SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

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	SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons
	Liu SL 1; Li YY 1; Lu JL 1; Su X 1; Tang M 1; Zhang R 1; Zhou LL 1; Zhou CR 1,2; Yang Q 1; Ji YQ 3
刊名	METHODS IN ECOLOGY AND EVOLUTION
	2013
卷号	4 期号:12 页码:1142-1150
关键词	high-throughput sequencing metabarcoding next-generation-sequencing operational taxonomic units phylogenetic diversity species richness standard barcode
通讯作者	xinzhou@genomics.cn
合作状况	其它
英文摘要	Metabarcoding of mixed arthropod samples for biodiversity assessment has mostly been carried out on the 454 GS FLX sequencer (Roche, Branford, Connecticut, USA), due to its ability to produce long reads (400bp) that are believed to allow higher taxonomic resolution. The Illumina sequencing platforms, with their much higher throughputs, could potentially reduce sequencing costs and improve sequence quality, but the associated shorter read length (typically <150bp) has deterred their usage in next-generation-sequencing (NGS)-based analyses of eukaryotic biodiversity, which often utilize standard barcode markers (e.g. COI, rbcL, matK, ITS) that are hundreds of nucleotides long. We present a new Illumina-based pipeline to recover full-length COI barcodes from mixed arthropod samples. Our new assembly program, SOAPBarcode, a variant of the genome assembly program SOAPdenovo, uses paired-end reads of the standard COI barcode region as anchors to extract the correct pathways (sequences) out of otherwise chaotic de Bruijn graphs', which are caused by the presence of large numbers of COI homologs of high sequence similarity. Two bulk insect samples of known species composition have been analysed in a recently published 454 metabarcoding study (Yu etal. 2012) and are re-analysed by our analysis pipeline. Compared to the results of Roche 454 (c.400-bp reads), our pipeline recovered full-length COI barcodes (658bp) and 17-31% more species-level operational taxonomic units (OTUs) from bulk insect samples, with fewer untraceable (novel) OTUs. On the other hand, our PCR-based pipeline also revealed higher rates of contamination across samples, due to the Illumina's increased sequencing depth. On balance, the assembled full-length barcodes and increased OTU recovery rates resulted in more resolved taxonomic assignments and more accurate beta diversity estimation. The HiSeq 2000 and the SOAPBarcode pipeline together can achieve more accurate biodiversity assessment at a much reduced sequencing cost in metabarcoding analyses. However, greater precaution is needed to prevent cross-sample contamination during field preparation and laboratory operation because of greater ability to detect non-target DNA amplicons present in low-copy numbers.
收录类别	SCI
资助信息	This study is supported by the National High-tech Research and Development Project (863) of China (2012AA021601) and by BGI. YQJ and DWY were sup- ported by Yunnan Province (20080A001), the Chinese Academy of Sciences (0902281081,KSCX2-YW-Z-1027),theNationalNaturalScienceFoundationof China (31170498), the Ministry of Science and Technology of China (2012FY110800),theUniversityofEastAnglia,andtheStateKeyLaboratoryof GeneticResourcesandEvolutionattheKunmingInstituteofZoology.
语种	英语
WOS记录号	WOS:000327997900005
公开日期	2013-12-30
内容类型	期刊论文
源URL	[http://159.226.149.42:8088/handle/152453/7751]
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.China National Gene Bank, BGI-Shenzhen,Bei shan IndustrialZone,YantianDistrict,Shenzhen,GuangdongProvince 518083,China; 2.College of Life Sciences,Sichuan University,Chengdu,SichuanProvince610000,China 3.State Key Laboratory of Genetic Resources and Evolution,KunmingInstituteofZoology,ChineseAcademyofSciences,Kunming, Yunnan650223,China 4.School of Biological Sciences,University of East Anglia,NorwichResearchPark,Norwich, NorfolkNR47TJ,UK
推荐引用方式 GB/T 7714	Liu SL,Li YY,Lu JL,et al. SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons[J]. METHODS IN ECOLOGY AND EVOLUTION,2013,4(12):1142-1150.
APA	Liu SL.,Li YY.,Lu JL.,Su X.,Tang M.,...&Zhou X[*].(2013).SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons.METHODS IN ECOLOGY AND EVOLUTION,4(12),1142-1150.
MLA	Liu SL,et al."SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons".METHODS IN ECOLOGY AND EVOLUTION 4.12(2013):1142-1150.