Begonia is one of the most species-rich angiosperm genera with c. 1500 species
currently identified and a pantropical distribution. Although Begonia are
predominantly found in ever wet rain forests, they can also be found in other habitats
including dry, desert scrub, and at altitudes from sea level to over 3000 meters.
Begonia can also exhibit huge morphological variation between closely related
species thus making them an ideal system for the study of the ecology, biogeography
and developmental evolution of tropical plants.
Previous work carried out at the Royal Botanic Gardens, Edinburgh focused on the
phylogenetic framework and biogeographic history of African and Asian Begonias.
This work on the Neotropical Begonia Section Gireoudia, aims to complement those
studies and to provide a framework for determining how macro- and micro-evolutionary processes have contributed to the high level of diversity in Begonia
worldwide.
Traditionally used nuclear and chloroplast markers for phylogenetics failed to resolve
species level relationships within sect. Gireoudia, therefore an alternative approach
using next-generation sequencing technology was developed.
A multiplexed, massively parallel sequencing approach was developed to sequence
sixteen Begonia chloroplast genomes on the Illumina GAIIx genome analyser in order
to identify chloroplast regions with sufficient phylogenetic information to resolve a
species-level phylogeny. The lack of a reference chloroplast genome sequence for
Begonia led to the development of a new method combining sequence from
conserved angiosperm chloroplast genome sequences together with long-range PCR
to generate the samples. Eighteen, overlapping long-range PCR amplicons for each
Begonia species were used in a multiplexed sequencing reaction on an Illumina
GAIIx and the chloroplast sequence reads were assembled using a de novo approach.
A selection of potentially, phylogenetically informative regions, determined from the
large-scale chloroplast alignment generated during this study, were assessed. Two of
these regions were chosen for further phylogenetic analysis and resulted in improved
resolution of American Begonia, sect. Gireoudia.
This study successfully demonstrates a new innovative approach to that normally
taken in traditional molecular systematics. The research presented provides a
framework for the development of new molecular markers that are suitable for low-level phylogenetic studies, especially where recent radiations make resolution of
species groups difficult, such as Begonia. New sequencing technologies such as those
used here will provide powerful new tools for students of molecular evolution,
phylogenetics and taxonom
