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Abstract Detail

Ecological Section

Wei, Na [1], Dick, Christopher  [2].

In silico evaluation of microsatellite development effectiveness using next-generation sequencing: a practical guide for ecologists.

Microsatellites are repetitive short DNA sequences that are scattered throughout the genomes of prokaryotes and eukaryotes. Due to their hypervariability, these molecular markers have seen extensive use in ecological investigations, such as dispersal, parentage inference, mating system, and clonal structure. The advent of next-generation sequencing (NGS) technologies has transformed the way microsatellites are isolated, by providing many more candidate markers than using traditional methods, and with substantial reductions in time and capital investment. Recent attempts to employ NGS for microsatellite detection have used the 454, Illumina, Ion Torrent, and Pacific Biosciences (PacBio) RS platforms. Independently from specific platforms, the development of microsatellite markers is in general influenced by read length, quality, and quantity. Based on simulations, we found increases in read lengths are associated with improvements in primer design success, microsatellite throughput, and genomic redundancy detection. In addition, the simulations revealed a detrimental effect of sequencing errors on the efficiency of converting microsatellite loci into functional makers. 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 circular consensus sequencing may be optimal for rapid, small-scale microsatellite development due to its flexibility in scaling sequencing effort, while platforms such as Illumina MiSeq will provide cost-efficient solutions for multi-species microsatellite projects.

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1 - University Of Michigan, Ecology And Evolutionary Biology, 830 N. University Ave., 2010 Kraus Building, Ann Arbor, MI, 48109, USA
2 - University Of Michigan, Ecology And Evolutionary Biology, 830 N. University Ave., 2011 Kraus Building, Ann Arbor, MI, 48109, USA

next-generation sequencing
read length simulation
sequencing error simulation
error trimming simulation.

Presentation Type: Poster:Posters for Sections
Session: P
Location: Eyrie/Boise Centre
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PEC024
Abstract ID:182
Candidate for Awards:Ecological Section Best Graduate Student Poster

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