Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity

doi:10.1186/s12864-022-08532-6

	Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
	Zhang, Mengjia1,2,3,4 ; Chen, Nansheng 1,2,4,5
	2022-04-27
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	23 期号:1 页码:17
通讯作者	Chen, Nansheng([email protected])
摘要	The cosmopolitan Thalassionema species are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marine environment based primarily on morphological features and essentially ignored their genomic information, hindering in-depth investigation on Thalassionema biodiversity. In this project, we constructed the complete chloroplast genomes (cpDNAs) of seven Thalassionema strains representing three different species, which were also the first cpDNAs constructed for any species in the order Thalassionematales that includes 35 reported species and varieties. The sizes of these Thalassionema cpDNAs, which showed typical quadripartite structures, varied from 124,127 bp to 140,121 bp. Comparative analysis revealed that Thalassionema cpDNAs possess conserved gene content inter-species and intra-species, along with several gene losses and transfers. Besides, their cpDNAs also have expanded inverted repeat regions (IRs) and preserve large intergenic spacers compared to other diatom cpDNAs. In addition, substantial genome rearrangements were discovered not only among different Thalassionema species but also among strains of a same species T. frauenfeldii, suggesting much higher diversity than previous reports. In addition to confirming the phylogenetic position of Thalassionema species, this study also estimated their emergence time at approximately 38 Mya. The availability of the Thalassionema species cpDNAs not only helps understand the Thalassionema species, but also facilitates phylogenetic analysis of diatoms.
关键词	Thalassionema species Chloroplast genome Comparative genomics Divergence time
DOI	10.1186/s12864-022-08532-6
收录类别	SCI
语种	英语
资助项目	Strategic Priority Research Program of 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]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000788306800001
出版者	BMC
引用统计	被引频次：3[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/337002/178868
专题	海洋生态与环境科学重点实验室
通讯作者	Chen, Nansheng
作者单位	1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266200, Peoples R China 3.Univ Chinese Acad Sci, Coll Marine Sci, Beijing 10039, Peoples R China 4.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao 266071, Peoples R China 5.Simon Fraser Univ, Dept Mol Biol & Biochem, 8888 Univ Dr, Burnaby, BC V5A 1S6, Canada
第一作者单位	海洋生态与环境科学重点实验室
通讯作者单位	海洋生态与环境科学重点实验室
推荐引用方式 GB/T 7714	Zhang, Mengjia,Chen, Nansheng. Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity[J]. BMC GENOMICS,2022,23(1):17.
APA	Zhang, Mengjia,&Chen, Nansheng.(2022).Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity.BMC GENOMICS,23(1),17.
MLA	Zhang, Mengjia,et al."Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity".BMC GENOMICS 23.1(2022):17.

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