DOI: 10.1101/489989Dec 8, 2018Paper

Genome-wide recombination map construction from single individuals using linked-read sequencing

BioRxiv : the Preprint Server for Biology
Andreea DreauFelicity C. Jones

Abstract

Meiotic recombination is a major molecular mechanism generating genomic diversity. Recombination rates vary across the genome, often involving localized crossover "hotspots" and "coldspots". Studying the molecular basis and mechanism underlying this variation within and among individuals has been challenging due to the high cost and effort required to construct individualized genome-wide maps of recombination crossovers. In this study we introduce a new method to detect recombination crossovers across the genome from sperm DNA using Illumina sequencing of linked-read libraries produced using 10X Genomics technology. We leverage the long range information provided by the linked short reads to phase and assign haplotype states to each DNA molecule. When applied to DNA from gametes of a diploid organism, the majority of linked-read molecules can be used to faithfully reconstruct an individual's two haplotypes present at each location in the genome. A valuable rare fraction of molecules that span meiotic crossovers between the two chromosome haplotypes can then be isolated from the broader population of nonrecombinant molecules. Our pipeline, called ReMIX, allows us to characterize the genomic location and intensity of meiotic cros...Continue Reading

Related Concepts

Chromosomes
DNA
Genome
Laboratory mice
Recombination, Genetic
Sperm Cell
Sticklebacks
Location
cDNA Library
Genomics

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