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Comparative analysis of single-cell genome sequencing techniques toward the characterization of germline and somatic genomes in ciliated protists.
Lyu, Liping; Asghar, Usman; Fu, Jinyu; Gao, Yunyi; Zhang, Xue; Al-Farraj, Saleh A; Chen, Zigui; Gao, Feng.
Affiliation
  • Lyu L; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China.
  • Asghar U; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China.
  • Fu J; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China.
  • Gao Y; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China.
  • Zhang X; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China.
  • Al-Farraj SA; Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
  • Chen Z; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China. Electronic address: zigui.chen@cuhk.edu.hk.
  • Gao F; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture (OUC), Ministry of Education, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China. Electronic address: gaof@ouc.edu.cn.
Eur J Protistol ; 88: 125969, 2023 Apr.
Article in En | MEDLINE | ID: mdl-36822126
Ciliated protists contain both germline micronucleus (MIC) and somatic macronucleus (MAC) in a single cytoplasm. Programmed genome rearrangements occur in ciliates during sexual processes, and the extent of rearrangements varies dramatically among species, which lead to significant differences in genomic architectures. However, genomic sequences remain largely unknown for most ciliates due to the difficulty in culturing and in separating the germline from the somatic genome in a single cell. Single-cell whole genome amplification (WGA) has emerged as a powerful technology to characterize the genomic heterogeneity at the single-cell level. In this study, we compared two single-cell WGA, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in characterizing the germline and somatic genomes in ciliates with different genomic architectures. Our results showed that: 1) MALBAC exhibits strong amplification bias towards MAC genome while MDA shows bias towards MIC genome of ciliates with extensively fragmented MAC genome; 2) both MDA and MALBAC could amplify MAC genome more efficiently in ciliates with moderately fragmented MAC genome. Moreover, we found that more sample replicates could help to obtain more genomic data. Our work provides a reference for selecting the appropriate method to characterize germline and somatic genomes of ciliates.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Ciliophora / Genomics Language: En Journal: Eur J Protistol Journal subject: BIOLOGIA Year: 2023 Document type: Article Affiliation country: China Country of publication: Germany

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Ciliophora / Genomics Language: En Journal: Eur J Protistol Journal subject: BIOLOGIA Year: 2023 Document type: Article Affiliation country: China Country of publication: Germany