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Microsatellite markers from the I on T orrent: a multi‐species contrast to 454 shotgun sequencing
Author(s) -
Elliott Carole P.,
Enright Neal J.,
Allcock Richard J. N.,
Gardner Michael G.,
Meglécz Emese,
Anthony Janet,
Krauss Siegfried L.
Publication year - 2014
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12192
Subject(s) - biology , microsatellite , shotgun sequencing , computational biology , dna sequencing , shotgun , primer (cosmetics) , genetics , metagenomics , evolutionary biology , dna , gene , allele , chemistry , organic chemistry
Abstract The development and screening of microsatellite markers have been accelerated by next‐generation sequencing ( NGS ) technology and in particular GS ‐ FLX pyro‐sequencing (454). More recent platforms such as the PGM semiconductor sequencer ( I on T orrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS ‐ FLX pyro‐sequencing for two gymnosperm (a conifer and a cycad) and one angiosperm species. We show that these NGS platforms differ in the quantity of returned sequence data, unique microsatellite data and primer design opportunities, mostly consistent with the differences in read length. The strength of the PGM lies in the large amount of data generated at a comparatively lower cost and time. The strength of GS ‐ FLX lies in the return of longer average length sequences and therefore greater flexibility in producing markers with variable product length, due to longer flanking regions, which is ideal for capillary multiplexing. These differences need to be considered when choosing a NGS method for microsatellite discovery. However, the ongoing improvement in read lengths of the NGS platforms will reduce the disadvantage of the current short read lengths, particularly for the PGM platform, allowing greater flexibility in primer design coupled with the power of a larger number of sequences.