bioRxiv preprint doi: https://doi.org/10.1101/774018; this version posted September 18, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 To be submitted to: Scientific Reports 3 Running title: Plastid phylogenomics of the orchid family 4 5 Plastid phylogenomics of the orchid family: Solving phylogenetic ambiguities 6 within Cymbidieae and Orchidoideae 7 8 Maria Alejandra Serna-Sáncheza,b, Astrid Catalina Alvarez-Yelac, Juliana Arcilaa, Oscar A. Pérez- 9 Escobar d, Steven Dodsworthe and Tatiana Ariasa* 10 11 a Laboratorio de Biología Comparativa. Corporación para Investigaciones Biológicas (CIB), Cra. 12 72 A No. 78 B 141, Medellín, Colombia. 13 b Biodiversity, Evolution and Conservation. EAFIT University, Cra. 49, No. 7 sur 50, Medellín, 14 Colombia 15 c Centro de Bioinformática y Biología Computacional (BIOS). Ecoparque Los Yarumos Edificio 16 BIOS, Manizales, Colombia. 17 d Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3AE, London, UK. 18 e School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK. 19 * Corresponding Author: T.A.: Corporación para Investigaciones Biológicas, Cra. 72 A No. 78 B 20 141, Medellín, Colombia. E-mail:
[email protected] 21 22 All data have been deposited in Bioproject (XXXXXXX) and SRA (XXXXXXX, Appendix 1). 23 24 ABSTRACT 25 Recent phylogenomic analyses have solved evolutionary relationships between most of the 26 Orchidaceae subfamilies and tribes, yet phylogenetic relationships remain unclear within the 27 hyperdiverse tribe Cymbidieae and within the Orchidoideae subfamily. Here we address these 28 knowledge-gaps by focusing taxon sampling on the Cymbidieae subtribes Stanhopeinae, 29 Maxillariinae, Zygopetalinae, Eulophiinae, Catasetinae, and Cyrtopodiinae.