Less is more: Extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

Pukk, Lilian, Ahmad, Freed, Hasan , Shihab, Kisand, Veljo, Gross, Riho and Vasemagi, Anti (2015) Less is more: Extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology. Molecular Ecology Resources, 15 5: 1145-1152. doi:10.1111/1755-0998.12392

Author Pukk, Lilian
Ahmad, Freed
Hasan , Shihab
Kisand, Veljo
Gross, Riho
Vasemagi, Anti
Title Less is more: Extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology
Journal name Molecular Ecology Resources   Check publisher's open access policy
ISSN 1755-0998
Publication date 2015-03-10
Year available 2015
Sub-type Article (original research)
DOI 10.1111/1755-0998.12392
Volume 15
Issue 5
Start page 1145
End page 1152
Total pages 8
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell Publishing Ltd
Collection year 2016
Language eng
Abstract Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction-site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare-cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth. We applied this approach to a common freshwater fish species, the Eurasian perch (Perca fluviatilis L.), and generated over 2.2 MB of novel sequence data consisting of ~17 000 contigs, identified 1259 single nucleotide polymorphisms (SNPs). We also estimated genetic differentiation between the DNA pools from freshwater (Lake Peipus) and brackish water (the Baltic Sea) populations and identified SNPs with the strongest signal of differentiation that could be used for robust individual assignment in the future. This work represents an important step towards developing genomic resources and genetic tools for the Eurasian perch. We expect that our ddRAD sequencing protocol for semiconductor sequencing technology will be useful alternative for currently available RAD protocols.
Keyword De novo assembly
DNA pooling
Eurasian perch (Perca fluviatilis L.)
Next-generation sequencing
Population genomics
SNP development and validation
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2016 Collection
UQ Diamantina Institute Publications
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