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Open Access Research article

Refinement of Bos taurus sequence assembly based on BAC-FISH experiments

Giulia Partipilo1, Pietro D'Addabbo1, Giovanni M Lacalandra2, George E Liu3 and Mariano Rocchi1*

Author Affiliations

1 Department of Biology, University of Bari, Via Orabona 4, 70125 Bari, Italy

2 Department of Animal Production, Faculty of Veterinary Medicine, University of Bari, SP. Casamassima-Valenzano, Valenzano, BA 70010, Italy

3 Bovine Functional Genomics Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA

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BMC Genomics 2011, 12:639  doi:10.1186/1471-2164-12-639

Published: 30 December 2011

Abstract

Background

The sequencing of the cow genome was recently published (Btau_4.0 assembly). A second, alternate cow genome assembly (UMD2), based on the same raw sequence data, was also published. The two assemblies have been subsequently updated to Btau_4.2 and UMD3.1, respectively.

Results

We compared the Btau_4.2 and UMD3.1 alternate assemblies. Inconsistencies were grouped into three main categories: (i) DNA segments showing almost coincidental chromosomal mapping but discordant orientation (inversions); (ii) DNA segments showing a discordant map position along the same chromosome; and (iii) sequences present in one chromosomal assembly but absent in the corresponding chromosome of the other assembly. The latter category mainly consisted of large amounts of scaffolds that were unassigned in Btau_4.2 but successfully mapped in UMD3.1. We sampled 70 inconsistencies and identified appropriate cow BACs for each of them. These clones were then utilized in FISH experiments on cow metaphase or interphase nuclei in order to disambiguate the discrepancies. In almost all instances the FISH results agreed with the UMD3.1 assembly. Occasionally, however, the mapping data of both assemblies were discordant with the FISH results.

Conclusions

Our work demonstrates how FISH, which is assembly independent, can be efficiently used to solve assembly problems frequently encountered using the shotgun approach.

Keywords:
Cow genome; alternate assemblies of cow genomes; genomic comparison; unassigned scaffolds; BAC-FISH mapping