Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics

doi:10.3389/fmicb.2023.1203780

	Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics
	Liu, Feng 1,2,3; Wang, Yichao4 ; Huang, Hailong 5; Chen, Nansheng 1,2,3
	2023-06-15
发表期刊	FRONTIERS IN MICROBIOLOGY
卷号	14 页码:13
通讯作者	Liu, Feng(liufeng@qdio.ac.cn) ; Chen, Nansheng(chenns@qdio.ac.cn)
摘要	To understand the evolution of coscinodiscophycean diatoms, plastome sequences of six coscinodiscophycean diatom species were constructed and analyzed in this study, doubling the number of constructed plastome sequences in Coscinodiscophyceae (radial centrics). The platome sizes varied substantially in Coscinodiscophyceae, ranging from 119.1 kb of Actinocyclus subtilis to 135.8 kb of Stephanopyxis turris. Plastomes in Paraliales and Stephanopyxales tended to be larger than those in Rhizosoleniales and Coscinodiacales, which were due to the expansion of the inverted repeats (IRs) and to the marked increase of the large single copy (LSC). Phylogenomic analysis indicated that Paralia and Stephanopyxis clustered tightly to form the Paraliales-Stephanopyxales complex, which was sister to the Rhizosoleniales-Coscinodiscales complex. The divergence time between Paraliales and Stephanopyxales was estimated at 85 MYA in the middle Upper Cretaceous, indicating that Paraliales and Stephanopyxales appeared later than Coscinodiacales and Rhizosoleniales according to their phylogenetic relationships. Frequent losses of housekeeping protein-coding genes (PCGs) were observed in these coscinodiscophycean plastomes, indicating that diatom plastomes showed an ongoing reduction in gene content during evolution. Two acpP genes (acpP1 and acpP2) detected in diatom plastomes were found to be originated from an early gene duplication event occurred in the common progenitor after diatom emergence, rather than multiple independent gene duplications occurring in different lineages of diatoms. The IRs in Stephanopyxis turris and Rhizosolenia fallax-imbricata exhibited a similar trend of large expansion to the small single copy (SSC) and slightly small contraction from the LSC, which eventually led to the conspicuous increase in IR size. Gene order was highly conserved in Coscinodiacales, while multiple rearrangements were observed in Rhizosoleniales and between Paraliales and Stephanopyxales. Our results greatly expanded the phylogenetic breadth in Coscinodiscophyceae and gained novel insights into the evolution of plastomes in diatoms.
关键词	diatom plastome Coscinodiscophyceae gene duplication inverted repeats phylogenomic analysis
DOI	10.3389/fmicb.2023.1203780
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[42176162] ; National Natural Science Foundation of China[42276133] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDB42000000] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDA23050302] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDA23050403] ; Science and Technology Basic Resources Investigation Program of China[2018FY100200] ; Chinese Academy of Sciences Pioneer Hundred Talents Program ; Taishan Scholar Project Special Fund
WOS研究方向	Microbiology
WOS类目	Microbiology
WOS记录号	WOS:001018023200001
出版者	FRONTIERS MEDIA SA
WOS关键词	PLASTID GENOMES ; CHLOROPLAST GENOME ; THALASSIOSIRA-PSEUDONANA ; SEQUENCE ; ALIGNMENT ; GENE ; PERFORMANCE ; TIMESCALE ; TOOL
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/182331
专题	海洋生态与环境科学重点实验室
通讯作者	Liu, Feng; Chen, Nansheng
作者单位	1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao, Shandong, Peoples R China 2.Laoshan Lab, Marine Ecol & Environm Sci Lab, Qingdao, Shandong, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao, Shandong, Peoples R China 4.Chinese Acad Fishery Sci, Beijing, Peoples R China 5.Ningbo Univ, Sch Marine Sci, Ningbo, Zhejiang, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Liu, Feng,Wang, Yichao,Huang, Hailong,et al. Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics[J]. FRONTIERS IN MICROBIOLOGY,2023,14:13.
APA	Liu, Feng,Wang, Yichao,Huang, Hailong,&Chen, Nansheng.(2023).Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics.FRONTIERS IN MICROBIOLOGY,14,13.
MLA	Liu, Feng,et al."Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics".FRONTIERS IN MICROBIOLOGY 14(2023):13.