大粒香水稻叶绿体基因组特征分析

吴朝昕; 刘雪薇<sup>*</sup>; 李祖军; 龙武华; 宫彦龙; 朱速松

引用本文:	吴朝昕, 刘雪薇, 李祖军, 龙武华, 宫彦龙, 朱速松.大粒香水稻叶绿体基因组特征分析[J].广西植物,2022,42(11):1830-1839.[点击复制]
	WU Chaoxin, LIU Xuewei, LI Zujun, LONG Wuhua, GONG Yanlong, ZHU Susong.Analysis of chloroplast genome of rice Dalixiang[J].Guihaia,2022,42(11):1830-1839.[点击复制]

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大粒香水稻叶绿体基因组特征分析
吴朝昕, 刘雪薇^*, 李祖军, 龙武华, 宫彦龙, 朱速松
贵州省农业科学院水稻研究所, 贵阳 550006

摘要:

大粒香作为贵州重要的优质稻资源,推广种植面积大,并且在乡村振兴过程中为社会带来了较高的经济效益。然而,目前对大粒香基因组学的理论研究报道较少。为揭示大粒香水稻叶绿体基因组(cpDNA)特征及系统发育关系,该研究对大粒香叶绿体进行测序,并分析其基因组特征。结果表明:(1)大粒香水稻cpDNA全长134 563 bp,包括1个大单拷贝区(LSC,80 864 bp)、1个小单拷贝区(SSC,12 347 bp)和2个反向重复序列区(IR_s,20 676 bp)。(2)注释到129个基因,可分为蛋白编码、tRNA和rRNA三类基因,数量分别为85个、36个和8个。(3)密码子偏好分析显示,大粒香cpDNA密码子偏好A碱基或U(T)碱基,亮氨酸密码子使用了1 944次,使用次数最多; 半胱氨酸的密码子仅使用198次,使用次数最少。(4)检测到129个SSR,其中有95个单核苷酸重复且大部分SSR序列由A/T碱基组成。(5)系统发育分析结果显示,大粒香与热带粳稻亲缘关系最近,聚为一类。该研究结果揭示了大粒香叶绿体基因组信息,并确定了大粒香系统发育所属分支。

关键词: 水稻, 大粒香, 叶绿体基因, SSR, 系统发育分析

DOI：10.11931/guihaia.gxzw202105024

分类号:Q943

文章编号:1000-3142(2022)11-1830-10

基金项目:黔农科院青年基金([2018]101号); 贵州省科技基础项目(黔科合基础[2020]1Y101); 黔农科院引导项目[2018]03号; 黔科合支撑项目([2019]2304号); 黔科中引地项目([2019]4001); 黔科合平台人才项目([2017]5719); 黔科合基础(ZK[2021]124)[Supported by Youth Fund of Guizhou Academy of Agricultural Sciences([2018]101); Project of Guizhou Science and Technology(QianKeHeJiChu[2020]1Y101); Project of Guizhou Academy of Agricultural Sciences([2018]03); Project of Guizhou Science and Technology Cooperation [2019]2304; Central Guided by Guizhou Science and Technology Cooperation([2019]4001); Platform Talent of Guizhou Science and Technology Cooperation([2017]5719); Project of Guizhou Science and Technology(QianKeHeJiChu-ZK[2021]124])]。

Analysis of chloroplast genome of rice Dalixiang

WU Chaoxin, LIU Xuewei^*, LI Zujun, LONG Wuhua, GONG Yanlong, ZHU Susong

Guizhou Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China

Abstract:

As an important high-quality rice resource in Guizhou Province, Dalixiang has a large planting area, and has brought higher economic benefits to society in the process of rural revitalization. However, there are few theoretical researches on the genomics of Dalixiang. In order to reveal the characteristics and phylogenetic relationships of chloroplast genome of rice Dalixiang, the chloroplasts of Dalixiang were sequenced and their genomic characteristics were analyzed. The results were as follows:(1)The chloroplast genome of Dalixiang was 134 563 bp, including LSC(80 864 bp),SSC(12 347 bp)and two IR_s(20 676 bp).(2)There were 129 genes annotated in the chloroplast genome of Dalixiang, which could be divided into protein coding, tRNA and rRNA, with 85, 36 and 8 genes respectively.(3)Codon bias analysis of Dalixiang showed that leucine was most frequently used(1 944 times)and that of cysteine was used least frequently(198 times), and most codons ended in A/U(T).(4)The total number of SSR loci in the cpDNA of Dalixiang was 129, ninety-five of which were mononucleotide and most of SSR were composed of nucleobase A/T.(5)Phylogenetic analysis showed the closest affiliation relationship between Dalixiang and Tropical Japonica, and these two were clustered into one group. This study reveals the characteristic information of Dalixiang chloroplast genome, and identifies the phylogenetic status of Dalixiang.

Key words: rice, Dalixiang, chloroplast genome, SSR, phylogenetic analysis