Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation

doi:10.3390/ijerph191610024

	Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation
	Wang, Yichao1,2,3,4 ; Wang, Jing1,2,4 ; Chen, Yang1,2,3,4 ; Liu, Shuya 1,2,4; Zhao, Yongfang 2,5; Chen, Nansheng 1,2,4,6
	2022-08-01
发表期刊	INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
卷号	19 期号:16 页码:20
通讯作者	Chen, Nansheng([email protected])
摘要	The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
关键词	diatom class Bacillariophyceae chloroplast genome phylogenetic analysis super barcode
DOI	10.3390/ijerph191610024
收录类别	SCI
语种	英语
资助项目	Natural Science Foundation of China[42176162]; Strategic Priority Research Program of the Chinese Academy of Sciences[XDB42000000]; Chinese Academy of Sciences Pioneer Hundred Talents Program; Taishan Scholar Project Special Fund; Qingdao Innovation and Creation Plan (Talent Development Program-5th Annual Pioneer and Innovator Leadership Award)[19-3-2-16-zhc]; National Key Research and Development Program of China[2017YFC1404300]
WOS研究方向	Environmental Sciences & Ecology ; Public, Environmental & Occupational Health
WOS类目	Environmental Sciences ; Public, Environmental & Occupational Health
WOS记录号	WOS:000845862000001
出版者	MDPI
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/337002/180841
专题	海洋生态与环境科学重点实验室胶州湾海洋生态系统国家野外研究站
通讯作者	Chen, Nansheng
作者单位	1.Chinese Acad Sci, CAS Key Lab Marine Ecol & Environm Sci, Inst Oceanol, Qingdao 266071, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266237, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao 266071, Peoples R China 5.Chinese Acad Sci, Inst Oceanol, Jiaozhou Bay Natl Marine Ecosyst Res Stn, Qingdao 266071, Peoples R China 6.Simon Fraser Univ, Dept Mol Biol & Biochem, 8888 Univ Dr, Burnaby, BC V5A 1S6, Canada
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	Wang, Yichao,Wang, Jing,Chen, Yang,et al. Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation[J]. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH,2022,19(16):20.
APA	Wang, Yichao,Wang, Jing,Chen, Yang,Liu, Shuya,Zhao, Yongfang,&Chen, Nansheng.(2022).Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation.INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH,19(16),20.
MLA	Wang, Yichao,et al."Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation".INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 19.16(2022):20.