PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

CORC > 昆明动物研究所 > 昆明动物研究所 > 遗传资源与进化国家重点实验室 > 动物生态学研究中心

	PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation
	Ramirez-Gonzalez R 1; Yu DW 2,3; Bruce C 3; Heavens D 1; Caccamo M 1; Emerson BC[*]3
刊名	PLOS ONE
	2013
卷号	8 期号:3 页码:e57615
通讯作者	bemerson@ipna.csic.es
合作状况	其它
英文摘要	High-throughput parallel sequencing is a powerful tool for the quantification of microbial diversity through the amplification of nuclear ribosomal gene regions. Recent work has extended this approach to the quantification of diversity within otherwise difficult-to-study metazoan groups. However, nuclear ribosomal genes present both analytical challenges and practical limitations that are a consequence of the mutational properties of nuclear ribosomal genes. Here we exploit useful properties of protein-coding genes for cross-species amplification and denoising of 454 flowgrams. We first use experimental mixtures of species from the class Collembola to amplify and pyrosequence the 59 region of the COI barcode, and we implement a new algorithm called PyroClean for the denoising of Roche GS FLX pyrosequences. Using parameter values from the analysis of experimental mixtures, we then analyse two communities sampled from field sites on the island of Tenerife. Cross-species amplification success of target mitochondrial sequences in experimental species mixtures is high; however, there is little relationship between template DNA concentrations and pyrosequencing read abundance. Homopolymer error correction and filtering against a consensus reference sequence reduced the volume of unique sequences to approximately 5% of the original unique raw reads. Filtering of remaining non-target sequences attributed to PCR error, sequencing error, or numts further reduced unique sequence volume to 0.8% of the original raw reads. PyroClean reduces or eliminates the need for an additional, time-consuming step to cluster reads into Operational Taxonomic Units, which facilitates the detection of intraspecific DNA sequence variation. PyroCleaned sequence data from field sites in Tenerife demonstrate the utility of our approach for quantifying evolutionary diversity and its spatial structure. Comparison of our sequence data to public databases reveals that we are able to successfully recover both interspecific and intraspecific sequence diversity.
收录类别	SCI
资助信息	This work was supported by a Research Fellowship to Brent Emerson from The Leverhulme Trust, project support from The Genome Analysis Centre (TGAC), the University of East Anglia, and the Consejo Superior de Investigaciones Cientı ´ficas. Doug Yu was supported by Yunnan Province (20080A001), the Chinese Academy of Sciences (0902281081, KSCX2-YW- Z-1027, Y002731079), the National Natural Science Foundation of China (31170498), the Ministry of Science and Technology of China (2012FY110800), the University of East Anglia, and the State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology.
语种	英语
WOS记录号	WOS:000315897100027
公开日期	2013-05-09
内容类型	期刊论文
源URL	[http://159.226.149.42:8088/handle/152453/7418]
专题	昆明动物研究所_动物生态学研究中心昆明动物研究所_遗传资源与进化国家重点实验室
作者单位	1.The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom 2.Ecology, Conservation, and Environment Center, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China 3.School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
推荐引用方式 GB/T 7714	Ramirez-Gonzalez R,Yu DW,Bruce C,et al. PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation[J]. PLOS ONE,2013,8(3):e57615.
APA	Ramirez-Gonzalez R,Yu DW,Bruce C,Heavens D,Caccamo M,&Emerson BC[*].(2013).PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation.PLOS ONE,8(3),e57615.
MLA	Ramirez-Gonzalez R,et al."PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation".PLOS ONE 8.3(2013):e57615.