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SEPALLATA 3 Genes: Molecular Evolution and Development of Grass Flowers Lori Glenwinkel Advisor: Simon Malcomber, Plant Evolution Lab Overview -Overview of Grass flower morphology -Floral organ identity and the evolution of the Grass flower -SEPALLATA3 genes and floral organ developent -Prelimary Data pinpointing the SEP3 duplication event in the grasses SEP3 expression and the evolution of the lodicule -Molecular Evolution of duplicate Genes(Current and future projects) Positive selection analysis Noncoding regulatory region analysis of SEP3 genes Zanis 2007 wo Two structures may be considered homologous if they are connected by a series of transitional forms (Whipple 2007) SEPALLATA Genes were first characterized in Arabidopsis sep1sep2sep3sep4 quadruple mutant Malcomber 2005 SEPALLATA genes encode MADS box Transcription factors Homeotic family of transcription factors required for vegetative and reproductive development SEPALLATA genes interact with B and C class transcription factors to specify the inner three whorls (carpels, stamen, lodicules) (Malcomber and Kellogg 2005) SEP3A and SEP3B, a grass specific Duplication? Pinpointing the SEP3 Duplication Event 9 AP3 and PI are B class Heterodimers known to interact with SEPALLATA3 genes in Arabidopsis (Takashi 2001) WSEP Shitsukawa 2007 Models of Duplicate Gene Evolution: New and Old Paradigm: one of the duplicates is either lost (pseudogenization) or gains a new function (neofunctionalization) Problems with this model: • deleterious mutations are more probable than advantageous mutations • Moore 2005 fails to account for the preponderance of retained duplicates in whole genomes Models of Duplicate Gene Evolution: New and Old Newer Subfucntionalization Model: duplicate genes acquire debilitating yet complementary mutations that alter one or more subfunctions of the single gene progenitor Strengths of this Model: does not rely on the sparse occurrence of beneficial mutations, but on more frequently occurring loss-of-function mutations in regulatory regions Moore 2005 Investigating SEP3A and SEP3 genes for subfuctionalization rVISTA and Expression analysis rVISTA, online program for comparing noncoding regulatory sequenced If fordifferential conserved andregulation non conservedisTFBSs. Significance: established, Collect genomic sequences grasses with enough of a role for•- SEP3A and SEP3B inforthe development their genome sequenced. and evolution of the grass flower will be better - Search TRANSFAC database using rVISTA understood. Expression analysis: isolating SEP3A and SEP3B from disparate grass species, comparing expression between the lineages Investigating Neofunctionalziation Model in SEP3A and SEP3B lineages, PAML (Positive selection Analysis using Maximum Likelihood) PAML uses increasing complex models of evolution to estimate whether positive selection is acting on an amino acid site Significance: If positive selection is acting on the SEP3A or lineages,or(n) atto the base of the (s) twomutations clades, then Ratio ofSEP3B nonsynonymous synonymous used to predict amino acid neofunctionalization is suggested lending support to a role for site changes in a lineage over time. the evolution of the grass spikelet. dn/ds >1 indicates positive selection (suggests neofunctionalization) dn/ds <1 indicate negative selection dn/ds = 1 neutral selection • Conclusions Preliminary studies SEP3A/SEP3B duplication occurred prior to the evolution of the spikelet clade (indicating it may contribute to the unique grass flower morphology) SEP3 genes may have played a role the evolution of the lodicules. (SEP3A and B class gene expression) Future projects Molecular evolution analysis may suggest Subfunctionalization or Neofunctionalization fates for the SEP3 dupliate genes in the grasses. A strong case for SEP3A and SEP3B’s role in the evolution of the lodicules will result in a better understanding of how grass flower develop. This has potential value agriculturally considering that crop yeild is proportional to flower size.