Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae)

Analyses of genome scale data sets are beginning to clarify the phylogenetic relationships of species with complex evolutionary histories. Broad sampling across many genes allows for both large concatenated data sets to improve genome-scale phylogenetic resolution and also for independent analysis of gene trees and detection of phylogenetic incongruence. Recent sequencing projects in Oryza sativa and its wild relatives have positioned rice as a model system for such “phylogenomic” studies. We describe the assembly of a phylogenomic data set from 800,000 bacterial artificial chromosome (BAC) end sequences, producing an alignment of 2.4 million nucleotides for 10 diploid species of Oryza. A supermatrix approach confirms the broad outline of previous phylogenetic studies, although the non-phylogenetic signal and high levels of missing data must be handled carefully. Phylogenetic analysis of 12 chromosomes and nearly 2000 genes finds strikingly high levels of incongruence across different g...