Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers.

Details

Serval ID
serval:BIB_70E88EA3A25F
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers.
Journal
Nature Biotechnology
Author(s)
Nordström K.J., Albani M.C., James G.V., Gutjahr C., Hartwig B., Turck F., Paszkowski U., Coupland G., Schneeberger K.
ISSN
1546-1696 (Electronic)
ISSN-L
1087-0156
Publication state
Published
Issued date
2013
Volume
31
Number
4
Pages
325-330
Language
english
Abstract
Genes underlying mutant phenotypes can be isolated by combining marker discovery, genetic mapping and resequencing, but a more straightforward strategy for mapping mutations would be the direct comparison of mutant and wild-type genomes. Applying such an approach, however, is hampered by the need for reference sequences and by mutational loads that confound the unambiguous identification of causal mutations. Here we introduce NIKS (needle in the k-stack), a reference-free algorithm based on comparing k-mers in whole-genome sequencing data for precise discovery of homozygous mutations. We applied NIKS to eight mutants induced in nonreference rice cultivars and to two mutants of the nonmodel species Arabis alpina. In both species, comparing pooled F2 individuals selected for mutant phenotypes revealed small sets of mutations including the causal changes. Moreover, comparing M3 seedlings of two allelic mutants unambiguously identified the causal gene. Thus, for any species amenable to mutagenesis, NIKS enables forward genetics without requiring segregating populations, genetic maps and reference sequences.
Pubmed
Web of science
Open Access
Yes
Create date
26/08/2013 13:45
Last modification date
20/08/2019 14:29
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