INSIGHTS INTO THE EVOLUTION OF THE CHLOROPLAST GENOME AND THE PHYLOGENY OF BEGONIA

Authors

  • Y.-H. Tseng Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115201, Taiwan./Department of Life Sciences, National Chung Hsing University, 145 Xingda Road, South District, Taichung City 402202, Taiwan. https://orcid.org/0000-0002-8166-5690
  • C.L. Hsieh Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115201, Taiwan. https://orcid.org/0000-0002-3342-3654
  • L. Campos-Domínguez Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK./ Institute of Molecular Plant Sciences, Rutherford Building, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3BF, Scotland, UK./ Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3FL, Scotland, UK. https://orcid.org/0000-0002-8998-3394
  • A.Q. Hu Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115201, Taiwan./Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, England, UK. https://orcid.org/0000-0001-9564-878X
  • C.C. Chang Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115201, Taiwan. https://orcid.org/0000-0002-3035-7348
  • Y. T. Hsu Department of Life Sciences, National Cheng Kung University, 1 University Road, Tainan 701401, Taiwan. https://orcid.org/0000-0002-6862-4747
  • C.A. Kidner Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK./ Institute of Molecular Plant Sciences, Rutherford Building, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3BF, Scotland, UK. https://orcid.org/0000-0001-6426-3000
  • M. Hughes Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK. https://orcid.org/0000-0002-2168-0514
  • P.W. Moonlight Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK. https://orcid.org/0000-0003-4342-2089
  • C.H. Hung Department of Life Sciences, National Cheng Kung University, 1 University Road, Tainan 701401, Taiwan.
  • Y.C. Wang School of Forestry and Resource Conservation, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106319, Taiwan. https://orcid.org/0000-0002-6544-3473
  • Y.T. Wang Department of Horticulture, National Chung Hsing University, 145 Xingda Road, Taichung 402202, Taiwan. https://orcid.org/0000-0003-3668-219X
  • S.H. Liu Department of Biological Sciences, National Sun-Yat-sen University, 70 Lienhai Road, Kaohsiung 804201, Taiwan. https://orcid.org/0000-0002-5429-6869
  • D. Girmansyah https://orcid.org/0000-0002-3096-8763
  • K.-F. Chung Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115201, Taiwan. https://orcid.org/0000-0003-3628-2567

DOI:

https://doi.org/10.24823/ejb.2022.408

Keywords:

Begonia, Begoniaceae, Hillebrandia, IR expansion, Plastome, Species barcode

Abstract

Begonia (Begoniaceae) is one of the largest angiosperm genera, comprising more than 2000 species; this makes it ideal as a model to investigate the genomic basis of species radiations. Here we present the results of the first genus-wide comparative study of plastid genome structure, sequence diversity, and phylogenetics of Begoniaceae, in which 44 complete Begoniaceae plastomes, including those of Begonia’s sister group, Hillebrandia, a monotypic genus endemic to Hawai‘i, and 43 species representing 42 sections of Begonia, were assembled. Our results reveal that Begoniaceae plastome size ranges from 167,123 to 170,852 bp, displaying the typical quadripartite structure. Structures of most Begoniaceae plastomes are highly conserved but differ from the plastomes of the majority of angiosperms in having a unique inverted repeat (IR) expansion, from IRa to large single copy (LSC), resulting from a duplicated fragment of the trnH–GUG gene to the trnR–UCU gene. Additionally, comparison between plastomes of Hillebrandia and Begonia shows that the former genus has fewer simple sequence repeats than most Begonia species analysed, suggesting that species of Begonia have more repetitive and dynamic plastomes than those of its sister genus. We also identified six highly variable regions suitable for phylogenetic analysis and as potential DNA barcodes for species identification. Our robust hypothesis of plastome phylogenomic relationships provides new insights into infrageneric classification and highlights potential classification issues in Begonia

A gene map of Begonia and Hillebrandia

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Published

2022-08-18

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Section

Original Research Articles