Multi-tissue transcriptome analysis of two Begonia species

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.

This research address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. The team 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 maximizing the use of variable light levels in tropical plants. The team 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.

The team identified the chalcone synthase gene family members in the 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 the team 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 indicates that lineage-specific differences are already beginning to accumulate since the divergence of the study species. The team concludes that there is evidence for a role of gene duplication in generating diversity through the sequence and expression divergence in Begonia.

Read the complete research at

Emelianova, K., Martínez Martínez, A., Campos-Dominguez, L. et al. Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family. Sci Rep 11, 17773 (2021). 

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