IDENTIFICATION OF GENOMIC REGIONS CARRYING A CAUSAL MUTATION IN UNORDERED GENOMES

BioRxiv : the Preprint Server for Biology
Pilar Corredor-MorenoDan MacLean

Abstract

Whole genome sequencing using high-throughput sequencing (HTS) technologies offers powerful opportunities to study genetic variation. Mapping the mutations responsible for different phenotypes is generally an involved and time-consuming process so researchers have developed user-friendly tools for mapping-by-sequencing, yet they are not applica- ble to organisms with non-sequenced genomes. We introduce SDM (SNP Distribution Method), a reference independent method for rapid discovery of mutagen-induced muta- tions in typical forward genetic screens. SDM aims to order a disordered collection of HTS reads or contigs such that the fragment carrying the causative mutation can be identified. SDM uses typical distributions of homozygous SNPs that are linked to a phenotype-altering SNP in a non-recombinant region as a model to order the fragments. To implement and test SDM, we created model genomes with an idealised SNP density based on Arabidop- sis thaliana chromosome 1 and analysed fragments with size distribution similar to reads or contigs assembled from HTS sequencing experiments. SDM groups the contigs by their normalised SNP density and arranges them to maximise the fit to the expected SNP distribution. We tested the procedure ...Continue Reading

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