The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral populus diploid.

Chunfang Zheng, P. Kerr Wall, Jim Leebens-Mack, Victor A. Albert, Claude Walker Depamphilis, David Sankoff

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

We improve on guided genome halving algorithms so that several thousand gene sets, each containing two paralogs in the descendant T of the doubling event and their single ortholog from an undoubled reference genome R, can be analyzed to reconstruct the ancestor A of T at the time of doubling. At the same time, large numbers of defective gene sets, either missing one paralog from T or missing their ortholog in R, may be incorporated into the analysis in a consistent way. We apply this genomic rearrangement distance-based approach to the recently sequenced poplar (Populus trichocarpa) and grapevine (Vitis vinifera) genomes, as T and R respectively.

Original languageEnglish (US)
Pages (from-to)261-271
Number of pages11
JournalComputational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
Volume7
StatePublished - Jan 1 2008

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Populus
Diploidy
Genome
Genes
Vitis

All Science Journal Classification (ASJC) codes

  • Medicine(all)

Cite this

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AU - Wall, P. Kerr

AU - Leebens-Mack, Jim

AU - Albert, Victor A.

AU - Depamphilis, Claude Walker

AU - Sankoff, David

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