Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae

doi:10.1111/tpj.15028

	Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae
	Kang, Jong-Soo ; Zhang, Hong-Rui ; Wang, Ya-Rong ; Liang, Si-Qi ; Mao, Zhi-Yuan ; Zhang, Xian-Chun; Xiang, Qiao-Ping
	2020
发表期刊	PLANT JOURNAL
ISSN	0960-7412
卷号	104 期号:6 页码:1657-1672
摘要	Plastids and mitochondria are endosymbiotic organelles that store genetic information. The genomes of these organelles generally exhibit contrasting patterns regarding genome architecture and genetic content. However, they have similar genetic features in Selaginellaceae, and little is known about what causes parallel evolution. Here, we document the multipartite plastid genomes (plastomes) and the highly divergent mitochondrial genomes (mitogenomes) from spikemoss obtained by combining short- and long-reads. The 188-kb multipartite plastome has three ribosomal operon copies in the master genomic conformation, creating the alternative subgenomic conformation composed of 110- and 78-kb subgenomes. The long-read data indicated that the two different genomic conformations were present in almost equal proportions in the plastomes of Selaginella nipponica. The mitogenome of S. nipponica was assembled into 27 contigs with a total size of 110 kb. All contigs contained directly arranged repeats at both ends, which introduced multiple conformations. Our results showed that plastomes and mitogenomes share high tRNA losses, GC-biased nucleotides, elevated substitution rates and complicated organization. The exploration of nuclear-encoded organelle DNA replication, recombination and repair proteins indicated that, several single-targeted proteins, particularly plastid-targeted recombinase A1, have been lost in Selaginellaceae; conversely, the dual-targeted proteins remain intact. According to the reported function of recombinase A1, we propose that the plastomes of spikemoss often fail to pair homologous sequences during recombination, and the dual-targeted proteins play a key role in the convergent genetic features of plastomes and mitogenomes. Our results provide a distinctive evolutionary pattern of the organelle genomes in Selaginellaceae and evidence of their convergent evolution.
关键词	Selaginella plastid genome mitochondrial genome genome evolution convergent evolution RecA
学科领域	Plant Sciences
DOI	10.1111/tpj.15028
收录类别	SCI
语种	英语
WOS关键词	CHLOROPLAST DNA ; MITOCHONDRIAL GENOME ; INVERTED REPEAT ; PLANT MITOCHONDRIAL ; COMPLETE SEQUENCE ; LINEAR-MOLECULES ; PLASTID GENOMES ; COPY NUMBER ; GENE ; RECOMBINATION
WOS研究方向	Plant Sciences
WOS记录号	WOS:000589870500001
出版者	WILEY
文献子类	Article
出版地	HOBOKEN
EISSN	1365-313X
资助机构	National Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31770237, 31670205]
作者邮箱	qpxiang@ibcas.ac.cn
引用统计	被引频次：24[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/21520
专题	系统与进化植物学国家重点实验室
作者单位	1.[Kang, Jong-Soo 2.Zhang, Hong-Rui 3.Wang, Ya-Rong 4.Liang, Si-Qi 5.Zhang, Xian-Chun 6.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 7.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 8.Chinese Acad Sci, Inst Bot, Photosynth Res Ctr, Key Lab Photobiol, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Kang, Jong-Soo,Zhang, Hong-Rui,Wang, Ya-Rong,et al. Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae[J]. PLANT JOURNAL,2020,104(6):1657-1672.
APA	Kang, Jong-Soo.,Zhang, Hong-Rui.,Wang, Ya-Rong.,Liang, Si-Qi.,Mao, Zhi-Yuan.,...&Xiang, Qiao-Ping.(2020).Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae.PLANT JOURNAL,104(6),1657-1672.
MLA	Kang, Jong-Soo,et al."Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae".PLANT JOURNAL 104.6(2020):1657-1672.

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