Genetic anchoring of whole-genome shotgun assemblies.

Martin Mascher,Nils Stein

doi:10.3389/fgene.2014.00208

Abstract

The recent advances in sequencing throughput and genome assembly algorithms have established whole-genome shotgun (WGS) assemblies as the cornerstone of the genomic infrastructure for many species. WGS assemblies can be constructed with comparative ease and give a comprehensive representation of the gene space even of large and complex genomes. One major obstacle in utilizing WGS assemblies for important research applications such as gene isolation or comparative genomics has been the lack of chromosomal positioning and contextualization of short sequence contigs. Assigning chromosomal locations to sequence contigs required the construction and integration of genome-wide physical maps and dense genetic linkage maps as well as synteny to model species. Recently, methods to rapidly construct ultra-dense linkage maps encompassing millions of genetic markers from WGS sequencing data of segregating populations have made possible the direct assignment of genetic positions to short sequence contigs. Here, we review recent developments in the integration of WGS assemblies and sequence-based linkage maps, discuss challenges for further improvement of the methodology and outline possible applications building on genetically anchored WGS assemblies.

Highlights

Next-generation sequencing (NGS) has facilitated the rapid collection of vast amounts of genomic sequence data, enabling whole-genome shotgun (WGS) assemblies in species with huge genomes (Li et al, 2010; Jia et al, 2013; Ling et al, 2013; Nystedt et al, 2013)
Sequence-based high-throughput genotyping and its applications such as genome-wide association or population genetic studies rely on the visualization of features [single-nucleotide polymorphisms (SNPs), peaks of summary statistics] along the chromosomes, often applying sliding-windows to aggregate the information of neighboring contigs (Luikart et al, 2003; Schneeberger et al, 2009; Andrews and Luikart, 2014; Ellegren, 2014)
If extensive physical mapping resources are not available, reference genomes of related species may serve as proxy to order WGS assemblies, but approaches based on genome collinearity (Mayer et al, 2009) are restricted to genic regions and their accuracy is bounded by the degree of syntenic conservation between related species

Summary

INTRODUCTION

Next-generation sequencing (NGS) has facilitated the rapid collection of vast amounts of genomic sequence data, enabling whole-genome shotgun (WGS) assemblies in species with huge genomes (Li et al, 2010; Jia et al, 2013; Ling et al, 2013; Nystedt et al, 2013). High-quality reference sequences continue to be constructed with the help of physical maps and sequencing single bacterial artificial chromosomes (BACs; Groenen et al, 2012; Amborella Genome Project, 2013). This hierarchical shotgun approach entails the laborious and expensive steps of BAC library construction, finger-printing and clone-by-clone sequencing (Ariyadasa and Stein, 2012). If extensive physical mapping resources are not available (as is the case for many non-model species), reference genomes of related species may serve as proxy to order WGS assemblies, but approaches based on genome collinearity (Mayer et al, 2009) are restricted to genic regions and their accuracy is bounded by the degree of syntenic conservation between related species. Recent translocations or duplications of single genes or larger genomic regions may reduce interspecific collinearity and www.frontiersin.org

Mascher and Stein

Findings

CONCLUSION