Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

Frank Nicholas,Tim Smith,Ewen F Kirkness,Wes Barris,Jillian F Maddox,Mikhail Nefedov,Sean Mcwilliam,Jyoti Shetty,Brian P Dalrymple,Allan M Crawford,Shaying Zhao,Margaret O'Grady,Pieter J De Jong,Abhirami Ratnakumar,John Mcewan,V Hutton Oddy,Noelle E Cockett

doi:10.1186/gb-2007-8-7-r152

Abstract

Using BAC-end sequences, a sparse marker map and the sequences of the human, dog and cow genomes, an accurate and detailed sub-gene level map of the sheep genome has been constructed.

Highlights

Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?
We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited
Construction, characterization, and end sequencing of the sheep BAC library A Texel ram was chosen as the source of the DNA for the construction of the BAC library, because the Texel is a popular terminal sire breed for meat production in several countries, and a Texel was the paternal grandsire breed of the sheep international mapping flock [3]

Summary

Introduction

Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?. Sheep are a major farmed species, producing meat, pelts, and wool. They are closely related to cattle, which is both an advantage and a disadvantage for researchers. The downside is that the sheep genome sequence would be of great benefit to the sheep research community, the sheep has not yet been prioritized by funding agencies for whole genome sequencing. The first version of the sheep linkage map, released in 1995, contained 246 markers and covered 2,070 cM [3]. The addition of markers to the map has been slow, and the focus has changed from microsatellites to single nucleotide polymorphisms (SNPs) and expressed sequence tags in order to benefit from new genotyping technology, as well as to allow easier cross-species genomic comparisons. The current sheep maps lack the resolution required for effective use of modern genomics tools, such as SNP-based whole genome scans

Methods

Results

Discussion

Conclusion