Relaxed Selection Among Duplicate Floral Regulatory Genes in Lamiales

Abstract

Abstract. Polyploidization is a prevalent mode of genome diversification within plants. Most gene duplicates arising from polyploidization (paralogs) are typically lost, although a subset may be maintained under selection due to dosage, partitioning of gene function, or acquisition of novel functions. Because they experience selection in the presence of other duplicate loci across the genome, interactions among genes may also play a significant role in the maintenance of paralogs resulting from polyploidization. Previously, we identified duplicates of the genes LFY/FLO and AP3/DEF that directly interact in a floral regulatory pathway and are thought to be the result of ancient polyploidization in the Lamiales (> 50 mya). Although duplicates of MADS box genes including AP3/DEF are common throughout the angiosperm lineage, LFY/FLO duplicates in Lamiales are the first reported outside of tetraploid taxa. In order to explore hypotheses for the joint preservation of these interacting floral regulatory genes including novel LFY/FLO paralogs, here we clone FLO and DEF duplicates from additional Lamiales taxa and apply codon substitution models to test how selection acts on both genes following duplication. We find acceleration in the ratio of nonsynonymous-to-synonymous nucleotide substitutions for one (FLO) or both (DEF) paralogs that appears to be due to relaxed purifying selection as opposed to positive selection and shows a different pattern among functional domains of these genes. Several mechanisms are discussed that might be responsible for preservation of co-orthologs of FLO and DEF in Lamiales, including interactions among the genes of this regulatory pathway.

The LEAFY Floral Regulators in Angiosperms: Conserved Proteins with Diverse Roles

“…They either result from polyploidy, as in Nicotiana tabaccum, or from smaller-scale duplication events, as the two paralogs did not persist long enough to be inherited by multiple species (Baum et al 2005;Kelly et al 1995). There are only two documented cases (Maize and Lamiales) where a second copy seems to have been kept unusually long (Aagaard et al 2006;Bomblies et al 2003). The reason why LFY copies are not more often maintained is not understood.…”

“…LFY homologues have been cloned in more than 200 species and LFY is mostly found as a single copy gene. It is clear that LFY experienced duplication as any other genes since there are traces of copies being eliminated (Aagaard et al 2006;Baum et al 2005;Bomblies and Doebley 2005;Bomblies and Doebley 2006;Southerton et al 1998). Moreover, several species exhibit two or three LEAFY-like genes but the phylogeny studies demonstrate that the paralogs are recent copies (Archambault and Bruneau 2004;Shu et al 2000;Southerton et al 1998;Wada et al 2002;Wang et al 2008;Yoon and Baum 2004).…”

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

“…Partial sequences of HaGI and HaTFL1 were obtained with degenerate primers designed for alignments of homologs from other species in GenBank (supporting information, Table S1). Previously published degenerate primers successfully amplified partial sequences of HaLFY (Aagaard et al 2006) and HaCOL2 (Hecht et al 2005). Partial sequence of HaSOC1 was obtained with primers designed for a Chrysanthemum 3 morifolium SOC1-like sequence (GenBank accession no.…”

The PI/GLO-like locus in orchids: Duplication and purifying selection at synonymous sites within Orchidinae (Orchidaceae)

“…However, paralogs of genes involved in transcriptional regulation, signal transduction, and development can persist within genomes through subfunctionalization or, less frequently, neo-functionalization (Aagaard et al, 2006). Gene duplication events and positive selection have driven the functional diversification of gene families encoding developmental transcription factors (e.g., Hox genes and MADS-box genes) (Kuraku and Meyer, 2009;Shan et al, 2009).…”