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

Cranston, K. A., Hurwitz, B. L., Sanderson, M. J., Ware, D. H., Wing, R. A., Stein, L. D. (2010) Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae). Systematic Botany, 35 (3). pp. 512-523.

DOI: 10.1600/036364410792495872


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 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 phylogenetic inference using data from next-generation sequencing protocols but that attention to methodological issues arising inevitably in these data sets is critical. © 2010 by the American Society of Plant Taxonomists.

Item Type: Paper
Uncontrolled Keywords: BAC-end sequencing gene trees missing data Oryza Phylogenomics rice.
Subjects: bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation
organism description > plant > Oryza
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
CSHL Authors:
Communities: CSHL labs > Stein lab
CSHL labs > Ware lab
Depositing User: CSHL Librarian
Date: 2010
Date Deposited: 28 Sep 2011 14:01
Last Modified: 02 Mar 2018 15:16

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