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Author
Lee, Ernest KCibrian-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
Journal title
PLoS geneticsDate Published
2011-12-15Publication Volume
7Publication Issue
12Publication Begin page
e1002411
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Show full item recordAbstract
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.Citation
Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R. A functional phylogenomic view of the seed plants. PLoS Genet. 2011 Dec;7(12):e1002411. doi: 10.1371/journal.pgen.1002411. Epub 2011 Dec 15. PMID: 22194700; PMCID: PMC3240601.DOI
10.1371/journal.pgen.1002411ae974a485f413a2113503eed53cd6c53
10.1371/journal.pgen.1002411
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