石蒜属植物叶绿体基因组结构及系统学研究

FU Wen-fo; XIAO Tao; ZHANG Yong-hong

doi:10.3969/j.issn.1009-7791.2023.04.001

亚热带植物科学 >

2023 , Vol. 52 >Issue 4: 271 - 286

DOI: https://doi.org/10.3969/j.issn.1009-7791.2023.04.001

植物生理生化与分子生物学

石蒜属植物叶绿体基因组结构及系统学研究

FU Wen-fo ,
XIAO Tao ,
ZHANG Yong-hong

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(1. 云南师范大学生命科学学院，云南昆明 650500；2. 个旧市第十三中学，云南个旧 661011)

收稿日期: 2023-06-18

录用日期: 2023-08-21

网络出版日期: 2023-11-28

基金资助

国家自然科学基金项目(31760048)

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Chloroplast Genome Characteristics and Phylogeny of the Genus Lycoris (Amaryllidaceae)

付文佛，肖涛，张永洪

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(1. School of Life Sciences, Yunnan Normal University, Kunming 650500, Yunnan China; 2. Gejiu No. 13 Middle School, Gejiu 661011, Yunnan China)

Received date: 2023-06-18

Accepted date: 2023-08-21

Online published: 2023-11-28

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摘要

对17种石蒜属Lycoris植物的叶绿体全基因组序列基本特征及其系统发育关系进行分析。结果显示，石蒜属植物的叶绿体基因组具有典型的四分体环状结构，全长158 335～158 761 bp，总GC含量37.7%～37.8%。基因数量为133～137个，蛋白质编码基因、核糖体RNA基因、转运RNA基因数目稳定。含有散在重复序列41～57个，检测到66～74个SSR位点，其中单核苷酸A/T重复最多。密码子偏好性分析发现，编码密码子数量在26 448～26 740个之间，共有31 个密码子的 RSCU 值大于1，而其中29 个密码子的第三位碱基为A或U，表明17个石蒜属植物偏好A或U结尾的密码子。叶绿体全基因组比对和共线性分析结果显示，石蒜属植物叶绿体基因组不存在重排和倒置，具有较高的保守性，非编码区的变异频率高于编码区。IR边界分析表明，由于IR区的收缩和扩张，部分物种中的rpl22、rps19、ndhF基因均出现跨过JLB或JSB边界的情况。核苷酸多态性分析筛选出trnG-UCC、atpF-atpH、psbC-trnS-UGA-psbZ、trnG-GCC-psbZ、rpl32、trnL-UAG-rpl32-ccsA、rps15-ycf1等高变基因和基因间隔区可作为分子标记用于系统发育分析。以叶绿体全基因组序列构建的分子系统树显示，石蒜属物种形成单系，支持该属独立的分类地位。传统的基于雄蕊和花冠形态划分的整齐花亚属和石蒜亚属的物种均未形成单系，基于雄蕊与花被片的位置关系对石蒜属植物属下物种进行分类仍值得商榷。同时，系统发育分析支持安徽石蒜L. anhuiensis、江苏石蒜L. houdyshelii、稻草石蒜L. straminea、玫瑰石蒜L. rosea杂交起源的观点，并揭示了它们可能的母本。

关键词： 石蒜属; 叶绿体; 基因组; 单系; 系统发育

本文引用格式

FU Wen-fo , XIAO Tao , ZHANG Yong-hong . 石蒜属植物叶绿体基因组结构及系统学研究[J]. 亚热带植物科学, 2023 , 52(4) : 271 -286 . DOI: 10.3969/j.issn.1009-7791.2023.04.001

Abstract

In this study, the basic characteristics and phylogenetic relationship of chloroplast genome sequences from 17 species of Lycoris were analyzed. The results showed that the chloroplast genomes of Lycoris had a typical quadripartite circle structure with a total length of 158 335–158 761 bp and a total GC content of 37.7%–37.8%. The number of genes was 133–137, and the number of protein-coding genes, rRNA genes, and tRNA genes were identical in different species. There were 41–57 interspersed repeats and 66–74 SSR loci detected, among which single nucleotide A/T repeats were the most frequent. Codon preference analysis showed that the number of coding codons ranged from 26 448 to 26 740. The RSCU values of 31 codons were greater than 1 and the third base of 29 codons were A or U, which indicated that Lycoris plant preferred codons ended with A or U. The results of chloroplast genome alignment and collinearity analysis exhibited highly conservative with no rearrangement and inversion observed. Higher variation frequency of non-coding regions versus coding regions was detected. The IR boundary analysis showed that rpl22, rps19 and ndhF genes in some species crossed the JLB or JSB boundary due to the contraction and expansion of the IR region. Nucleotide polymorphism analysis detected 7 highly variable genes or intergenic regions, trnG-UCC, atpF-atpH, psbC-trnS-UGA-psbZ, trnG-GCC-psbZ, rpl32, trnL-UAG- rpl32-ccsA, rps15-ycf1, which could be used as molecular markers for phylogenetic analysis. The molecular phylogenetic tree showed that all Lycoris species clustered closely and formed a monophyly, which supported the independent taxonomic status of the genus. Two traditional subgenera, Symmanthus and Lycoris, didn’t form monophyly separately, although distinguished in stamen and corolla. And it was still doubtable on the intrageneric circumscription based on the relative position of stamens and perianth. In addition, the phylogenetic analysis supported the perspective of the hybrid origin of L. anhuiensis, L. houdyshelii, L. straminea and L. rosea, with potential maternal species recommended.

Key words： Lycoris; chloroplast; genome; monophyly; phylogeny

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