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

Cibrian-Jaramillo, A., De la Torre-Barcena, J. E., Lee, E. K., Katari, M. S., Little, D. P., Stevenson, D. W., Martienssen, R. A., Coruzzi, G. M., DeSalle, R. (March 2010) Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution. Genome Biology and Evolution, 2. pp. 225-239. ISSN 1759-6653

URL: http://www.ncbi.nlm.nih.gov/pubmed/20624728
DOI: 10.1093/gbe/evq012

Abstract

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.

Item Type: Paper
Uncontrolled Keywords: phylogenomics orthologs partition metrics gene ontology micro-RNAs small interfering RNAs POSITIVE SELECTION COP9 SIGNALOSOME SEED PLANTS FLOWERING PLANTS DATA SETS FUNCTIONAL PREDICTIONS MONOCOT RELATIONSHIPS NUCLEAR GENES SEQUENCE DATA ANGIOSPERMS
Subjects: bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA expression
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
organism description > plant
CSHL Authors:
Communities: CSHL labs > Martienssen lab
Depositing User: CSHL Librarian
Date: 24 March 2010
Date Deposited: 28 Sep 2011 14:16
Last Modified: 09 Apr 2014 19:46
PMCID: PMC2997538
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15391

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