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

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.

Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species.

The Philippine island of Palawan is highly biodiverse. During fieldwork there in 2011 & 2014 we found five unknown species in the large genus Begonia. The species are similar in their rhizomatous stems, four-tepaled flowers, inferior two- or three-locular ovaries with bilamellate placentas, and are assignable to Begonia sect. Baryandra. Our observations support the recognition of these as five new species endemic to Palawan: B. elnidoensis, B. gironellae, B. quinquealata, B. tabonensis and B. tenuibracteata which are described here. The five new species were added to phylogenies based Bayesian analysis of nrDNA (ITS) and chloroplast DNA (ndhA, ndhF-rpl32, rpl32-trnL, trnC-trnD), along with 45 other allied ingroup species. A majority of the species show incongruent positions in the two phylogenies, with evidence of prevalent chloroplast capture. Models show chloroplast capture is more likely in plant populations with high levels of inbreeding following a reduction in selfing rate after hybridisation; we suggest that this is a possible explanation for the massive amount of chloroplast exchange seen in our phylogeny, as Begonia species often exist as small isolated populations and may be prone to inbreeding depression. Our data also indicate a level of nuclear genetic exchange between species. The high prevalence of hybrid events in Begonia is potentially an important factor in driving genomic change and species evolution in this mega-diverse genus.

Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics.

Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.

Maintenance of species boundaries in a Neotropical radiation of Begonia.

A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by-product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later-generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.

[Study on wild germplasm resoures of Begonia fimbristipula in Dinghu District, Zhaoqing City, Guangdong Province].

OBJECTIVE: A systematical investigation on the distribution of wild germplasm of Regonia fimbristipula in Dinghu District, Zhaoqing City, Guangdong Province was conducted at 8 sites. METHODS: Field quadrat survey method was carried out. RESULTS: Begonia fimbristipula had obvious phenotypical plasticity showing three phenotypes with red, green and bicolor leaf, respectively. Its populations lived in the ecological environment of rock. The growth and building of Begonia fimbristipula population were mutually influenced by many ecological factors such as natural habitat, slope-exposure, soil thickness, sunlight, air humidity as well as soil physical and chemical properties. CONCLUSION: Living environment vulnerability and human activities are the main reason causing sharp decrease of wild resources of Begonia fimbristipula. Evaluation on regional distribution of wild Begonia fimbristipula and its protection and use of the rationalization have important value.

Isolation of compound microsatellite markers in Begonia fenicis (Begoniaceae) endemic to East and Southeast Asian islands.

PREMISE OF THE STUDY: We developed compound microsatellite markers for Begonia fenicis, a species endemic to eastern and southeastern Asian islands, to investigate geographical genetic structure. METHODS AND RESULTS: Using the compound microsatellite marker technique, 21 markers were developed and six polymorphic markers were characterized for samples from four islands in Taiwan and southern Japan. The number of alleles per locus ranged from two to six (mean = 4.33). Observed and expected heterozygosities were 0.125-0.725 (0.383) and 0.498-0.719 (0.641), and polymorphic information content was 0.371-0.664 (0.567). The interspecific transferability of the 21 markers was evaluated for eight species of the section Diploclinium from the Philippines; 15 markers were successfully amplified in one to eight species. CONCLUSIONS: These results indicate the utility of the six microsatellite markers in B. fenicis to investigate geographical genetic structure. The transferable markers are potentially useful for other species of the section.

First macrofossil record of Begonia (Begoniaceae).

PREMISE OF THE STUDY: Begonia is the sixth-largest genus of flowering plants, with about 1400-1500 species in 66 sections. Several species are popular with horticulturalists, mainly for their colorful flowers and leaves. However, the evolutionary history of the genus is debated, and until now there has been no macrofossil record. Here, we report on a fossil winged capsule from the Pliocene of Alabama and interpret it as a Begonia fruit, which represents the first convincing macrofossil evidence of the genus. METHODS: Identification required extensive literature and herbarium searches to compare features of the fossil with those of other recognized fossil and extant taxa that have winged fruits. KEY RESULTS: The fossil is identified as a Begonia fruit on the basis of a combination of characters, including the presence of two unequally developed wings, at least one additional inferred wing, details of the wing venation, a prominent marginal vein, a locule opening associated with a wing, and a persistent pedicel. CONCLUSIONS: Although too young to provide a calibration point for molecular divergence-time estimates, this fossil is noteworthy as the first macrofossil record of Begonia. It may represent a species that initially arrived from the south via Mexico after the closing of the Central American Straits. We propose that this fossil should stimulate a reexamination of other unidentified fossil winged fruits, as older records of Begonia may be forthcoming.

A non-coding plastid DNA phylogeny of Asian Begonia (Begoniaceae): evidence for morphological homoplasy and sectional polyphyly.

