Journal Article

Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

Angélica Cibrián-Jaramillo, Jose E. De la Torre-Bárcena, Ernest K. Lee, Manpreet S. Katari, Damon P. Little, Dennis W. Stevenson, Rob Martienssen, Gloria M. Coruzzi and Rob DeSalle

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 2, issue , pages 225-239
Published in print January 2010 |
Published online March 2010 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evq012

More Like This

Show all results sharing these subjects:

  • Bioinformatics and Computational Biology
  • Evolutionary Biology
  • Genetics and Genomics

GO

Show Summary Details

Preview

We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.

Keywords: phylogenomics; orthologs; partition metrics; gene ontology; micro-RNAs; small interfering RNAs

Journal Article.  8646 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.