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鉴定、比较和系统发育分析大戟属植物叶绿体基因组。

Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species.

机构信息

Department of Biology Education, College of Education, Chosun University, Gwangju, 61452, Republic of Korea.

Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, 11186, Republic of Korea.

出版信息

Sci Rep. 2024 Jul 4;14(1):15352. doi: 10.1038/s41598-024-66102-0.

Abstract

The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.

摘要

大戟属(大戟科)分布广泛,是观赏和药用的重要资源。尽管具有经济重要性,但大戟属的分类学长期以来一直受到表现出高度趋同的形态特征的复杂性质的挑战。虽然分子标记对于系统发育研究至关重要,但它们在大戟属中的可用性有限。为了解决这一差距,我们进行了比较分析,重点关注 9 种大戟属物种的叶绿体(CP)基因组,其中包括 3 个新测序和注释的样本。此外,还计算了系统发育信息量和核苷酸多样性,以确定在属内近缘分类群中进行系统发育分析的候选标记。我们的研究发现,在所研究的物种中,CP 基因组的大小和结构相对保守,主要在非编码区域和 IR/SC 边界观察到种间变异。通过利用系统发育信息量和核苷酸多样性,我们确定 rpoB 基因为物种划分和属内浅层系统发育推断的最佳候选标记。通过对多个分类群的 CP 基因组进行全面分析,我们的研究揭示了大戟属的进化动态和分类学复杂性,为其 CP 基因组进化和分类学提供了有价值的见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1763/11222452/68122f82819a/41598_2024_66102_Fig1_HTML.jpg

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