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Begonia  is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that  Begonia  has a highly variable genome size, and analysis of paralog pairs has previously suggested that  Begonia  underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in  Begonia  using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species,  Begonia conchifolia  and  B. plebeja , yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our  Begonia  study species, as well as in  Hillebrandia sandwicensis , the monotypic sister genus to  Begonia ,  Cucumis sativus ,  Arabidopsis thaliana , and  Zea mays . Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in  Begonia  arising recently, after the divergence of  Begonia  and  Cucumis . Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in  Begonia .

Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family