Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing

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 (Ion Torrent) 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.