[1]赵振宁,孙浩田,宋雨茹,等.山楂属植物叶绿体基因组特征与密码子偏好性分析[J].江苏农业学报,2023,(02):504-517.[doi:doi:10.3969/j.issn.1000-4440.2023.02.024]
　ZHAO Zhen-ning,SUN Hao-tian,SONG Yu-ru,et al.Chloroplast genome characteristics and codon usage bias analysis of Crataegus L.[J].,2023,(02):504-517.[doi:doi:10.3969/j.issn.1000-4440.2023.02.024]
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山楂属植物叶绿体基因组特征与密码子偏好性分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2023年02期
页码:
504-517
栏目:
园艺
出版日期:
2023-04-30

文章信息/Info

Title:
Chloroplast genome characteristics and codon usage bias analysis of Crataegus L.
作者:
赵振宁1; 孙浩田2; 宋雨茹1; 余潇3
（1.西南林业大学林学院，云南昆明650224；2.西南林业大学生态与环境学院，云南昆明650224；3.湖北工程学院建筑学院，湖北孝感432000）
Author(s):
ZHAO Zhen-ning1; SUN Hao-tian2; SONG Yu-ru1; YU Xiao3
(1.College of Forestry, Southwest Forestry University, Kunming 650224, China;2.College of Ecology and Environment, Southwest Forestry University, Kunming 650224, China;3.School of Architecture, Hubei Engineering University, Xiaogan 432000, China)
关键词:
山楂属; 叶绿体基因组; 密码子偏好性; 系统进化
Keywords:
Crataegus L.; chloroplast genome; codon usage bias; system evolution
分类号:
S661.5
DOI:
doi:10.3969/j.issn.1000-4440.2023.02.024
文献标志码:
A
摘要:
为明确山楂属植物叶绿体基因组结构与编码蛋白质的基因密码子偏好性特征，本研究利用第二代高通量测序技术对云南山楂[Crataegus scabrifolia (Franch.) Rehd.]的叶绿体基因组进行测序、组装和注释，并对山楂属11个种植物的叶绿体基因组结构、遗传多样性以及密码子偏好性进行了分析。结果显示，山楂属植物的叶绿体基因组长度为159 607～159 875 bp，G+C含量为36.6%～36.7%，为标准的四分体结构，G+C含量和结构变异均保守，边界扩张收缩稳定，未发现基因组的倒置和重排现象，11个种植物的简单重复序列和离散重复序列的种类和数量存在一定的差异。综合中性绘图分析、有效密码子数分析（ENC-plot）、奇偶校验分析（PR2-plot）和对应性（COA）分析的结果，发现山楂属植物叶绿体基因组密码子使用不但受到碱基突变的影响，还受到选择压力的深刻影响。对叶绿体基因组的最优密码子进行筛选，最优密码子数量为17～20个，其中C. kansuensis、C. oresbia、C. pinnatifida的最优密码子数量最多，C. marshallii的最优密码子数量最少，分析它们的最优密码子数据发现，山楂属植物的最优密码子大多以A或U作为第三位碱基。基于CDS(蛋白质编码序列)和叶绿体全基因组构建的系统发育关系既具有一定的相似性，也存在一些差异。本研究结果为山楂属植物的系统发育研究和分子标记开发等工作提供了参考依据。
Abstract:
In order to clarify the chloroplast genome structure and codon usage bias of Crataegus, this study used the next-generation sequencing to sequence, assemble and annotate the chloroplast genome of Crataegus scabrifolia (Franch.) Rehd., and analyzed the chloroplast genome structure, genetic diversity and codon preference of 11 species of Crataegus. The results showed that the length of chloroplast genome was between 159 607 bp and 159 875 bp, the G+C content and structural variation were conservative, the G+C content was between 36.6% and 36.7%, the boundary expansion and contraction were stable, no inversion and rearrangement of the genome were found, and there were differences in the type and number of simple sequence repeats and interspersed repeated sequences. Based on the results of neutrality plot analysis, ENC-plot, PR2-plot and correspondence analysis, it was found that the chloroplast genome codon usage in Crataegus was not only affected by base mutation, but also by selective pressure. The optimal codons of the chloroplast genome were screened, and the optimal number of codons was between 17 and 20. C. kansuensis, C. oresbia, and C. pinnatifida had the largest number of optimal codons, and C. marshallii had the least number of optimal codons. The analysis of their optimal codon data revealed that the optimal codons of Crataegus mostly used A or U as the third base. The phylogenetic relationships constructed based on protein coding sequence and complete chloroplast genome had certain similarities and differences. The results of this study can provide a reference for the phylogenetic research and molecular marker development of Crataegus.

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备注/Memo

备注/Memo:
收稿日期：2022-10-17 基金项目：云南省第二次国家重点保护野生植物资源调查项目（09930-216304）；2021年度云南省大学生创新创业国家级项目（202110677046） 作者简介：赵振宁（2003-），男，山东泰安人，本科，主要从事植物生物信息学研究。（E-mail）zzn1529370396@163.com 通讯作者：余潇，（E-mail）yuxiao19920215@163.com
更新日期/Last Update: 2023-05-12