Evolution of the gene lineage and expression analyses in the basal eudicot, L. (Papaveraceae).

Background: () and () are recent paralogs that belong to the large bHLH transcription factor family. Orthologs of these genes have been found in all core eudicots, whereas pre-duplication genes, named , have been found in basal eudicots, monocots, basal angiosperms and gymnosperms. Nevertheless, functional studies have only been performed in , where and are partially redundant in carpel and valve margin development and has a unique role in the dehiscence zone. Further analyses of pre-duplication genes are necessary to assess the functional evolution of this gene lineage.

Results: We isolated additional genes from , , and from our transcriptome libraries and performed phylogenetic analyses. We identified the previously described bHLH domain in all analyzed sequences and also new conserved motifs using the MEME suite. Finally, we analyzed the expression of three genes () from , a basal eudicot in the Papaveraceae. To determine the developmental stages at which these genes were expressed, pre- and post-anthesis carpels and fruits of were collected, sectioned, stained, and examined using light microscopy. Using in situ hybridization we detected that genes are expressed in floral buds, early sepal initiation, stamens and carpel primordia and later during fruit development in the dehiscence zone of the opercular fruit.

Conclusions: Our expression results, in comparison with those available for core eudicots, suggest conserved roles of members of the gene lineage across eudicots in the specification of carpel margins and the dehiscence zone of the mature fruits. Although there is some redundancy between and , these gene clades seem to have undergone some degree of sub-functionalization in the core eudicots, likely by changes in cis regulatory regions and to some extent in coding sequences, at least in Brassicaceae. Our results also indicate that in , paleo genes may play a role in early floral organ specification that was subsequently lost in core eudicot lineages.