Complete Chloroplast Genome Sequence and Characteristics Analysis of Medicago sativa ‘Deqin’

doi:10.11733/j.issn.1007-0435.2022.02.008

Acta Agrestia Sinica ›› 2022, Vol. 30 ›› Issue (2): 320-328.DOI: 10.11733/j.issn.1007-0435.2022.02.008

Complete Chloroplast Genome Sequence and Characteristics Analysis of Medicago sativa ‘Deqin’

SUN Zhi-xuan¹, AO Ping-xing¹, BI Yu-fen², ZHAO Yan¹

1. College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan Province 650201, China;
2. College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province 650201, China

Received:2021-07-16 Revised:2021-09-16 Published:2022-03-10

德钦’紫花苜蓿叶绿体基因组序列及特征分析

孙志轩¹, 敖平星¹, 毕玉芬², 赵雁¹

1. 云南农业大学园林园艺学院, 云南昆明 650201;
2. 云南农业大学动物科学技术学院, 云南昆明 650201

通讯作者: 赵雁,E-mail:744234036@qq.com
作者简介:孙志轩(1996-),男,汉族,河南新乡人,硕士研究生,主要从事园林植物资源利用与创新研究,E-mail:dg3114@163.com
基金资助:
国家自然科学基金项目(31660683);云南农业大学第十四届学生科技创新创业行动基金项目(2021ZKX086)资助

Abstract

Abstract: Medicago sativa ‘Deqin’ (hereinafter referred to as ‘Deqin’) is an excellent alfalfa local variety with strong drought,heat,and aluminum-acid toxicity resistance. In this study,the whole chloroplast genome of ‘Deqin’ was sequenced by Illumina second-generation high-throughput sequencing technology (NCBI accession number:MN218692),and its structure and characteristics were analyzed. The results showed that the chloroplast genome of ‘Deqin’,with a total length of 125 470 bp,has one inverted repeat region and belongs to IR lacking clad. A total of 110 coding genes,including 76 protein-coding genes,30 tRNAs and 4 rRNAs,and 3 genes (rps16,rpl22 and infA) are absent,with an overall GC content of 33.9%. Relative synonymous codon usage showed that 70.74% of codons RSCU>1 in ‘Deqin’,with preference ending with A and T. SSRs analysis identified 115 SSRs loci. Different SSRs loci from ‘Deqin’ were identified in the gene of clpP. The phylogenetic tree shows that ‘Deqin’ and M. sativa L. were clustered into one group with 75% support. The results have reference value for Medicago chloroplast genome engineering and further identification and utilization of specific genes of ‘Deqin’.

Key words: Medicago sativa ‘Deqin’, Chloroplast genome, Characteristic analysis, High-throughput sequencing, Phylogenetic analysis

摘要： ‘德钦’紫花苜蓿(Medicago sativa L. ‘Deqin’，以下简称‘德钦’苜蓿)是一种优良的地方品种，具有特异耐旱性、耐热性和耐酸铝性。本研究利用Illumina第二代高通量测序技术对其叶绿体全基因组进行测序(NCBI登录号：MN218692)，并对其结构及特征进行分析。结果显示：‘德钦’苜蓿叶绿体基因组含有一个反向重复区，属于IR缺失型；总长为125 470 bp，共有110个基因，其中蛋白质编码基因76个、tRNA 30个和rRNA 4个，缺失3个基因(rps16，rpl22和infA)，总GC含量为33.9%；相对同义密码子使用度显示，‘德钦’苜蓿70.74%的密码子使用度>1，偏好以A和T结尾；共鉴定出115个SSRs位点，其中clpP基因鉴定出与紫花苜蓿不同SSRs位点；最大似然树结果显示‘德钦’苜蓿与紫花苜蓿聚在一起，支持率为75%。研究结果将对苜蓿属叶绿体基因组工程研究及‘德钦’苜蓿特异基因的进一步鉴定利用提供一定的参考价值。

关键词: 德钦’紫花苜蓿, 叶绿体基因组, 高通量测序, 特征分析, 系统发育分析

CLC Number:

S541

SUN Zhi-xuan, AO Ping-xing, BI Yu-fen, ZHAO Yan. Complete Chloroplast Genome Sequence and Characteristics Analysis of Medicago sativa ‘Deqin’[J]. Acta Agrestia Sinica, 2022, 30(2): 320-328.

孙志轩, 敖平星, 毕玉芬, 赵雁. 德钦’紫花苜蓿叶绿体基因组序列及特征分析[J]. 草地学报, 2022, 30(2): 320-328.

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Complete Chloroplast Genome Sequence and Characteristics Analysis of Medicago sativa ‘Deqin’

德钦’紫花苜蓿叶绿体基因组序列及特征分析

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