Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling

BMC Bioinformatics

Research

David Sankoff¹  Chunfang Zheng¹  Baoyong Wang¹  Carlos Fernando Buen Abad Najar² 

[1] Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada;Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Distrito Federal, México;

关键词: whole genome doubling;    fractionation;    run length statistics;    gene loss;    gene duplication;   

DOI  :  10.1186/1471-2105-16-S17-S9

来源: Springer

【 摘 要 】

BackgroundThe loss of duplicate genes - fractionation - after whole genome doubling (WGD) is the subject to a debate as to whether it proceeds gene by gene or through deletion of multi-gene chromosomal segments.ResultsWGD produces two copies of every chromosome, namely two identical copies of a sequence of genes. We assume deletion events excise a geometrically distributed number of consecutive genes with mean µ ≥ 1, and these events can combine to produce single-copy runs of length l. If µ = 1, the process is gene-by-gene. If µ > 1, the process at least occasionally excises more than one gene at a time. In the latter case if deletions overlap, the later one simply extends the existing run of single-copy genes. We explore aspects of the predicted distribution of the lengths of single-copy regions analytically, but resort to simulations to show how observing run lengths l allows us to discriminate between the two hypotheses.ConclusionsDeletion run length distributions can discriminate between gene-by-gene fractionation and deletion of segments of geometrically distributed length, even if µ is only slightly larger than 1, as long as the genome is large enough and fractionation has not proceeded too far towards completion.

【 授权许可】

CC BY   
© Sankoff et al. 2015