海洋科学2024，Vol.48Issue(4)：83-96,14.DOI:10.11759/hykx20220823001
基于高通量测序的表层水体纤毛虫多样性评估方法比较与优化
Comparison and optimization of high-throughput sequence processing strategies:a case study regarding ciliate diversity in surface seawater
摘要
Abstract
High-throughput amplicon sequencing has been widely employed for studying microbial diversity.Dif-ferent sequencing methods and data analysis processes influence the analysis results of microbial biodiversity and community structure.Therefore,this study aimed to investigate the effects of different methods,the key steps in-volved in data analysis of the chimera removal and rare taxa,and the merging of similar taxonomic units.Results revealed that the main species detected by DNA sequencing,RNA sequencing,and morphological methods were similar.Moreover,fewer species were detected by RNA sequencing than by DNA sequencing;however,the differ-ence was not significant.Community structural analysis showed a similar community structure based on the opera-tional taxonomic unit(OTU)clustering on a similarity of 97%,98%,99%,and 100%.Both methods of the single-nucleotide variation and cluster based on sequence similarity were able to detect a similar relative abundance of different taxa to that by the morphological method.The species richness detected by OTU clustering under 99%similarity was similar to that detected by morphological results.Furthermore,chimera removal and rare taxa(re-moval thresholds:0.05%for DNA sequencing and 0.07%for RNA sequencing)can improve the issue of inflated molecular diversity.Thus,this study provides a scientific analysis process to investigate ciliate molecular diversity and provides guidelines for future research on eukaryotic microbial diversity.关键词
高通量测序/扩增子分析/方法学比较/纤毛虫/分子多样性Key words
high-throughput sequencing/amplicon sequencing analysis/methodology comparison/ciliate/molecular diversity分类
生物科学引用本文复制引用
万圆圆,赵峰,王超锋,张越,徐奎栋..基于高通量测序的表层水体纤毛虫多样性评估方法比较与优化[J].海洋科学,2024,48(4):83-96,14.基金项目
国家自然科学基金资助项目(41976099) （41976099）
中国科学院青年创新促进会(2022206)National Natural Science Foundation of China,No.41976099 （2022206）
Youth Innovation Promotion Association CAS,No.2022206 （）
