Acta Agrestia Sinica

Acta Agrestia Sinica ›› 2025, Vol. 33 ›› Issue (12): 3933-3943.DOI: 10.11733/j.issn.1007-0435.2025.12.007

• 2025-12-28 • Previous Articles    

Analysis of the Sequence Characteristics of the Chloroplast Genome of Microphysa elongata

YU Wei1, ZHOU Xin-xin2,3, YANG Li-e4, PENG De-li1   

  1. 1. College of Life Sciences, Yunnan Normal University, Kunming, Yunnan Province 650500, China;
    2. South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province 510650, China;
    3. Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou, Guangdong Province 510650, China;
    4. Faculty of Geography, Yunnan Normal University, Kunming, Yunnan Province 650500, China
  • Received:2025-01-03 Revised:2025-04-20 Published:2025-12-01

泡果茜草叶绿体基因组序列特征分析

余伟1, 周欣欣2,3, 杨丽娥4, 彭德力1   

  1. 1. 云南师范大学/生命科学学院, 云南 昆明 650500;
    2. 中国科学院华南植物园, 广东 广州 510650;
    3. 华南植物迁地保护与利用国家林业和草原局重点实验室, 广东 广州 510650;
    4. 云南师范大学/地理学部, 云南 昆明 650500
  • 通讯作者: 杨丽娥，E-mail：lieyang90@163.com；彭德力，E-mail：pengdeli@ynnu.edu.cn
  • 作者简介:余伟（1998-），男，土家族，湖南永顺人，硕士研究生，主要从事植物系统分类研究，E-mail：yuwei202209@163.com；
  • 基金资助:
    国家自然科学基金项目（31900185，32360057）资助

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Abstract: This study utilized Illumina high-throughput technology sequenced the chloroplast genome of Microphysa elongata （Schrenk） Pobed. and annotated its chloroplast genome. The structural features， and its phylogenetic relationships were analyzed. The results show that the Microphysa genus possesses a typical quadripartite structure， with a genome length of 155 087 bp. Among them， the large single-copy region （LSC） is 85 399 bp， the small single-copy region （SSC） is 17 110 bp， and both inverted repeat regions （IR） are 26 289 bp in length. This genome contains 87 protein-coding genes， 37 transfer RNA （tRNA） genes， and 8 ribosomal RNA （rRNA） genes. Variations in the lengths of rps19， ndhF， and ycf1 genes， along with their distances from the boundaries， lead to differences in the IR regions among Pseudogalium and Microphysa. The degree of variation in non-coding regions is significantly greater than that in coding regions. A total of 60 dispersed repeat sequences， 86 simple sequence repeat （SSR） loci， and 27 029 codons were identified in Microphysa elongata， with the most common codon being UUU， which encodes phenylalanine （Phe）， and a preference for A/U-ending codons. Phylogenetic analysis indicates that Microphysa elongata forms an independent clade and is nested within the broadly defined genus Galium. The results of this study could provide references for further study on genetic structure and diversity， specific gene mining， and phylogenetic studies of the tribe of Rubieae.

Key words: Microphysa elongata （Schrenk） Pobed, Chloroplast genome, Sequence structure, Phylogenetic analysis

摘要： 本研究基于Illumina高通量技术对泡果茜草（Microphysa elongata （Schrenk） Pobed.）叶绿体基因组进行测序，并对其叶绿体基因组进行注释，结构特征及其系统发育关系分析。结果显示：泡果茜草叶绿体基因组具有典型的四分体结构，基因组长度为155 087 bp。其中，大单拷贝区（Large single-copy region，LSC）长度是85 399 bp，小单拷贝区（Small single-copy region，SSC）长度是17 110 bp，两个反向重复区（Inverted repeat regions，IR）的长度均是26 289 bp。该基因组有87个蛋白质编码基因、37个转运RNA基因和8个核糖体RNA基因。在奇异拉拉藤属（Pseudogalium）和泡果茜草属（Microphysa）中，rps19，ndhF和ycf1基因的长度及其与边界的距离是导致反向重复区差异的原因。非编码区的变异程度显著大于编码区。泡果茜草共检测到60个散在重复序列、86个简单重复序列位点和27 029个密码子，最常用的密码子是苯丙氨酸（Phe）的UUU且偏好使用A/U结尾。系统发育分析表明：泡果茜草形成独立分支，并嵌套于广义拉拉藤属（Galium）中。本研究可为茜草族植物遗传结构与多样性、特异基因挖掘以及系统发育等研究提供参考。

关键词: 泡果茜草, 叶绿体基因组, 序列结构, 系统发育分析

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