Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data.
Mol Ecol
; 22(11): 3141-50, 2013 Jun.
Article
in En
| MEDLINE
| ID: mdl-23432348
ABSTRACT
In this study, we used restriction site-associated DNA (RAD) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the Eurasian beaver (Castor fibre) to Scotland. In the absence of a reference genome for beaver, we built contigs and discovered SNPs within them using paired-end RAD data, so as to have sufficient flanking region around the SNPs to conduct marker design. To do this, we used a simple pipeline which catalogued the Read 1 data in stacks and then used the assembler cortex_var to conduct de novo assembly and genotyping of multiple samples using the Read 2 data. The analysis of around 1.1 billion short reads of sequence data was reduced to a set of 2579 high-quality candidate SNP markers that were polymorphic in Norwegian and Bavarian beaver. Both laboratory validation of a subset of eight of the SNPs (1.3% error) and internal validation by confirming patterns of Mendelian inheritance in a family group (0.9% error) confirmed the success of this approach.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Rodentia
/
Sequence Analysis, DNA
/
High-Throughput Nucleotide Sequencing
Type of study:
Risk_factors_studies
Limits:
Animals
Country/Region as subject:
Asia
/
Europa
Language:
En
Journal:
Mol Ecol
Journal subject:
BIOLOGIA MOLECULAR
/
SAUDE AMBIENTAL
Year:
2013
Type:
Article
Affiliation country:
United kingdom