数字农科院2.0

Disruption of recombination machinery alters the mutational landscape in plant organellar genomes

文献类型： 外文期刊

作者： Waneka, Gus;Broz, Amanda K.;Wold-McGimsey, Forrest;Zou, Yi;Wu, Zhiqiang;Sloan, Daniel B.

作者机构：

关键词： organelle mutation;Duplex Sequencing;mitochondria;plastid;recombination;single nucleotide variant;indel;repair;structural variant

期刊名称： G3-GENES GENOMES GENETICS

ISSN： 2160-1836

年卷期： 2025 年

页码：

收录情况： SCIE（2025版）

摘要： Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made toward understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar-targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild-type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.

分类号：

  • 相关文献

[1]Cytonuclear Interactions and Subgenome Dominance Shape the Evolution of Organelle-Targeted Genes in the Brassica Triangle of U. Shenglong Kan,Xuezhu Liao,Lan Lan,Jiali Kong,Jie Wang,Liyun Nie,Jun Zou,Hong An,Zhiqiang Wu. 2024

[2]非RIG-I依赖的鸡STING介导干扰素产生的信号通路. 程玉强,孙英杰,王恒安,严亚贤,丁铲,孙建和. 2015

[3]A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants. Shaofang Li,Lang Liu,Wenxian Sun,Xueping Zhou,Huanbin Zhou. 2022

[4]All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. Liu, Lei,Zhang, Kang,Bai, Jinrui,Lu, Jinghua,Lu, Xiaoxiao,Hu, Junling,Pan, Chunyang,He, Shumin,Yuan, Jiale,Zhang, Yiyue,Zhang, Min,Guo, Yanmei,Wang, Xiaoxuan,Huang, Zejun,Du, Yongchen,Cheng, Feng,Li, Junming. 2022

[5]The emerging role of tissue regulatory T cells in tissue repair and regeneration. Abdul Raheem,Ilyas Khan,Iqbal Ahmad,Abdul Wajid,Mohammad Y. Alshahrani,Fuad M. Alzahrani,Khalid J. Alzahrani,Abdul Qadeer,I. Chuang Liao,Chien Chin Chen. 2025

[6]MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes. Waneka, Gus,King, Connor R.,Sloan, Daniel B.,Wu, Zhiqiang,Broz, Amanda K.,Wu, Zhiqiang. 2020

[7]Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates. Amanda K. Broz,Gus Waneka,Zhiqiang Wu,Matheus Fernandes Gyorfy,Daniel B. Sloan. 2021

[8]基于重测序开发的InDel标记定位陆地棉矮化突变体. 季高翔,何守朴,潘兆娥,龚文芳,贾银华,王立如,王朋朋,耿晓丽,杜雄明. 2018

[9]8个水稻抗条纹叶枯病分子标记有效性的验证及评价. 张亚东,朱镇,陈涛,赵庆勇,周丽慧,于新,王才林. 2012

[10]番茄粉红色果实相关基因的dCAPS和InDel标记开发与应用. 董淑芳,王孝宣,高建昌,国艳梅,黄泽军,杜永臣. 2016

[11]大刍草渐渗系雌穗表型统计及SNP分子标记开发. 曹立超,樊双虎,张春义,陈茹梅. 2014

[12]玉米Rubisco活化酶基因ZmRCA1的序列变异分析. 宋燕春,石云素,程伟东,吴子恺,王天宇,黎裕. 2011

[13]应用InDel标记进行软枣猕猴桃杂交子代真实性鉴定. 孙世航,林苗苗,齐秀娟,孙雷明,钟云鹏,方金豹. 2018

[14]基于BSA-seq技术对豌豆花色基因的精细定位. 严昕,项超,刘荣,李冠,李孟伟,李正丽,宗绪晓,杨涛. 2022

[15]花生InDel标记开发及其在含油量QTL定位中的应用. 陶顺玉,吴贝,刘念,罗怀勇,黄莉,周小静,陈伟刚,郭建斌,喻博伦,雷永,廖伯寿,姜慧芳. 2022

[16]Nif gene transfer and expression in chloroplasts: Prospects and problems. Dixon, R,Cheng, Q,Shen, GF,Day, A,DowsonDay, M. 1997

[17]FLOURY ENDOSPERM24, a heat shock protein 101 (HSP101), is required for starch biosynthesis and endosperm development in rice. Wu, Hongming,Ren, Yulong,Dong, Hui,Xie, Chen,Zhao, Lei,Wang, Xin,Zhang, Fulin,Zhang, Binglei,Jiang, Xiaokang,Huang, Yunshuai,Jing, Ruonan,Wang, Jian,Miao, Rong,Bao, Xiuhao,Yu, Mingzhou,Nguyen, Thanhliem,Mou, Changling,Wang, Yunlong,Wang, Yihua,Lei, Cailin,Cheng, Zhijun,Jiang, Ling,Wan, Jianmin. 2024

[18]Identification of leaf chloroplast-specific promoter to efficiently control of Colorado potato beetle with reduced dsRNA accumulation in potato tubers. Liao, Jianghua,Rong, Haoling,You, Lili,Xia, Kai,Wang, Minghui,Han, Peng,Li, Chao,Zhang, Jiang. 2023

[19]Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes. Jie Wang,Shenglong Kan,Jiali Kong,Liyun Nie,Weishu Fan,Yonglin Ren,Wayne Reeve,Jeffrey P. Mower,Zhiqiang Wu. 2024

[20]ZmPTOX1, a plastid terminal oxidase, contributes to redox homeostasis during seed development and germination. Peng, Yixuan,Liang, Zhi,Cai, Minghao,Wang, Jie,Li, Delin,Chen, Quanquan,Du, Xuemei,Gu, Riliang,Wang, Guoying,Schnable, Patrick S.,Wang, Jianhua,Li, Li. 2024

作者其他论文 更多>>