IHB OpenIR  > 水生生物分子与细胞生物学研究中心  > 期刊论文
Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila
Chen, Kai1,2; Wang, Guangying1; Xiong, Jie1; Jiang, Chuanqi1; Miao, Wei1,2,3,4
2019-06-30
Source PublicationJOURNAL OF EUKARYOTIC MICROBIOLOGY
ISSN1066-5234
Issue1Pages:12
Abstract

Ciliates are unicellular eukaryotes with separate germline and somatic genomes and diverse life cycles, which make them a unique model to improve our understanding of population genetics through the detection of genetic variations. However, traditional sequencing methods cannot be directly applied to ciliates because the majority are uncultivated. Single-cell whole-genome sequencing (WGS) is a powerful tool for studying genetic variation in microbes, but no studies have been performed in ciliates. We compared the use of single-cell WGS and bulk DNA WGS to detect genetic variation, specifically single nucleotide polymorphisms (SNPs), in the model ciliate Tetrahymena thermophila. Our analyses showed that (i) single-cell WGS has excellent performance regarding mapping rate and genome coverage but lower sequencing uniformity compared with bulk DNA WGS due to amplification bias (which was reproducible); (ii) false-positive SNP sites detected by single-cell WGS tend to occur in genomic regions with particularly high sequencing depth and high rate of C:G to T:A base changes; (iii) SNPs detected in three or more cells should be reliable (an detection efficiency of 83.4-97.4% was obtained for combined data from three cells). This analytical method could be adapted to measure genetic variation in other ciliates and broaden research into ciliate population genetics.

KeywordCiliated protozoa population genetics single-cell resequencing variation detection whole-genome amplification
DOI10.1111/jeu.12746
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[91631303] ; National Natural Science Foundation of China[31525021] ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China
WOS Research AreaMicrobiology
WOS SubjectMicrobiology
WOS IDWOS:000474131200001
WOS KeywordDNA ; AMPLIFICATION ; NUCLEOTIDE ; MUTATION
PublisherWILEY
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China ; Wuhan Branch, Supercomputing Center, Chinese Academy of Science, China
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/31714
Collection水生生物分子与细胞生物学研究中心_期刊论文
Corresponding AuthorWang, Guangying; Miao, Wei
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Hubei, Peoples R China
4.CAS Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
Recommended Citation
GB/T 7714
Chen, Kai,Wang, Guangying,Xiong, Jie,et al. Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila[J]. JOURNAL OF EUKARYOTIC MICROBIOLOGY,2019(1):12.
APA Chen, Kai,Wang, Guangying,Xiong, Jie,Jiang, Chuanqi,&Miao, Wei.(2019).Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila.JOURNAL OF EUKARYOTIC MICROBIOLOGY(1),12.
MLA Chen, Kai,et al."Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila".JOURNAL OF EUKARYOTIC MICROBIOLOGY .1(2019):12.
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