TY - GEN
T1 - Internal validation of ancestral gene order reconstruction in angiosperm phylogeny
AU - Sankoff, David
AU - Zheng, Chunfang
AU - Wall, P. Kerr
AU - DePamphilis, Claude
AU - Leebens-Mack, Jim
AU - Albert, Victor A.
PY - 2008
Y1 - 2008
N2 - Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiopsperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, including an unbiased version of the guided genome halving algorithm, reference to two related genomes instead of only one to guide the reconstruction, use of draft genome sequences in contig form only, incorporation of incomplete sets of homology correspondences among the genomes and addition of large numbers of "singleton" correspondences. We make use of genomic distance, breakpoint reuse rate, dispersion of sets of alternate solutions and other means to evaluate these techniques, while reconstructing the pre-WGD ancestor of Populus trichocarpa as well as an early rosid ancestor.
AB - Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiopsperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, including an unbiased version of the guided genome halving algorithm, reference to two related genomes instead of only one to guide the reconstruction, use of draft genome sequences in contig form only, incorporation of incomplete sets of homology correspondences among the genomes and addition of large numbers of "singleton" correspondences. We make use of genomic distance, breakpoint reuse rate, dispersion of sets of alternate solutions and other means to evaluate these techniques, while reconstructing the pre-WGD ancestor of Populus trichocarpa as well as an early rosid ancestor.
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U2 - 10.1007/978-3-540-87989-3_19
DO - 10.1007/978-3-540-87989-3_19
M3 - Conference contribution
AN - SCOPUS:70350536711
SN - 3540879889
SN - 9783540879886
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 252
EP - 264
BT - Comparative Genomics, International Workshop, RECOMB-CG 2008, Proceedings
T2 - RECOMB Workshop on Comparative Genomics, RECOMB-CG 2008
Y2 - 13 October 2008 through 15 October 2008
ER -