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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. 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,但也有学者根据它们的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,本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的差异,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: |
基金项目:国家自然科学基金项目(面上项目,重点项目,重大项目) |
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Characterization of genetic difference and phylogenetic relationship between Schizocapsa guangxiensis and Tacca plantaginea |
MA Yunying1, DENG Yongbiao1, Lü Huqian1, ZHOU Qianru1, LI Jingjian1, LU Zhaocen3*, XIE Wenjuan1*
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Abstract: |
The taxonomy of Tacca remains controversial. Schizocapsa guangxiensis is considered to be the same species as T. 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 S. guangxiensis and T. plantanginea, this study conducted high-throughput DNA sequencing of S. guangxiensis, assembled a complete chloroplast genome using bioinformatics software, and compared it with the published T. plantanginea chloroplast genome. The results showed that: (1) The chloroplast genome size of S. guangxiensis and T. plantanginea is 162 149 bp and 160 749 bp, respectively, and they have the same GC content (36.90%). Notably, the gene types and gene amount are exactly the same in these two species, including 89 protein-coding genes and 37 tRNA genes, and 6 rRNA genes. (2) Codon preference analysis shows that there are certain differences in the codon frequencies used by the two species, but they both prefer codons ending in A/T(U). (3) Compared with T. plantanginea, the SSC boundary of S. guangxiensis has obvious expansion, which is the main factor leading to the length variant in chloroplast genome between the two species. (4) There are some sequence divergences between S. guangxiensis and T. plantanginea in the LSC and SSC regions, especially the intergenic region, which can be exploited as species-specific molecular marker. (5) Phylogenetic results show that S. guangxiensis and T. plantanginea have a rather distant genetic relationship. Although S. guangxiensis is 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 |