Analysis of the Complete Chloroplast Genome Sequence Characteristics and Its Code Usage Bias of Sorghum bicolor

doi:10.11733/j.issn.1007-0435.2023.12.008

Acta Agrestia Sinica ›› 2023, Vol. 31 ›› Issue (12): 3636-3650.DOI: 10.11733/j.issn.1007-0435.2023.12.008

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Analysis of the Complete Chloroplast Genome Sequence Characteristics and Its Code Usage Bias of Sorghum bicolor

HONG Sen-rong^1,2,3,4, LIN Shun-lai¹, LI Ying-ping¹, LI Yun-yun¹, LI He-yue¹, ZHANG Qing-bao¹

1. College of Life Sciences, Shangrao Normal University, Shangrao, Jiangxi Province 334001, China;
2. Shangrao Agricultural Technology Innovation Research Institute, Shangrao, Jiangxi Province 334001, China;
3. Key Laboratory of protection and utilization of medicinal and edible plant resources in Shangrao City, Shangrao, Jiangxi Province 334001, China;
4. Key Laboratory of germplasm conservation and utilization of potato and taro crops in Shangrao City, Shangrao, Jiangxi Province 334001, China

Received:2023-07-03 Revised:2023-08-10 Online:2023-12-15 Published:2024-01-03

甜高粱叶绿体基因组特征及密码子偏好性分析

洪森荣^1,2,3,4, 林顺来¹, 李盈萍¹, 李芸芸¹, 李和月¹, 张庆宝¹

1. 上饶师范学院生命科学学院, 江西上饶 334001;
2. 上饶农业技术创新研究院, 江西上饶 334001;
3. 上饶市药食同源植物资源保护与利用重点实验室, 江西上饶 334001;
4. 上饶市薯芋类作物种质保存与利用重点实验室, 江西上饶 334001

作者简介:洪森荣(1974-)，男，汉族，江西永新人，硕士，教授，主要从事植物生物技术研究工作，E-mail：hongsenrong@163.com
基金资助:
国家自然科学基金资助目(31960079)；江西省科技厅重点研发计划一般项目(20202BBG73010)；江西省教育厅科学技术研究项目(GJJ201704；GJJ211729)；江西省现代农业产业技术体系建设专项(JXARS-13-赣东站)；上饶市科技局平台载体建设项目(2020J001)；上饶师范学院2023年大学生创新创业训练计划项目(202310416013)资助

Abstract

Abstract: The chloroplast genome of Sorghum bicolor was sequenced by high-throughput sequencing technology,and its structure,gene composition and codon preference of the assembled and annotated chloroplast genome were analyzed in this study. The results showed that the chloroplast genome length of S. bicolor was 140 644 bp,encoding 86 CDS genes,38 tRNA genes,and 8 rRNA genes. 31 SSR loci and 42 long repeat sequences were detected. The chloroplast genome of S. bicolor and its 14 related species showed little change,and the IR region boundary had no significant contraction or expansion. The codon preference of Sorghum bicolor chloroplast genome ended with A and U,and the codon usage bias was largely affected by natural selection,but was less affected by mutation pressure. There were 14 optimal codons (ACU,UAG,CCU,CUA,GCU,AGU,GAU,UUA,CGU,GAA,GUU,UCA,CAU,UGU) in the chloroplast genome of S. bicolor. S. bicolor had close genetic relationship with S. bicolor MT333845 (origin:Korea,cultivated species Donganme),S. bicolor MT333848 (origin:Korea,cultivated species Sodam Chal),and S. bicolor MT459453 (origin:Korea,cultivated species ATx623). The research results would provide reference for improving molecular breeding techniques and exploring the phylogenetic development of Sorghum plants.

Key words: Sweet sorghum, Chloroplast genome, Sequence characteristics, Codon bias, Optimal codons, Phylogenetic analysis

摘要： 本研究采用高通量测序技术对甜高粱叶绿体基因组进行测序，对组装和注释后的叶绿体基因组进行结构、基因组成及密码子偏好性分析。结果表明，甜高粱(Sorghum bicolor)叶绿体基因组长度为140 644 bp，编码86个CDS基因、38个tRNA基因和8个rRNA基因，检测到31个SSR位点和42个Long repeat序列。甜高粱及其14个近缘种的叶绿体基因组变化不大，IR区边界未发生明显的收缩与扩张。甜高粱叶绿体基因组密码子偏好以A，U结尾，其密码子使用偏性很大程度上受自然选择的影响，而受突变压力的影响小。甜高粱叶绿体基因组的最优密码子14个(ACU，UAG，CCU，CUA，GCU，AGU，GAU，UUA，CGU，GAA，GUU，UCA，CAU，UGU)。甜高粱与高粱Sorghum bicolor MT333845(产地：韩国，栽培种Donganme)、MT333848(产地：韩国，栽培种Sodam Chal)、MT459453(产地：韩国，栽培种ATx623)亲缘关系较近。研究结果将为完善高粱属植物分子育种技术和探究高粱属植物系统发育提供参考。

关键词: 甜高粱, 叶绿体基因组, 序列特征, 密码子偏好性, 最优密码子, 系统发育分析

CLC Number:

S344+.13

HONG Sen-rong, LIN Shun-lai, LI Ying-ping, LI Yun-yun, LI He-yue, ZHANG Qing-bao. Analysis of the Complete Chloroplast Genome Sequence Characteristics and Its Code Usage Bias of Sorghum bicolor[J]. Acta Agrestia Sinica, 2023, 31(12): 3636-3650.

洪森荣, 林顺来, 李盈萍, 李芸芸, 李和月, 张庆宝. 甜高粱叶绿体基因组特征及密码子偏好性分析[J]. 草地学报, 2023, 31(12): 3636-3650.

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Analysis of the Complete Chloroplast Genome Sequence Characteristics and Its Code Usage Bias of Sorghum bicolor

甜高粱叶绿体基因组特征及密码子偏好性分析

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