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Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions

文献类型： 外文期刊

作者： Fan, Weishu 1 ; Liu, Fang 1 ; Jia, Qiaoya 1 ; Du, Haiyuan 1 ; Chen, Wu 1 ; Ruan, Jiwei 4 ; Lei, Jiajun 5 ; Li, De-Zhu 1 ; Mower, Jeffrey P. 6 ; Zhu, Andan 1 ;

作者机构： 1.Chinese Acad Sci, Germplasm Bank Wild Species, Kunming Inst Bot, Kunming 650201, Yunnan, Peoples R China

2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China

3.Yunnan Univ, Sch Life Sci, Kunming 650500, Yunnan, Peoples R China

4.Yunnan Acad Agr Sci, Flower Res Inst, Kunming 650205, Yunnan, Peoples R China

5.Shenyang Agr Univ, Coll Hort, Shenyang 110866, Liaoning, Peoples R China

6.Univ Nebraska, Ctr Plant Sci Innovat, Lincoln, NE 68588 USA

7.Univ Nebraska, Dept Agron & Hort, Lincoln, NE 68583 USA

关键词： Fragaria; homologous noncoding sequences; mitochondrial genome; multinucleotide substitutions; mutation rates; structural variations

期刊名称：NEW PHYTOLOGIST （ 影响因子：10.323； 五年影响因子：10.768 ）

ISSN： 0028-646X

年卷期：

页码：

收录情况： SCI

摘要： Plant mitochondrial DNA has been described as evolving rapidly in structure but slowly in sequence. However, many of the noncoding portions of plant mitogenomes are not homologous among species, raising questions about the rate and spectrum of mutations in noncoding regions. Recent studies have suggested that the lack of homology in noncoding regions could be due to increased sequence divergence. We compared 30 kb of coding and 200 kb of noncoding DNA from 13 sequenced Fragaria mitogenomes, followed by analysis of the rate of sequence divergence, microinversion events and structural variations. Substitution rates in synonymous sites and nongenic sites are nearly identical, suggesting that the genome-wide point mutation rate is generally consistent. A surprisingly high number of large multinucleotide substitutions were detected in Fragaria mitogenomes, which may have resulted from microinversion events and could affect phylogenetic signal and local rate estimates. Fragaria mitogenomes preferentially accumulate deletions relative to insertions and substantial genomic arrangements, whereas mutation rates could positively associate with these sequence and structural changes among species. Together, these observations suggest that plant mitogenomes exhibit low point mutations genome-wide but exceptionally high structural variations, and our results favour a gain-and-loss model for the rapid loss of homology among plant mitogenomes.

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