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Using comparative genomics to reorder the human genome sequence into a virtual sheep genome
Brian P Dalrymple1, Ewen F Kirkness, Mikhail Nefedov
1CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia. brian.dalrymple@csiro.au
Genome Biology
|August 1, 2007
Summary
Researchers created a detailed sheep genome map using bacterial artificial chromosome (BAC) end sequences and comparative genomics. This method enables subgene-level mapping for species with limited genomic resources.
Area of Science:
- Comparative genomics
- Genomic mapping
- Bioinformatics
Background:
- Developing accurate subgene-level genome maps is challenging, especially for species with limited genomic resources.
- Bacterial artificial chromosomes (BACs) offer a potential tool for genome mapping.
Purpose of the Study:
- To construct an accurate and detailed subgene-level map of the sheep genome.
- To assess the feasibility of using BAC end sequences, sparse marker maps, and related genome sequences for genome mapping.
Main Methods:
- Construction of a sheep BAC library (CHORI-243) and determination of BAC end sequences.
- Mapping sheep BAC end sequences onto human, dog, and cow genome frameworks, with coordinate conversion to human genome equivalents.
- Integration of BAC end sequence data, comparative genome contigs (CGCs), synteny information, and a sheep marker map to build a virtual sheep genome.
Main Results:
- Over 1,172 sheep BAC-CGCs were constructed, covering 91.2% of the human genome.
- BAC-CGC linkage information and synteny data were used to link contigs, covering approximately 70% of the genome.
- A virtual sheep genome was constructed, enabling the transfer of human genes and features for display on a genome browser.
Conclusions:
- Limited BAC sequencing, combined with positioning on a reference genome and integration of data from other genomes, can generate detailed subgene-level maps.
- This approach is effective for creating genomic resources for mammalian species with currently limited genomic data.
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