Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes

BMC Bioinformatics

Proceedings

David Sankoff¹  Chunfang Zheng¹ 

[1] Department of Mathematics and Statistics, University of Ottawa, Canada;

关键词: Whole Genome Duplication;    Synteny Block;    Ancestral Node;    Blue Edge;    Whole Genome Duplication Event;   

DOI  :  10.1186/1471-2105-13-S10-S9

来源: Springer

【 摘 要 】

BackgroundAncestral gene order reconstruction for flowering plants has lagged behind developments in yeasts, insects and higher animals, because of the recency of widespread plant genome sequencing, sequencers' embargoes on public data use, paralogies due to whole genome duplication (WGD) and fractionation of undeleted duplicates, extensive paralogy from other sources, and the computational cost of existing methods.ResultsWe address these problems, using the gene order of four core eudicot genomes (cacao, castor bean, papaya and grapevine) that have escaped any recent WGD events, and two others (poplar and cucumber) that descend from independent WGD s, in inferring the ancestral gene order of the rosid clade and those of its main subgroups, the fabids and malvids. We improve and adapt techniques including the OMG method for extracting large, paralogy-free, multiple orthologies from conflated pairwise synteny data among the six genomes and the PATHGROUPS approach for ancestral gene order reconstruction in a given phylogeny, where some genomes may be descendants of WGD events. We use the gene order evidence to evaluate the hypothesis that the order Malpighiales belongs to the malvids rather than as traditionally assigned to the fabids.ConclusionsGene orders of ancestral eudicot species, involving 10,000 or more genes can be reconstructed in an efficient, parsimonious and consistent way, despite paralogies due to WGD and other processes. Pairwise genomic syntenies provide appropriate input to a parameter-free procedure of multiple ortholog identification followed by gene-order reconstruction in solving instances of the "small phylogeny" problem.

【 授权许可】

CC BY   
© Zheng and Sankoff et al; licensee BioMed Central Ltd. 2012