Maximum likelihood and Bayesian analyses of non-coding plastid DNA sequence data based on a broad sampling of all major Asian Begonia sections (ndhA intron, ndhF-rpl32 spacer, rpl32-trnL spacer, 3977 aligned characters, 84 species) were used to reconstruct the phylogeny of Asian Begonia and to test the monophyly of major Asian Begonia sections. Ovary and fruit characters which are crucial in current sectional circumscriptions were mapped on the phylogeny to assess their utility in infrageneric classifications. The results indicate that the strong systematic emphasis placed on single, homoplasious characters such as undivided placenta lamellae (section Reichenheimia) and fleshy pericarps (section Sphenanthera), and the recognition of sections primarily based on a suite of plesiomorphic characters including three-locular ovaries with axillary, bilamellate placentae and dry, dehiscent pericarps (section Diploclinium), has resulted in the circumscription of several polyphyletic sections. Moreover, sections Platycentrum and Petermannia were recovered as paraphyletic. Because of the homoplasy of systematically important characters, current classifications have a certain diagnostic, but only poor predictive value. The presented phylogeny provides for the first time a reasonably resolved and supported phylogenetic framework for Asian Begonia which has the power to inform future taxonomic, biogeographic and evolutionary studies.

Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: implications for morphological and sexual system evolution.

The Cucurbitales are a clade of rosids with a worldwide distribution and a striking heterogeneity in species diversity among its seven family members: the Anisophylleaceae (29-40 species), Begoniaceae (1400 spp.), Coriariaceae (15 spp.), Corynocarpaceae (6 spp.), Cucurbitaceae (800 spp.), Datiscaceae (2 spp.), and Tetramelaceae (2 spp.). Most Cucurbitales have unisexual flowers, and species are monoecious, dioecious, andromonoecious, or androdioecious. To resolve interfamilial relationships within the order and to polarize morphological character evolution, especially of flower sexual systems, we sequenced nine plastids (atpB, matK, ndhF, rbcL, the trnL-F region, and the rpl20-rps12 spacer), nuclear (18S and 26S rDNA), and mitochondrial (nad1 b/c intron) genes (together approximately 12,000 bp) of 26 representatives of the seven families plus eight outgroup taxa from six other orders of the Eurosids I. Cucurbitales are strongly supported as monophyletic and are closest to Fagales, albeit with moderate support; both together are sister to Rosales. The deepest split in the Cucurbitales is that between the Anisophylleaceae and the remaining families; next is a clade of Corynocarpaceae and Coriariaceae, followed by Cucurbitaceae, which are sister to a clade of Begoniaceae, Datiscaceae, and Tetramelaceae. Based on this topology, stipulate leaves, inferior ovaries, parietal placentation, and one-seeded fruits are inferred as ancestral in Cucurbitales; exstipulate leaves, superior ovaries, apical placentation, and many-seeded fruits evolved within the order. Bisexual flowers are reconstructed as ancestral, but dioecy appears to have evolved already in the common ancestor of Begoniaceae, Cucurbitaceae, Datiscaceae, and Tetramelaceae, and then to have been lost repeatedly in Begoniaceae and Cucurbitaceae. Both instances of androdioecy (Datisca glomerata and Schizopepon bryoniifolius) evolved from dioecious ancestors, corroborating recent hypotheses about androdioecy often evolving from dioecy.

Pleistocene and pre-Pleistocene Begonia speciation in Africa.

This paper presents a historical biogeographic analysis of African Begonia based on combined internal transcribed spacer (ITS) and trnL intron sequences. Age range estimates for Begonia in Africa ranged from only 1.5 Ma for some terminal nodes to 27 Ma for basal nodes when the ages of Réunion (2 Ma) andMayotte (5.4 Ma) were used to date the split between Begonia salaziensis and Begonia comorensis. Assuming a more recent origin age for Begonia salaziensis (2 Ma) provided age estimates in other parts of the phylogeny which agreed with patterns observed in other African organisms. A large proportion of the Begonia diversity seen today in Africa is of pre-Pleistocene origin. Species of Pleistocene origin are concentrated in species-rich groups such as sections Loasibegonia, Scutobegonia, and Tetraphila, which have their centre of diversity in western Central Africa. Phylogenetically isolated taxa such as Begonia longipetiolata, Begonia iucunda, and Begonia thomeana date to the late Miocene, a period of extended aridification on the African continent that had severe effects on African rain forest species. A general pattern is identified where phylogenetically isolated species occur outside the main identified rain forest refuges. Endemic species on the island of São Tomé such as Begonia baccata, Begonia molleri, and Begonia subalpestris appear to be palaeoendemics. Of these species, the most recent age estimate is for B. baccata, which is dated at ca. 3 Ma. Therefore, São Tomé appears to have functioned as an important (if previously unrecognised) pre-Pleistocene refuge. On the mainland, areas such as the Massif of Chaillu in Gabon, southern Congo (Brazzaville), and far western areas of Congo (Kinshasa) have played similar roles to São Tomé.