Supplementary data for MSc Thesis
Creators: name: Ivanov, Plamena
Publisher: name: Zenodo
Year: 2023

description: This repository contains the supplementary data for Plamena Ivanov's Thesis: “Utilizing Next Generation Sequencing data for biodiversity and taxonomy research: a case study in <em>Begonia</em> L.” <strong>1. DNA regions assembled for phylogenetics:</strong> <strong>DNA regions (chloroplast)</strong>: ndhA intron, ndhF-rpl32 spacer, and rpl32-trnL spacer <strong>Reference B. hatacoa</strong> - GenBank accessions: JF756354.1, JF756438.1, and JF756522.1 <strong>DNA regions (nuclear)</strong>: 18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2, and 28S rRNA gene <strong>Reference B. baviensis</strong> - GenBank accession: JF975957.1 <strong>DNA regions (mitochondrial)</strong>: matR gene, nad1 intron and gene, nad7 intron and gene, and rps14-cob spacer <strong>Reference B. chloroneura</strong> - GenBank accessions: GU397184.1, GU397215.1, GU397246.1, and GU397308.1 <strong>DNA regions (chloroplast)</strong>: ndhA intron, ndhF-rpL32 spacer, rpL32-trnL spacer, trnC-ycf6 spacer, ycf6-psbM spacer, and psbM-trnD spacer <strong>Reference B. luzonensis</strong> - GenBank accessions: KR186484.1, KR186571.1, KR186744.1, KR186831.1, KR186918.1, and KR186658.1 <strong>DNA regions (nuclear)</strong>: ITS1, 5.8S rRNA gene, and ITS2 <strong>Reference B. luzonensis</strong> - GenBank accession: KR186988.1 <strong>2. Draft chloroplast genomes:</strong> Begonia sp. - sample <strong>MH5</strong> (Collection number - AR1023) Begonia U192 Martin’s Mystery - sample <strong>MH8 </strong> Begonia U192 Mindanao - sample <strong>MH10</strong> Begonia aff. luzonensis - sample <strong>MH11</strong> Begonia sp. - sample <strong>MH13</strong> (Accession number in (E) - E00891527) <strong>3. BAM/BAI files of the mapped trimmed reads to Begonia hybrid capture bait set (Michel et al., 2022):</strong> <strong>sample MH8</strong> - Begonia U192 ’Martin’s Mystery’ <strong>sample MH9</strong> - Begonia U192 ’Marikina Cultivar’ <strong>sample MH10</strong> - Begonia U192 ’Mindanao Cultivar’ <strong>sample MH11</strong> - B. aff. luzonensis <strong>sample MH17</strong> - Begonia U192 ’Martin’s Mystery’ <strong>sample MH18</strong> - Begonia U192 ’Marikina Cultivar’ <strong>sample MH19</strong> - Begonia U192 ’Mindanao Cultivar’ <strong>sample MH20 </strong>- B. aff. luzonensis Begonia hybrid capture bait set from: <strong>Michel, T., Tseng, Y.-H., Wilson, H. P., Chung, K.-F., and Kidner, C. A. (2022).</strong> “A hybrid capture bait set for Begonia”. In: Edinburgh Journal of Botany 79 (1), pp. 1–14. doi: 10.24823/ejb.2022.409. <strong>4. Maximum likelihood phylogenies and sequence alignments for:</strong> 4.1. Phylogeny based on the concatenated ndhA intron, ndhF- rpl32 spacer, and rpl32-trnL spacer <strong>chloroplast</strong> regions The data for the original alignment are from the following paper: <strong>Moonlight, P. W., Ardi, W. H., Padilla, L. A., Chung, K.-F., Fuller, D., Girmansyah, D., Hollands, R., Jara-Munoz, A., Kiew, R., Leong, W.-C., Liu, Y., Mahardika, A., Marasinghe, L. D., O’Connor, M., Peng, C.-I., Perez, A. J., Phutthai, T., Pullan, M., Rajbhandary, S., Reynel, C., Rubite, R. R., Sang, J., Scherberich, D., Shui, Y.-M., Tebbitt, M. C., Thomas, D. C., Wilson, H. P., Zaini, N. H., and Hughes, M. (2018)</strong>. “Dividing and conquering the fastest growing genus: Towards a natural sectional classification of the mega diverse genus Begonia (Begoniaceae)”. In: TAXON 67 (2), pp. 267–323. doi: 10.12705/672.3. The data for Begonia sagaingensis, B. amnicola, B. mariachristinae, and B. dicressine were shared by Richard Moore (MSc student, RBGE/University of Edinburgh). 4.2.Phylogeny based on the concatenated ndhA intron, ndhF-rpl32 intergenic spacer, rpl32-trnL intergenic spacer, trnC-ycf6 intergenic spacer, ycf6-psbM intergenic spacer, and psbM-trnD intergenic spacer <strong>chloroplast</strong> regions; and phylogeny based on the concatenated ITS1, the 5.8S rRNA gene, and the ITS2 <strong>nuclear</strong> regions. Data for the original alignments are from the following paper: <strong>Hughes, M., Peng, C.-I., Lin, C.-W., Rubite, R., Blanc, P., and Chung, K.-F. (2018)</strong>. “Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species”. In: PLoS ONE 13 (5), e0194877. doi: 10.1371/journal.pone.0194877. 4.3. Phylogeny based on the concatenated ndhA intron, ndhF- rpl32 spacer, and rpl32-trnL spacer <strong>chloroplast</strong> regions, and phylogenybased on the concatenated matR gene, nad1 intron and gene, nad7 intron and gene, and the rps14-cob spacer <strong>mitochondrial</strong> regions. Data for the original alignments are from the following paper: <strong>Begonia Phylogeny Group (2022).</strong> “Resolving Phylogenetic and Taxonomic conflict in Begonia”. In: Edinburgh Journal of Botany. Begonia special issue 79. This paper was compiled by Ardi, W. H., L. Campos-Domínguez, K.-F. Chung, W.-K. Dong, E. Drinkwater, D. Fuller, J. Gagul, G. J. L. Garnett, D. Girmansyah, W. P. Goodall- Copestake, M. Hughes, E. L. Jacques, O. A. Jara-Muñoz, S. Julia, C. A. Kidner, R. Kiew, N. Krishna, R. Li, L. D. K. Marasinghe, M. B. Maw, H. T. Nguyen, H. Q. Nguyen, C. W. L. T. Phutthai, P. W. Moonlight, A. K. Pradeep, S. Rajbhandary, R. R. Rubite, K. Souvannakhoummane, M. Sreenath, M. Tebbitt, D. Scherberich, D. C. Thomas, D. Tian, Y.-H. Tseng, and H. P. Wilson, pp. 1–28. doi: 10.24823/EJB.2022.1928.