title: A functional phylogenomic view of the seed plants.
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.
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America.
authors.forename: Ernest K
authors.initials: EK
authors.lastname: Lee
authors.forename: Angelica
authors.initials: A
authors.lastname: Cibrian-Jaramillo
authors.forename: Sergios-Orestis
authors.initials: SO
authors.lastname: Kolokotronis
authors.forename: Manpreet S
authors.initials: MS
authors.lastname: Katari
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
authors.forename: Michael
authors.initials: M
authors.lastname: Ott
authors.forename: Joanna C
authors.initials: JC
authors.lastname: Chiu
authors.forename: Damon P
authors.initials: DP
authors.lastname: Little
authors.forename: Dennis Wm
authors.initials: DW
authors.lastname: Stevenson
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Robert A
authors.initials: RA
authors.lastname: Martienssen
authors.forename: Gloria
authors.initials: G
authors.lastname: Coruzzi
authors.forename: Rob
authors.initials: R
authors.lastname: Desalle
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D005075:Biological Evolution; D032462:Cycadopsida / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D023281:Genomics; D019684:Magnoliopsida / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010944:Plants; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics; D012639:Seeds
chemical_list: D034741:RNA, Small Interfering; D012321:DNA-Directed RNA Polymerases