Comparative transcriptome analysis of two closely related begonia species reveals divergent patterns in key light-regulated pathways

Begonia is one of the most diverse angiosperm genera, comprising more than 2000 described species. The wide morphological and ecological range represented in the genus makes it a good model for studying the generation and maintenance of diversity. Previous research has shown that strong population structure, poor seed dispersal, and high levels of drift contribute to high rates of speciation and morphological variation. In the present study, we used transcriptomics to compare two closely related but morphologically and ecologically divergent species, Begoniaconchifolia A.Dietr. and B. plebeja Liebm., to identify genes putatively involved in ecological divergence. Using publicly available multitissue RNA-seq data, we asked what genetic pathways show species-specific patterns of divergence between our two study species. The results of differential expression and gene ontology enrichment analyses showed species-specific enrichment of light-regulated functions in Begonia plebeja. Concomitant enrichment of ethylene and jasmonate pathways in Begonia plebeja indicate an increased shade avoidance response, suggesting that light availability may be a key factor in the divergent adaptation of B. conchifolia and B. plebeja