锦葵科Malvatheca分支的质体基因组演化及系统发育分析

雷翰霖<sup>1; 2; 5</sup>; 黎若竹<sup>1</sup>; 蔡 杰<sup>3</sup>; 杨俊波<sup>3</sup>; 张志荣<sup>3</sup>; 李德铢<sup>3</sup>; 郁文彬<sup>1; 2; 4*</sup>

引用本文:	雷翰霖, 黎若竹, 蔡杰, 杨俊波, 张志荣, 李德铢, 郁文彬.锦葵科Malvatheca分支的质体基因组演化及系统发育分析[J].广西植物,2025,45(12):2241-2254.[点击复制]
	LEI Hanlin, LI Ruozhu, CAI Jie, YANG Junbo, ZHANG Zhirong, LI Dezhu, YU Wenbin.Plastome evolution and phylogenetic analysis of the Malvatheca clade(Malvaceae)[J].Guihaia,2025,45(12):2241-2254.[点击复制]

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锦葵科Malvatheca分支的质体基因组演化及系统发育分析
雷翰霖^{1,2, 5}, 黎若竹¹, 蔡杰³, 杨俊波³, 张志荣³, 李德铢³, 郁文彬^1,2,4*
1. 中国科学院西双版纳热带植物园综合保护中心和云南省热带雨林与亚洲象保护重点实验室, 云南勐腊 666303;2. 中国科学院西双版纳热带植物园云南省热带珍贵用材树种保护与利用国际联合实验室, 云南勐腊 666303;3. 中国科学院昆明植物研究所中国西南野生生物种质资源库, 昆明 650201;4. 中国科学院东南亚生物多样性研究中心, 云南勐腊 666303;5. 中国科学院大学, 北京 100049

摘要:

广义锦葵科(Malvaceae s.l.)Malvatheca分支(含锦葵亚科和木棉亚科)具有重要经济和生态价值,但其内部系统发育关系存在争议,特别是绵绒树族、轻木族和南瓜榄族的系统位置。目前,Malvatheca分支的质体基因组多样性演化还缺乏较为全面的研究。该研究整合了Malvatheca分支8族38属142种的质体全基因组(WGM)数据,包括新组装77个质体基因组,开展了质体基因组比较及系统发育分析。结果表明:(1)Malvatheca分支的质体基因组大小变化范围为156 701～163 741 bp,其变化主要受反向重复(IR)区长度与重复序列的数量影响。(2)通过分析IR和SC区域边界基因的差异确定了4种IR边界类型,其中类型Ⅲa被推断为Malvatheca分支的祖先结构类型,相似的IR区收缩和扩张事件在该分支演化过程中独立发生多次。(3)锦葵亚科和木棉亚科分别检测到8个高变区,其中trnS^GCU-trnG^UCC、petA-psbJ、ndhD-ccsA及ycf1为2个亚科共有高变区。此外,trnS^GCU-trnG^UCC、ycf1及常用分子标记ndhF在2个亚科中均表现出较强的系统发育分辨力。(4)基于质体WGM矩阵与蛋白质编码序列(CDS)矩阵的系统发育拓扑结构基本一致,为Malvatheca分支提供了可靠的系统发育框架。结果显示,Malvatheca分支早期演化形成4个分支,其中绵绒树族为最早分化类群,随后为轻木族,锦葵亚科与木棉亚科互为姐妹。此外,猴面包树族、木棉族、木槿属和黄花稔属均非单系,这些类群的组成和分类学处理仍需进一步研究。该研究利用迄今为止取样最广泛的质体基因组数据集,揭示了Malvatheca分支内部的主要系统发育关系,并为理解该分支质体基因组特征与演化提供了新的见解。

关键词: Malvatheca分支, 系统发育, 质体基因组, 木棉亚科, 锦葵亚科, 锦葵科

DOI：10.11931/guihaia.gxzw202504008

分类号:Q949

文章编号:1000-3142(2025)12-2241-14

基金项目:云南省基金项目(202201AT070232, 202101BC070003); 科技基础性工作专项(2021FY100200); 海南省重点研发计划项目(ZDYF2023RDYL01); 海南国家公园研究院资助项目(KY-24ZK02); 兴滇人才创新团队(202405AS350019); 中国科学院重大科技基础设施开放研究项目(2017-LSF-GBOWS-02)。

Plastome evolution and phylogenetic analysis of the Malvatheca clade(Malvaceae)

LEI Hanlin^1,2,5, LI Ruozhu¹, CAI Jie³, YANG Junbo³, ZHANG Zhirong³, LI Dezhu³, YU Wenbin^1,2,4*

1. Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;2. Yunnan International Joint Laboratory for the Conservation and Utilization of Tropical Timber Tree Species, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China;3. The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;4. Southeast Asia Biodiversity Research Institute, Chinese Academy of Science, Mengla 666303, Yunnan, China;5. University of Chinese Academy of Sciences, Beijing 100049, China

Abstract:

The Malvatheca clade(encompassing Malvoideae and Bombacoideae within Malvaceae s.l.)possesses significant economic and ecological values. However, the phylogenetic relationships within this clade remain controversial, particularly concerning the phylogenetic placement of Fremontodendreae, Ochromeae and Matisieae. Moreover, comprehensive analyses of plastome structural variations and evolution within this clade remain poorly investigated. To resolve these research gaps, this study incorporated the plastid whole genome(WGM)data from 142 species representing 8 tribes and 38 genera of the Malvatheca clade, including 77 plastomes newly de novo assembled. We performed comparative genomic and phylogenetic analyses using the plastome datasets. The results were as follows:(1)The plastome size in the Malvatheca clade exhibit variation ranging from 156 701 bp to 163 741 bp, primarily attributed to differential lengths in the inverted repeat(IR)region and varying numbers of repetitive sequences.(2)Four IR boundary types were identified through analysis of gene variation at IR/SC junctions. The Type Ⅲa is inferred as the ancestral structure of the plastome within the Malvatheca clade, with identical IR expansion/contraction events evolving convergently multiple times during its diversification.(3)Eight highly variable regions were detected in both Malvoideae and Bombacoideae, with trnS^GCU-trnG^UCC, petA-psbJ, ndhD-ccsA and ycf1 being common to both clades. Notably, trnS^GCU-trnG^UCC, ycf1 and the commonly used molecular markers ndhF exhibited robust phylogenetic resolution.(4)The topologies inferred from both the plastid WGM matrix and protein coding sequence(CDS)matrix datasets were largely identical and well-resolved, and provided a reliable phylogenetic framework for Malvatheca clade. The result showed that the Malvatheca clade was divided into four lineages, with Fremontodendreae as the earliest divergent group, followed by Ochromeae, then Bombacoideae and Malvoideae formed as sister group. Additionally, our results revealed non-monophyly in tribes Adansonieae and Bombaceae, as well as the genera Sida and Hisbiscus. The composition and taxonomic treatment of these groups still require further research. This study clarifies critical phylogenetic relationships within the Malvatheca clade while providing new perspectives on the plastome characteristics and evolution through the most extensively sampled plastome dataset currently available for this clade.

Key words: Malvatheca clade, phylogeny, plastome, Bombacoideae, Malvoideae, Malvaceae