Study on the evolution of genome dynamics across the mega-diverse genus Begonia L. (Begoniaceae)
Creators: name: Campos Dominguez, Lucia
Publisher: name: The University of Edinburgh
Year: 2021

description: Understanding the drivers of angiosperm species diversity has always been one of the major goals of research in evolutionary biology. In this thesis, the genus Begonia L. (Begoniaceae) is used as a model to study some of these drivers. Begonia is one of the most species-rich angiosperm genera with 1991 pantropically distributed species currently identified. The current distribution of Begonia species abundance overlaps with angiosperm species richness, dominating the tropical areas and making this genus a good model for the study of large angiosperm radiations. Recent evolutionary work on Begonia provides a robust phylogenetic background for the analysis of evolutionary patterns across the group and confirms speciation in Begonia is not only driven by adaptive processes, but rather by a ”random walk”. As well as extensive phenotypic variation, previous research has established that Begonia is also very variable in genome size chromosome numbers. This suggests that large scale genomic re-arrangements and bursts of transposon activity may be common in Begonia evolution. This thesis investigates patterns of genome dynamics across the Begonia genus, and its potential role in rapid species diversification. To have a better overview of the genome structural variation present in Begonia, chro- mosome numbers for hundreds of species have been gathered and taxonomically con- firmed according to the latest phylogeny. Results show chromosome number diversity is higher in some but not all of the larger clades, and the most variable karyotypes belong to taxonomically complex or unresolved Begonia sections. Our results also indicate that genome size variation does not correlate with changes in chromosome number. This suggests that Begonia genome dynamics is not only caused by large-scale du- plications, rearrangements or changes in ploidy levels, but rather that changes in the repetitive fraction of the genome also play an important role, likely causing changes in chromosome size. Whole Genome Sequencing (WGS) has been used to identify TE content and variation among different Begonia clades. In addition, the genome of the only Begonia sister species Hillebrandia sandwicensis has been assembled to compare these two genera at a genomic level and better understand the specific factors involved in the repeated radiation events described in Begonia. Our results suggest that Begonia species show more complex, repetitive and dynamic genomes overall than Hillebrandia. There is a wide variation in both content and types of DNA repeats across the different Begonia clades. Our Long Terminal Repeat (LTR) dating results show that species from older and more depauperate clades show more stable and generally lower recent LTR activity. In contrast, we have identified LTR-Copia and Gypsy retrotransposon families being recently expanded in two different highly speciose South-East Asian sections, and LTR elements and satellite DNA families being expanded in three Neotropical radiations. One of the largest Neotropical Begonia radiations is represented by section Gireoudia. To further investigate the genomic factors involved in this radiation, the repeat content, variation and transposon insertion times of 32 Gireoudia species was studied. These results show recent LTR and wide satellite DNA expansions across Gireoudia species, in contrast with its species poor, closely related sections. Moreover, we found a common LTR-Gypsy expansion shared by all Gireoudia species studied, that dates to the origin of this section, suggesting TE dynamics may have played a role in the origin of the Gireoudia radiation. To additionally comprehend whether intra-specific genome structure variation drives speciation by introducing crossing barriers between populations, repeatomes from dif- ferent Begonia heracleifolia (B. section Gireoudia) accessions showing variable genome sizes have also been studied. This revealed a markedly higher satellite repeat and LTR-Gypsy content in the accessions with larger genome sizes, associated with the ex- pansion of a few abundant repeat lineages. Furthermore, experimental crosses between the accessions demonstrated that seed viability is impaired in crosses between indi- viduals with different genome sizes. Therefore, we have also identified an association between changes in genomic repeat content and genetic barriers to reproduction within a Begonia species.