Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation in Medicago sativa
文献类型： 外文期刊
作者： Zhang, Tianxiang 1 ; Chen, Xiuhua 2 ; Yan, Wei 3 ; Li, Manman 1 ; Huang, Wangqi 4 ; Liu, Qian 3 ; Li, Yanan 3 ; Guo, Changhong 1 ; Shu, Yongjun 1 ;
作者机构： 1.Harbin Normal Univ, Coll Life Sci & Technol, Key Lab Mol Cytogenet & Genet Breeding Heilongjian, Harbin 150025, Peoples R China
2.Int Agr Res Inst, Yunnan Acad Agr Sci, Kunming 650200, Peoples R China
3.Inst Trop & Subtrop Cash Crops, Yunnan Acad Agr Sci, Baoshan 678000, Peoples R China
4.Flower Res Inst, Yunnan Acad Agr Sci, Natl Engn Res Ctr Ornamental Hort, Yunnan Flower Breeding Key Lab, Kunming 650200, Peoples R China
关键词： alfalfa; chloroplast genome; population structure; genetic variation; cold stress
期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：5.6； 五年影响因子：6.2 ）
ISSN： 1661-6596
年卷期： 2024 年 25 卷 3 期
页码：
收录情况： SCI
摘要： Alfalfa (Medicago sativa) is a perennial forage legume that is widely distributed all over the world; therefore, it has an extremely complex genetic background. Though population structure and phylogenetic studies have been conducted on a large group of alfalfa nuclear genomes, information about the chloroplast genomes is still lacking. Chloroplast genomes are generally considered to be conservative and play an important role in population diversity analysis and species adaptation in plants. Here, 231 complete alfalfa chloroplast genomes were successfully assembled from 359 alfalfa resequencing data, on the basis of which the alfalfa chloroplast pan-genome was constructed. We investigated the genetic variations of the alfalfa chloroplast genome through comparative genomic, genetic diversity, phylogenetic, population genetic structure, and haplotype analysis. Meanwhile, the expression of alfalfa chloroplast genes under cold stress was explored through transcriptome analysis. As a result, chloroplast genomes of 231 alfalfa lack an IR region, and the size of the chloroplast genome ranges from 125,192 bp to 126,105 bp. Using population structure, haplotypes, and construction of a phylogenetic tree, it was found that alfalfa populations could be divided into four groups, and multiple highly variable regions were found in the alfalfa chloroplast genome. Transcriptome analysis showed that tRNA genes were significantly up-regulated in the cold-sensitive varieties, while rps7, rpl32, and ndhB were down-regulated, and the editing efficiency of ycf1, ycf2, and ndhF was decreased in the cold-tolerant varieties, which may be due to the fact that chloroplasts store nutrients through photosynthesis to resist cold. The huge number of genetic variants in this study provide powerful resources for molecular markers.
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