引用本文: | 麻云英, 邓永彪, 吕虎强, 周倩如, 李景剑, 陆昭岑, 谢文娟.基于叶绿体基因组解析广西裂果薯与裂果薯的遗传差异及亲缘关系[J].广西植物,2024,44(9):1707-1720.[点击复制] |
MA Yunying, DENG Yongbiao, LV Huqian, ZHOU Qianru,
LI Jingjian, LU Zhaocen, XIE Wenjuan.Characterization of genetic difference and phylogenetic relationship between Schizocapsa guangxiensis and Tacca plantaginea based on chloroplast genome[J].Guihaia,2024,44(9):1707-1720.[点击复制] |
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基于叶绿体基因组解析广西裂果薯与裂果薯的遗传差异及亲缘关系 |
麻云英1, 邓永彪1, 吕虎强1,2, 周倩如1, 李景剑1, 陆昭岑3*, 谢文娟1*
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1. 桂林医学院 药学院, 广西 桂林 541199;2. 中华全国供销合作总社西安生漆涂料研究所, 西安 710061;3. 广西壮族自治区
中国科学院 广西植物研究所, 广西 桂林 541006
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摘要: |
蒟蒻薯属(Tacca)植物的分类一直存在很大的争议,其中广西裂果薯(Schizocapsa guangxiensis)被认为应与裂果薯(Tacca plantanginea)归并为同一物种,但也有学者根据其形态差异划分为不同的物种。为了明确广西裂果薯与裂果薯的遗传差异和系统发育关系,该研究对广西裂果薯进行DNA高通量测序,利用生物信息软件组装了完整的叶绿体基因组,并与已发表的裂果薯叶绿体基因组进行比较及系统发育分析。结果表明:(1)广西裂果薯和裂果薯的叶绿体基因组大小分别为162 149 bp和160 749 bp,GC含量都是36.90%,两者注释后得到的基因种类和基因数目完全一致,包含89个蛋白质编码基因、37个tRNA基因、6个rRNA基因。(2)密码子的偏好性分析显示,两物种使用的密码子频率存在一定差异,但是都偏好以A/T(U)结尾的密码子。(3)与裂果薯相比,广西裂果薯的SSC边界发生明显的扩张现象,是导致两者叶绿体基因组长度差异的主要因素。(4)广西裂果薯与裂果薯在LSC和SSC区域内存在一些序列分歧,尤其是基因间隔区,可用于开发物种特异性分子标记。(5)系统发育结果显示,广西裂果薯与裂果薯的亲缘关系较远,尽管广西裂果薯寄定在蒟蒻薯属内,但是它们属于两个不同的物种。该研究丰富了广西裂果薯叶绿体基因组遗传信息,为广西裂果薯物种分类、遗传多样性分析和物种保护提供了理论依据。 |
关键词: 广西裂果薯, 蒟蒻薯属, 叶绿体基因组, 遗传差异, 系统发育分析 |
DOI:10.11931/guihaia.gxzw202312006 |
分类号:Q943; Q949 |
文章编号:1000-3142(2024)09-1707-14 |
基金项目:国家自然科学基金(32060351); 广西自然科学基金(2021GXNSFAA220032) |
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Characterization of genetic difference and phylogenetic relationship between Schizocapsa guangxiensis and Tacca plantaginea based on chloroplast genome |
MA Yunying1, DENG Yongbiao1, LV Huqian1,2, ZHOU Qianru1,
LI Jingjian1, LU Zhaocen3*, XIE Wenjuan1*
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1. College of Pharmacy, Guilin Medical University, Guilin 541199, Guangxi, China;2. Xi'an Research Institute of Chinese Lacquer
Under All China Federation of Supply and Marketing Cooperatives, Xi'an 710061, China;3. Guangxi Institute of Botany,
Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, Guangxi, China
1. College of Pharmacy, Guilin Medical University, Guilin 541199, Guangxi, China; 2. Xi'an Research Institute of Chinese Lacquer
Under All China Federation of Supply and Marketing Cooperatives, Xi'an 710061, China; 3. Guangxi Institute of Botany,
Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, Guangxi, China
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Abstract: |
The taxonomy of Tacca remains is controversial all the time. Schizocapsa guangxiensis is considered to be the same species as Tacca plantanginea, but some taxonomists classify them into different species based on their morphological differences. In order to clarify the genetic differences and phylogenetic relationship between Schizocapsa guangxiensis and Tacca plantanginea, this study conducted high-throughput DNA sequencing of Schizocapsa guangxiensis, assembled a complete chloroplast genome using bioinformatics software, and compared it with the published Tacca plantanginea chloroplast genome. The results were as follows:(1)The chloroplast genome size of Schizocapsa guangxiensis and Tacca plantanginea was 162 149 bp and 160 749 bp, respectively, and they had the same GC content(36.90%). Notably, the gene types and gene amount were exactly the same in these two species, including 89 protein-coding genes and 37 tRNA genes, and 6 rRNA genes.(2)Codon preference analysis showed that there were certain differences in the codon frequencies used by the two species, but they both prefered codons ending in A/T(U).(3)Compared with T. plantanginea, the SSC boundary of Schizocapsa guangxiensis had obvious expansion, which was the main factor leading to the length variant in chloroplast genome between the two species.(4)There were some sequence divergences between S. guangxiensis and Tacca plantanginea in the LSC and SSC regions, especially the intergenic region, which can be exploited as species-specific molecular marker.(5)Phylogenetic results showed that Schizocapsa guangxiensis and Tacca plantanginea had a rather distant genetic relationship. Although Schizocapsa guangxiensis was placed in Tacca, they belong to two different species. This study enriches the genetic information of the chloroplast genome of S. guangxiensis and provides a theoretical basis for species classification, genetic diversity analysis and species protection of S. guangxiensis. |
Key words: Schizocapsa guangxiensis, Tacca, chloroplast genome, genetic difference, phylogenetic analysis |
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