10.5061/DRYAD.22P7M
Schoebel, Corine
Swiss Federal Institute for Forest, Snow and Landscape Research
Brodbeck, Sabine
Swiss Federal Institute for Forest, Snow and Landscape Research
Buehler, Dominique
Swiss Federal Institute for Forest, Snow and Landscape Research
Cornejo, Carolina
Swiss Federal Institute for Forest, Snow and Landscape Research
Gajurel, Jyoti
Institute of Vertebrate Biology
Hartikainen, Hanna
Natural History Museum
Keller, Daniela
Swiss Federal Institute for Forest, Snow and Landscape Research
Leys, Marie
Swiss Federal Institute of Aquatic Science and Technology
Říčanová, Štěpánka
Institute of Vertebrate Biology
Segelbacher, Gernot
University of Freiburg
Werth, Silke
Swiss Federal Institute for Forest, Snow and Landscape Research
Csencsics, Daniela
Swiss Federal Institute for Forest, Snow and Landscape Research
Schoebel, C. N.
Swiss Federal Institute for Forest, Snow and Landscape Research
Data from: Lessons learned from microsatellite development for non-model
organisms using 454 pyrosequencing
Dryad
dataset
2014
Comparative studies
Shotgun sequencing
next generation sequencing technology
massively parallel sequencing
2014-11-17T02:38:36Z
2014-11-17T02:38:36Z
en
https://doi.org/10.1111/jeb.12077
186667 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Microsatellites, also known as simple sequence repeats (SSRs), are among
the most commonly used marker types in evolutionary and ecological
studies. Next Generation Sequencing techniques such as 454 pyrosequencing
allow the rapid development of microsatellite markers in nonmodel
organisms. 454 pyrosequencing is a straightforward approach to develop a
high number of microsatellite markers. Therefore, developing
microsatellites using 454 pyrosequencing has become the method of choice
for marker development. Here, we describe a user friendly way of
microsatellite development from 454 pyrosequencing data and analyse data
sets of 17 nonmodel species (plants, fungi, invertebrates, birds and a
mammal) for microsatellite repeats and flanking regions suitable for
primer development. We then compare the numbers of successfully lab-tested
microsatellite markers for the various species and furthermore describe
diverse challenges that might arise in different study species, for
example, large genome size or nonpure extraction of genomic DNA.
Successful primer identification was feasible for all species. We found
that in species for which large repeat numbers are uncommon, such as
fungi, polymorphic markers can nevertheless be developed from 454
pyrosequencing reads containing small repeat numbers (five to six
repeats). Furthermore, the development of microsatellite markers for
species with large genomes was also with Next Generation Sequencing
techniques more cost and time-consuming than for species with smaller
genomes. In this study, we showed that depending on the species, a
different amount of 454 pyrosequencing data might be required for
successful identification of a sufficient number of microsatellite markers
for ecological genetic studies.
Schoebel et al. R-scriptR script to use with MSATCOMMANDER output files
for microsatellite mining.Schoebel et al. supplementary materialsOnline
supplementary materialSupplementary materials dryad.pdf