Begoniaceae

Tseng, Yu-Hsin, Hsieh, Chia-Lun, Campos-Domínguez, Lucia, Hu, Ai-Qun, Chang, Chiung-Chih, Hsu, Yu-Ting, Kidner, Catherine Anne, Hughes, Mark, Moonlight, Peter, Hung, Cheng-Hsiang, Wang, Yen-Chiao, Wang, Yi-Tse, Liu, Shih-Hui, Girmansyah, Deden & Chung, Kuo-Fang, 2022, INSIGHTS INTO THE EVOLUTION OF THE CHLOROPLAST GENOME AND THE PHYLOGENY OF BEGONIA, Edinburgh Journal of Botany 79 (408), pp. 1-32 : 2-4

Plastomes in Begoniaceae

Begonia L. ( Begoniaceae ) is one of the largest angiosperm genera, and comprises more than 2000 species divided among 70 sections (Hughes et al., 2015–; Moonlight et al., 2018). It is distributed worldwide in tropical and subtropical Asia, Africa and the Americas ( Tebbitt, 2005; Dewitte et al., 2011). The high species diversity of Begonia is in contrast to its sister genus, Hillebrandia Oliv. , which is monotypic ( Hillebrandia sandwicensis Oliv. ) and the only taxon of the Begoniaceae native to the Hawaiian Islands ( Clement et al., 2004). Begonia exhibits a large range of morphological diversity, particularly with respect to leaf shape, colour and variegation. As a megadiverse, pantropically distributed genus, Begonia provides an excellent system for investigating the processes and patterns underlying the generation of biodiversity. To gain insight into the potential role that the plastid genome plays in species differences, a comparative analysis of plastome structure and repeat content was required.

9 Department of Horticulture, National Chung Hsing University, 145 Xingda Road, Taichung 402202, Taiwan.

10 Department of Biological Sciences, National Sun-Yat-sen University, 70 Lienhai Road, Kaohsiung 804201, Taiwan.

11 Research Center for Biosystematics and Evolution, Research Organization for Life Science and Environment, National Research and Innovation Agency (BRIN), Cibinong Science Center, Jalan Raya Jakarta Bogor, Km 46, Cibinong, West Java, 16911, Indonesia.

In addition to the knowledge of plastome structure and variation, a stable and natural infrageneric classification is required as a basis for studies investigating the factors influencing speciation in Begonia (Moonlight et al., 2018) . However, Begonia taxonomy is remarkably challenging because of the large number of species and the poor preservation of morphological features in specimens ( Hughes & Girmansyah, 2011; Chung et al., 2014).

To date, extensive phylogenetic studies of Begonia and the Begoniaceae have been carried out, examining biogeography, species delimitation, sectional assignment and population genetics. Such studies are generally based on plastid sequences, because nuclear DNA phylogenies provide insufficient resolution, due to substitution saturation across the genus and phylogenetic incongruence derived from frequent natural hybridisation (Moonlight et al., 2018).

Earlier works used plastid sequences from the trnL intron ( Plana, 2003; Plana et al.,

2004; in combination with nrITS) and the rbcL region ( Clement et al., 2004; Goodall-Copestake et al., 2009; in combination with the nrITS and 18S rRNA gene, respectively) to evaluate sectional delimitation, divergence time and biogeographical patterns. The results of a subsequent phylogenetic study of Begonia using five plastid sequences (trnK intron/ matK gene, petB–petD spacer, psbB gene, psbC–trnS spacer and trnL intron) with five mitochondrial sequences (cox1 gene, matR gene, nad1 gene, nad7 gene and rps14–cob spacer) suggested that extant Begonia lineages first diversified in Africa and that the closest African relatives of the American and Asian Begonia are seasonally dry adapted species ( Goodall-Copestake et al., 2010).

Later, Thomas et al. (2011) successfully amplified three highly variable plastid sequences (ndhA intron, ndhF–rpl32 spacer and rpl32–trnL spacer) to reconstruct the first supported phylogenetic framework for Asian Begonia . Moonlight et al. (2018) also utilised these three plastid markers, with a more comprehensive taxon sampling including 574 species of Begonia , to establish the first sectional classification based on phylogenetic data, in which 70 sections of Begonia were recognised. Additionally, more plastid markers have been applied for species-level phylogenetic studies in Begonia sect. Coelocentrum (rpl16 intron with nrITS; Chung et al., 2014); hybridisation detection and biogeography in Begonia sect. Baryandra (trnC–trnD spacer with ndhA intron, ndhF–rpl32 spacer and rpl32–trnL spacer; Hughes et al., 2015, 2018); identification of the first natural hybrid in Begonia sect. Petermannia (trnL–trnF spacer with nrITS; Liu et al., 2019); and population genetics in Begonia luzhaiensis T.C.Ku (trnC–ycf6 spacer; Tseng et al., 2019).

In summary, 13 plastid genes or spacer sequences have been utilised in studies of Begonia and Begoniaceae . Although these phylogenetic studies have provided sufficient resolution at the sectional level, resolution at the species level in most sections has proven recalcitrant ( Harrison et al., 2016).

Harrison et al. (2016) first attempted to assemble plastomes of 16 species of Begonia using long-range PCR, but only one nearly complete plastome assembly ( B. peltata Otto

& A.Dietr.) was successfully generated. Subsequently, five additional complete plastomes of Asian Begonia were reported ( Dong et al., 2019; Fan et al., 2019; Huang & Wang, 2020; Zhou et al., 2020; Wang et al., 2021) based on the high-copy fraction of plastome sequences using the NGS genome skimming method ( Straub et al., 2012). The sizes of these plastome assemblies ranged from 157,648 to 169,436 bp, and they have a typical quadripartite structure ( Dong et al., 2019; Fan et al., 2019; Huang & Wang, 2020; Zhou et al., 2020; Wang et al., 2021). Recently, Shui et al. (2019) used 115 taxa covering 98 species of Begonia to establish the first plastome phylogeny in the genus, based on which a new infrageneric classification was proposed, although the plastome sequences were not released. However, so far, no comparative study of Begonia plastid sequence diversity and structure has been carried out. Furthermore, there has to date been no analysis of plastid sequence diversity to inform the choice of appropriate phylogenetic markers in Begonia .

In the present study, we report complete plastomes of Hillebrandia sandwicensis and

43 species of Begonia , representing 42 of the 70 sections recognised by Moonlight et al. (2018). Using these data, we aimed to: (i) characterise and compare plastome structure and gene organisation; (ii) identify putative repeated regions; (iii) identify candidate molecular markers for further phylogenetic analyses; and (iv) reconstruct plastome phylogenomic relationships to improve our understanding of plastome characteristics, structural diversity and evolution in Begoniaceae .