Phylogenomic Analysis of BAC-end Sequence Libraries in Oryza (Poaceae)

Analyses of genome scale data sets ale beginning to clarity 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 nd 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 24 million nucleotides for 10 diploid species of Oryza A supermatrix approach confirms the broad outline of previous phylogenehc studies, although the nonphylogenetic signal and high levels of missing data must be handled carefully Phylogenetic analysis of 12 chromosomes and nearly 2,000 genes finds strikingly high levels of incongruence across different genomic scales, a result that is likely to apply to other low-level phylogenies in plants We conclude that there is great potential for phylogenehc inference using data from next-generation sequencing protocols but that attention to methodological issues arising inevitably in these data sets is critical