The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio
dc.contributor.author | Wei, N. | |
dc.contributor.author | Bemmels, J. B. | |
dc.contributor.author | Dick, C. W. | |
dc.date.accessioned | 2014-08-19T10:27:24Z | |
dc.date.available | 2014-08-19T10:27:24Z | |
dc.date.issued | 2014-09 | |
dc.identifier.citation | Molecular Ecology Resources 14: 953-965 <http://hdl.handle.net/2027.42/108219> | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/108219 | |
dc.description.abstract | The advent of next-generation sequencing (NGS) technologies has transformed the way microsatellites are isolated for ecological and evolutionary investigations. Recent attempts to employ NGS for microsatellite discovery have used the 454, Illumina, and Ion Torrent platforms, but other methods including single-molecule real-time DNA sequencing (Pacific Biosciences or PacBio) remain viable alternatives. We outline a workflow from sequence quality control to microsatellite marker validation in three plant species using PacBio circular consensus sequencing (CCS). We then evaluate the performance of PacBio CCS in comparison with other NGS platforms for microsatellite isolation, through simulations that focus on variations in read length, read quantity and sequencing error rate. Although quality control of CCS reads reduced microsatellite yield by around 50%, hundreds of microsatellite loci that are expected to have improved conversion efficiency to functional markers were retrieved for each species. The simulations quantitatively validate the advantages of long reads and emphasize the detrimental effects of sequencing errors on NGS-enabled microsatellite development. In view of the continuing improvement in read length on NGS platforms, sequence quality and the corresponding strategies of quality control will become the primary factors to consider for effective microsatellite isolation. Among current options, PacBio CCS may be optimal for rapid, smallscale microsatellite development due to its flexibility in scaling sequencing effort, while platforms such as Illumina MiSeq will provide cost-efficient solutions for multispecies microsatellite projects. | en_US |
dc.language.iso | en_US | en_US |
dc.publisher | John Wiley and Sons | en_US |
dc.subject | Circular Consensus Sequencing, Error Trimming Simulation, Microsatellites, Quality Control, Read Length Simulation, Sequencing Error Simulation | en_US |
dc.title | The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio | en_US |
dc.type | Article | en_US |
dc.subject.hlbsecondlevel | Ecology and Evolutionary Biology | |
dc.subject.hlbtoplevel | Science | |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Department of Ecology and Evolutionary Biology | en_US |
dc.contributor.affiliationumcampus | Ann Arbor | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/108219/1/Na2014.pdf | |
dc.identifier.doi | 10.1111/1755-0998.12245 | |
dc.identifier.source | Molecular Ecology Resources | en_US |
dc.description.mapping | 85 | en_US |
dc.description.filedescription | Description of Na2014.pdf : main article | |
dc.owningcollname | Ecology and Evolutionary Biology, Department of (EEB) |
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