Harmonized coexistence of intragenomic variations in diatom Skeletonema strains

doi:10.1016/j.envres.2024.119799

	Harmonized coexistence of intragenomic variations in diatom Skeletonema strains
	Liu, Shuya 1,2,3; Ding, Xiangxiang1,2,3,4 ; Liu, Kuiyan 1,2,3,4; Chen, Nansheng 1,2,3
	2024-12-01
发表期刊	ENVIRONMENTAL RESEARCH
ISSN	0013-9351
卷号	262 页码:12
通讯作者	Chen, Nansheng([email protected])
摘要	Metabarcoding analysis has been demonstrated to be an effective technology for monitoring diversity and dynamics of phytoplankton including Skeletonema species. Although molecular diversity uncovered in metabarcoding projects has generally been interpreted as sum of interspecies diversity and intraspecies diversity, accumulating evidence suggests that it also harbors unprecedentedly high levels of intra-genomic variations (IGVs). As up to thousands of amplicon sequence variants (ASVs) identified in a typical metabarcoding project can be annotated to be Skeletonema species, we hypothesize that substantial portions of these ASVs are contributed by IGVs. Here, the nature of IGVs in Skeletonema species was quantitatively analyzed by carrying out single-strain metabarcoding analysis of 18S rDNA V4 in 49 strains belonging to seven Skeletonema species. Results showed that each Skeletonema strain harbored a high level of IGVs as expected. While many Skeletonema strains each contained one dominant ASV and a substantial number of ASVs displaying much lower relative abundance, other Skeletonema strains each contained multiple ASVs with comparable or nearly equally abundances. Thus the co-existence of multiple dominant ASVs in a single cell indicated a tug-of-war of these variants in evolution, which may eventually result in harmonized coexistence of multiple dominant ASVs. A total of nine dominant ASVs and 652 non-dominant ASVs were found in 49 strains of seven Skeletonema species, indicating rich interspecies and intraspecies variations, and complex evolution of IGVs in genus of Skeletonema. The results confirmed that the extensive degree of IGVs was the main contributor to the high molecular diversity revealed by metabarcoding analysis. This study highlights the importance of quantitative characterization of IGVs in Skeletonema species for accurate interpretation of species diversity in metabarcoding analysis.
关键词	Skeletonema species Metabarcoding analysis Intra-genomic variations Molecular diversity 18S rDNA
DOI	10.1016/j.envres.2024.119799
收录类别	SCI
语种	英语
资助项目	National Key Research and Development (R&D) Program of China[2022YFC3105200]; Natural Science Foundation of China[42176162]; Natural Science Foundation of China[41906118]; Taishan Scholar Project Special Fund, China; Strategic Priority Research Program of Chinese Academy of Sciences, China[XDB42000000]; Chinese Academy of Sciences Pioneer Hundred Talents Program, China
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:001297899300001
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS关键词	RIBOSOMAL-RNA GENES ; CONCERTED EVOLUTION ; DIVERSITY ; DNA ; BACILLARIOPHYCEAE ; COSTATUM ; HETEROGENEITY ; REVEALS ; POLYMORPHISM ; VARIABILITY
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/198189
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 Marine Sci & Technol Ctr, Lab Marine Ecol & Environm Sci, Qingdao 266200, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao 266071, Peoples R China 4.Univ Chinese Acad Sci, Coll Adv Agr Sci, Beijing 100039, Peoples R China
推荐引用方式 GB/T 7714	Liu, Shuya,Ding, Xiangxiang,Liu, Kuiyan,et al. Harmonized coexistence of intragenomic variations in diatom Skeletonema strains[J]. ENVIRONMENTAL RESEARCH,2024,262:12.
APA	Liu, Shuya,Ding, Xiangxiang,Liu, Kuiyan,&Chen, Nansheng.(2024).Harmonized coexistence of intragenomic variations in diatom Skeletonema strains.ENVIRONMENTAL RESEARCH,262,12.
MLA	Liu, Shuya,et al."Harmonized coexistence of intragenomic variations in diatom Skeletonema strains".ENVIRONMENTAL RESEARCH 262(2024):12.