Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

Michelle Zavala-Páez, Leila do Nascimento Vieira, Valter Antônio de Baura, Eduardo Balsanelli, Emanuel Maltempi de Souza, Marco Cerna Cevallos, Mark W. Chase, Eric de Camargo Smidt

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Abstract

Pantropical Bulbophyllum, with ∼2,200 species, is one of the largest genera in Orchidaceae. Although phylogenetics and taxonomy of the ∼60 American species in the genus are generally well understood, some species complexes need more study to clearly delimit their component species and provide information about their evolutionary history. Previous research has suggested that the plastid genome includes phylogenetic markers capable of providing resolution at low taxonomic levels, and thus it could be an effective tool if these divergent regions can be identified. In this study, we sequenced the complete plastid genome of eight Bulbophyllum species, representing five of six Neotropical taxonomic sections. All plastomes conserve the typical quadripartite structure, and, although the general structure of plastid genomes is conserved, differences in ndh-gene composition and total length were detected. Total length was determined by contraction and expansion of the small single-copy region, a result of an independent loss of the seven ndh genes. Selection analyses indicated that protein-coding genes were generally well conserved, but in four genes, we identified 95 putative sites under positive selection. Furthermore, a total of 54 polymorphic simple sequence repeats were identified, for which we developed amplification primers. In addition, we propose 10 regions with potential to improve phylogenetic analyses of Neotropical Bulbophyllum species.

Original languageEnglish
Article number799
JournalFrontiers in Plant Science
Volume11
DOIs
StatePublished - 3 Jul 2020

Bibliographical note

Funding Information:
We thank Sistema de Autoriza??o e Informa??o em Biodiversidade/Instituto Chico Mendes de Conserva??o da Biodiversidade (SISBIO/ICMBio) for the collecting permits and the Universidad Polit?cnica Salesiana for the financial support. ECS would like to thank Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq) for grant Bolsa de Produtividade em Pesquisa CNPq-N?vel 2 (proc.311001/2014-9, 308460/2017-0) and Pos-doc grant (proc. 203304/2018-7) and Brazilian Program of National Institutes of Science and Technology-INCT/Brazilian Research Council-CNPq/MCT. Ana Victoria Mauad is thanked for her help in the lab and phylogenetic analyses.

Publisher Copyright:
© Copyright © 2020 Zavala-Páez, Vieira, Baura, Balsanelli, Souza, Cevallos, Chase and Smidt.

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

Keywords

  • molecular evolution
  • molecular markers
  • Neotropical orchids
  • next-generation sequencing
  • plastid genome

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