A functional phylogenomic view of the seed plants

Lee, E. K., Cibrian-Jaramillo, A., Kolokotronis, S. O., Katari, M. S., Stamatakis, A., Ott, M., Chiu, J. C., Little, D. P., Stevenson, D. W., McCombie, W. R., Martienssen, R. A., Coruzzi, G., Desalle, R. (2011) A functional phylogenomic view of the seed plants. PLoS genetics, 7 (12). e1002411. ISSN 1553-7404 (Electronic)1553-7390 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/22194700
DOI: 10.1371/journal.pgen.1002411

Abstract

A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.

Item Type: Paper
Uncontrolled Keywords: Angiosperms genetics Arabidopsis genetics Biological Evolution DNA-Directed RNA Polymerases Evolution Molecular Flowers genetics Genes Plant genetics Genome Plant Genomics Gymnosperms genetics Oryza sativa genetics Phylogeny Plants RNA Interference RNA Small Interfering/genetics Seeds
Subjects: bioinformatics
bioinformatics > genomics and proteomics
organism description > plant
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: Matt Covey
Date Deposited: 06 Feb 2013 16:00
Last Modified: 26 Dec 2014 20:08
PMCID: PMC3240601
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27166

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