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

Giulia Partipilo, Pietro D'Addabbo, Giovanni M. Lacalandra, George E. Liu, Mariano Rocchi

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number639
JournalBMC Genomics
Volume12
DOIs
Publication statusPublished - Dec 30 2011

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Chromosomes
Genome
DNA
Interphase
Firearms
Metaphase
Clone Cells

Keywords

  • Alternate assemblies of cow genomes
  • Bac-fish mapping
  • Cow genome
  • Genomic comparison
  • Unassigned scaffolds

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Partipilo, G., D'Addabbo, P., Lacalandra, G. M., Liu, G. E., & Rocchi, M. (2011). Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. BMC Genomics, 12, [639]. https://doi.org/10.1186/1471-2164-12-639

Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. / Partipilo, Giulia; D'Addabbo, Pietro; Lacalandra, Giovanni M.; Liu, George E.; Rocchi, Mariano.

In: BMC Genomics, Vol. 12, 639, 30.12.2011.

Research output: Contribution to journalArticle

Partipilo, G, D'Addabbo, P, Lacalandra, GM, Liu, GE & Rocchi, M 2011, 'Refinement of Bos taurus sequence assembly based on BAC-FISH experiments', BMC Genomics, vol. 12, 639. https://doi.org/10.1186/1471-2164-12-639
Partipilo G, D'Addabbo P, Lacalandra GM, Liu GE, Rocchi M. Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. BMC Genomics. 2011 Dec 30;12. 639. https://doi.org/10.1186/1471-2164-12-639
Partipilo, Giulia ; D'Addabbo, Pietro ; Lacalandra, Giovanni M. ; Liu, George E. ; Rocchi, Mariano. / Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. In: BMC Genomics. 2011 ; Vol. 12.
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