Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta)

doi:10.3389/fpls.2023.1126175

	Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta)
	Liu, Feng 1,2,3; Chen, Nansheng 1,2,3; Wang, Hongshu1,2,3 ; Li, Jiamin 1,2,3; Wang, Jing1,2,3 ; Qu, Fan 4
	2023-04-18
发表期刊	FRONTIERS IN PLANT SCIENCE
ISSN	1664-462X
卷号	14 页码:17
通讯作者	Liu, Feng(liufeng@qdio.ac.cn)
摘要	To understand the evolutionary driving forces of chloroplast (or plastid) genomes (plastomes) in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta), in this study, we sequenced and constructed seven complete chloroplast genomes from five Ulva species, and conducted comparative genomic analysis of Ulva plastomes in Ulvophyceae. Ulva plastome evolution reflects the strong selection pressure driving the compactness of genome organization and the decrease of overall GC composition. The overall plastome sequences including canonical genes, introns, derived foreign sequences and non-coding regions show a synergetic decrease in GC content at varying degrees. Fast degeneration of plastome sequences including non-core genes (minD and trnR3), derived foreign sequences, and noncoding spacer regions was accompanied by the marked decrease of their GC composition. Plastome introns preferentially resided in conserved housekeeping genes with high GC content and long length, as might be related to high GC content of target site sequences recognized by intron-encoded proteins (IEPs), and to more target sites contained by long GC-rich genes. Many foreign DNA sequences integrated into different intergenic regions contain some homologous specific orfs with high similarity, indicating that they could have been derived from the same origin. The invasion of foreign sequences seems to be an important driving force for plastome rearrangement in these IR-lacking Ulva cpDNAs. Gene partitioning pattern has changed and distribution range of gene clusters has expanded after the loss of IR, indicating that genome rearrangement was more extensive and more frequent in Ulva plastomes, which was markedly different from that in IR-containing ulvophycean plastomes. These new insights greatly enhance our understanding of plastome evolution in ecologically important Ulva seaweeds.
关键词	chloroplast genome Ulvophyceae comparative genomics GC content group I II intron genome rearrangement
DOI	10.3389/fpls.2023.1126175
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[42276133/41876165] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDA23050302/XDA23050403] ; Key Research Program of Frontier Sciences, Chinese Academy of Sciences[QYZDB-SSW-DQC023] ; Science and Technology Basic Resources Investigation Program of China[2018FY100200] ; Major Scientific and Technological Innovation Project of Shandong Province[2019JZZY020706] ; Natural Science Foundation of Shandong Province for Young Scholars[ZR2022QD066]
WOS研究方向	Plant Sciences
WOS类目	Plant Sciences
WOS记录号	WOS:000980084600001
出版者	FRONTIERS MEDIA SA
WOS关键词	TIDE-FORMING MACROALGA ; PLASTID GENOME ; ALGA ; MITOCHONDRIAL ; AUSTRALIS ; ALIGNMENT ; SEQUENCE ; INTRONS ; REVEALS ; PERTUSA
引用统计	被引频次：2[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/182973
专题	海洋生态与环境科学重点实验室
通讯作者	Liu, Feng
作者单位	1.Chinese Acad Sci IOCAS, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao, Shandong, Peoples R China 2.Marine Ecol & Environm Sci Lab, Pilot Natl Lab Marine Sci & Technol Qingdao, Qingdao, Shandong, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao, Shandong, Peoples R China 4.Harbin Univ Sci & Technol, Weihai, Shandong, 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,Chen, Nansheng,Wang, Hongshu,et al. Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta)[J]. FRONTIERS IN PLANT SCIENCE,2023,14:17.
APA	Liu, Feng,Chen, Nansheng,Wang, Hongshu,Li, Jiamin,Wang, Jing,&Qu, Fan.(2023).Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta).FRONTIERS IN PLANT SCIENCE,14,17.
MLA	Liu, Feng,et al."Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta)".FRONTIERS IN PLANT SCIENCE 14(2023):17.