SEPALLATA 3 Genes: Molecular Evolution SEPALLATA 3 Genes: Molecular Evolution and Development of Grass Flowersand Development of Grass Flowers

Lori GlenwinkelLori Glenwinkel

Advisor: Simon Malcomber, Plant Evolution LabAdvisor: 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

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Two structures may be considered homologous if they are connected by a series of transitional forms (Whipple 2007)

SEPALLATA genes encode MADS box Transcription factorsHomeotic family of transcription factors required for vegetative and reproductive development

SEPALLATA Genes were first characterized in Arabidopsis

sep1sep2sep3sep4 quadruple mutant

Malcomber 2005

SEPALLATA genes interact with B and C class transcription factors to specify the inner three whorls (carpels, stamen, lodicules)

SEP3A and SEP3B,

a grass specific Duplication?

(Malcomber and Kellogg 2005)

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Pinpointing the SEP3 Duplication Event

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

Moore 2005

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

• fails to account for the preponderance of retained duplicates in whole genomes

Models of Duplicate Gene Evolution: New and Old

Moore 2005

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

Investigating SEP3A and SEP3 genes for subfuctionalization

rVISTA and Expression analysis

rVISTA, online program for comparing noncoding regulatory sequenced for conserved and non conserved TFBSs.

•- Collect genomic sequences for grasses with enough of their genome sequenced.

- Search TRANSFAC database using rVISTA

Expression analysis: isolating SEP3A and SEP3B from disparate grass species, comparing expression between the lineages

Significance: If differential regulation is established, a role for SEP3A and SEP3B in the development and evolution of the grass flower will be better understood.

PAML uses increasing complex models of evolution to estimate whether positive selection is acting on an amino acid site

Ratio of nonsynonymous (n) to synonymous (s) mutations used to predict amino acid site changes in a lineage over time.

dn/ds >1 indicates positive selection (suggests neofunctionalization)

dn/ds <1 indicate negative selection

dn/ds = 1 neutral selection

Investigating Neofunctionalziation Model in SEP3A and SEP3B lineages,

PAML (Positive selection Analysis using Maximum Likelihood)

Significance: If positive selection is acting on the SEP3A or SEP3B lineages,or at the base of the two clades, then neofunctionalization is suggested lending support to a role for the evolution of the grass spikelet.

• Conclusions Preliminary studiesSEP3A/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 projectsMolecular 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.