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dc.contributor.authorLee, Ernest K
dc.contributor.authorCibrian-Jaramillo, Angelica
dc.contributor.authorKolokotronis, Sergios-Orestis
dc.contributor.authorKatari, Manpreet S
dc.contributor.authorStamatakis, Alexandros
dc.contributor.authorOtt, Michael
dc.contributor.authorChiu, Joanna C
dc.contributor.authorLittle, Damon P
dc.contributor.authorStevenson, Dennis Wm
dc.contributor.authorMcCombie, W Richard
dc.contributor.authorMartienssen, Robert A
dc.contributor.authorCoruzzi, Gloria
dc.contributor.authorDeSalle, Rob
dc.date.accessioned2022-08-30T19:51:08Z
dc.date.available2022-08-30T19:51:08Z
dc.date.issued2011-12-15
dc.identifier.citationLee 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.en_US
dc.identifier.eissn1553-7404
dc.identifier.doi10.1371/journal.pgen.1002411
dc.identifier.pmid22194700
dc.identifier.urihttp://hdl.handle.net/20.500.12648/7523
dc.description.abstractA 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.en_US
dc.language.isoenen_US
dc.relation.urlhttps://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002411en_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleA functional phylogenomic view of the seed plants.en_US
dc.typeArticle/Reviewen_US
dc.source.journaltitlePLoS geneticsen_US
dc.source.volume7
dc.source.issue12
dc.source.beginpagee1002411
dc.source.endpage
dc.source.countryUnited States
dc.source.countryUnited States
dc.description.versionVoRen_US
refterms.dateFOA2022-08-30T19:51:08Z
dc.description.institutionSUNY Downstateen_US
dc.description.departmentEpidemiology and Biostatisticsen_US
dc.description.degreelevelN/Aen_US
dc.identifier.journalPLoS genetics


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Attribution 4.0 International
Except where otherwise noted, this item's license is described as Attribution 4.0 International