Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates

doi:10.1016/j.hal.2021.102108

	Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates
	Liu, Yuyang 1; Hu, Zhangxi1,2,3 ; Deng, Yunyan 1,2,3; Shang, Lixia 1,2,3; Gobler, Christopher J.4; Tang, Ying Zhong 1,2,3
	2021-11-01
发表期刊	HARMFUL ALGAE
ISSN	1568-9883
卷号	109 页码:13
通讯作者	Hu, Zhangxi(zhu@qdio.ac.cn) ; Tang, Ying Zhong(yingzhong.tang@qdio.ac.cn)
摘要	Dinoflagellates are an ecologically important group of protists in aquatic environment and have evolved many unusual and enigmatic genomic features such as immense genome sizes, high repeated genes, and a large portion of hydroxymethyluracil in DNA. Although previous studies have observed positive correlations between the large subunit (LSU) rRNA gene copy number and genome size of a variety of eukaryotic organisms (e.g. higher plants and animals), or between cell volume and LSU rRNA gene copy number, and/or between genome size and cell size, which suggests a possible co-evolution among these three features in different lineages of life, it remains an open question regarding the relationships among these three parameters in dinoflagellates. For the first time, we estimated the copy numbers of the LSU rRNA gene, the genome sizes, and cell volumes within a broad range of dinoflagellates (covering 15 species of 11 genera) using single-cell qPCR-based assay (determining LSU rRNA gene copy number), FlowCAM (cell volume measurement), and ultraviolet spectrophotometry (genome size estimation). The measured copy number of LSU rRNA gene ranged from 398 +/- 184 (Prorocentrum minimum) to 152,078 +/- 33,555 copies center dot cell-1 (Alexandrium pacificum), while the genome size and the cell volume ranged from 5.6 +/- 0.2 (Karlodinium veneficum) to 853 +/- 19.9 pg center dot cell-1 (Pseliodinium pirum), and from 1,070 +/- 225 (Kar. veneficum) to 168,474 +/- 124,180 mu m3 (Ps. pirum), respectively. Together with the three parameters measured in literature, there are significant positive linear correlations between LSU rRNA gene copy numbers and genome sizes, cell volumes and LSU rRNA gene copy numbers, and between genome sizes and cell volumes via comparisons of multi-model regression analyses, suggesting a dependence of genome size and rRNA gene copy number on the cell volumes of dinoflagellates. Validation of the measurement methods was conducted via comparisons between reported data in the literature and that predicted using the linear equations we obtained, and between genome size measured by flow cytometry (FCM) and ultraviolet spectrophotometry (Nanodrop). These results provide insightful understandings of dinoflagellate evolution in terms of the relationships among genomes, gene copy number, and cell volume, and of rRNA gene-based studies in intra-populational and intraindividual genetic diversity, taxonomy, and diversity assessment in the environment of dinoflagellates. The results also provide a dataset useful for reads calibration in environmental metabarcoding studies of dinoflagellates and selection of candidate species for whole genome sequencing.
关键词	LSU rRNA gene copy number Genome size Cell volume Co-evolution Dinoflagellate
DOI	10.1016/j.hal.2021.102108
收录类别	SCI
语种	英语
WOS研究方向	Marine & Freshwater Biology
WOS类目	Marine & Freshwater Biology
WOS记录号	WOS:000710116900003
出版者	ELSEVIER
引用统计	被引频次：9[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/337002/176735
专题	海洋生态与环境科学重点实验室
通讯作者	Hu, Zhangxi; Tang, Ying Zhong
作者单位	1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, 7 Nanhai Rd, Qingdao 266071, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Peoples R China 4.SUNY Stony Brook, Sch Marine & Atmospher Sci, Stony Brook, NY 11790 USA
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; 中国科学院海洋大科学研究中心
推荐引用方式 GB/T 7714	Liu, Yuyang,Hu, Zhangxi,Deng, Yunyan,et al. Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates[J]. HARMFUL ALGAE,2021,109:13.
APA	Liu, Yuyang,Hu, Zhangxi,Deng, Yunyan,Shang, Lixia,Gobler, Christopher J.,&Tang, Ying Zhong.(2021).Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates.HARMFUL ALGAE,109,13.
MLA	Liu, Yuyang,et al."Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates".HARMFUL ALGAE 109(2021):13.

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