf1, and absence of trnH in some species. Comparative genome analysis revealed a ~ 24-kb inversion between trnC-GCA and trnF-GAA within the genus, a phenomenon first observed to involve at least three rearrangements. Furthermore, we identified three valuable molecular markers (trnT-UGU - trnL-UAA, psbE - petL, and rps11 - rpl36) that are suitable for phylogenetic inference within Sophora.

Conclusions: Phylogenetic analyses based on the chloroplast genomes robustly supported the monophyly of sect. Pseudosophora. Importantly, our phylogenetic results suggested that S. japonica and S. xanthantha should not be classified within the genus Sophora. These findings contribute significantly to the chloroplast genomic data of Sophora and provide valuable genetic resources and molecular markers for resolving taxonomic ambiguities and advancing future phylogenetic, evolutionary, and taxonomic investigations of Sophora.

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来源期刊
BMC Plant Biology
BMC Plant Biology 生物-植物科学
CiteScore
8.40
自引率
3.80%
发文量
539
审稿时长
3.8 months
期刊介绍: BMC Plant Biology is an open access, peer-reviewed journal that considers articles on all aspects of plant biology, including molecular, cellular, tissue, organ and whole organism research.
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