A functional phylogenomic view of the seed plants

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 th...

Full description

Saved in:
Bibliographic Details
Published in:PLoS genetics 2011-12, Vol.7 (12), p.e1002411-e1002411
Main Authors: Lee, Ernest K, Cibrian-Jaramillo, Angelica, Kolokotronis, Sergios-Orestis, Katari, Manpreet S, Stamatakis, Alexandros, Ott, Michael, Chiu, Joanna C, Little, Damon P, Stevenson, Dennis Wm, McCombie, W Richard, Martienssen, Robert A, Coruzzi, Gloria, Desalle, Rob
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Biological Evolution
Biology
Cycadopsida - genetics
DNA-Directed RNA Polymerases
Evolution
Evolution, Molecular
Flowers - genetics
Gene expression
Genes
Genes, Plant - genetics
Genetic aspects
Genetics
Genome, Plant
Genomics
Magnoliopsida - genetics
Oryza - genetics
Phanerogams
Phylogenetics
Phylogeny
Physiological aspects
Plants
RNA
RNA Interference
RNA, Small Interfering - genetics
Seeds
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1002411