Unraveling Darwin’s “abominable mystery”: using phylogenomics to identify proteins of importance in plant evolution - IBC 2011
Unraveling Darwin’s “abominable mystery”: using phylogenomics to identify proteins of importance in plant evolution
Angélica Cibrián-Jaramillo, New York University
Dennis Stevenson, New York Botanical Garden (presenting author)
This work is part of the The New York Plant Genomics Consortium: Gloria Coruzzi (New York University), Rob DeSalle (American Museum of Natural History AMNH), Dennis Stevenson (The New York Botanical Garden), Rob Martienssen and W. Richard McCombie (Cold Spring Harbor Laboratory), Ernest Lee (AMNH), Sergios-Orestis Kolokotronis (AMNH), Manpreet Katari (NYU), and Angelica Cibrian-Jaramillo (AMNH/NYBG).
Darwin was famously concerned that the sudden appearance and rapid diversification of flowering plants in the mid-Cretaceous could not have occurred by gradual change. Here I discuss a phylogeny among the major seed plant groups, i.e. cycads, ginkgo, conifers, gnetophytes, and flowering plants, and I provide a bioinformatic pipeline in which these phylogenetic relationships can be used as a platform for identifying genes of functional importance in plant diversification. Using complete genomes and unigenes from 16 plant species, genes with positive partitioned Bremer support at major nodes were used to identify overrepresented gene ontology (GO) terms. This is a novel method in which phylogenomic tools are used to postulate hypotheses of gene function in the evolution of major taxa. Although I focus on plants, it can be applied to any group of species with ESTs or genomes available. In this 16-taxa phylogeny, genes involved in post-transcriptional silencing via RNA interference were found to be overrepresented at several major nodes, including at the split of monocots and dicots during early angiosperm divergence. One of these genes, RNA-dependent RNA polymerase 6 is required for the biogenesis of trans-acting small interfering RNA (tasiRNA), confers heteroblasty and organ polarity, and restricts maternal specification of the germline. Processing of small RNA and transfer between neighboring cells underlies these roles, and may have contributed to distinct mutant phenotypes in plants, and in particular to the differences in embryo morphology that defines monocots and dicots. Functional hypotheses such as the role of these genes for plant diversification can be further coupled with expression and genetic data but their phylogenetic importance is identified with our approach first. This can lead to better gene searches, annotations, and functional analyses for genome level studies. This phylogenomic approach and those genes identified here guide plant ecological genomics studies and help understand the precise evolutionary mechanisms driving the diversification of plant species, gradually unraveling Darwin’s abiding and perplexing mystery.
