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The chloroplast genome of Hancornia speciosa Gomes: structural organization and phylogenomic studies in Rauvolfioideae (Apocynaceae)

  • Elvia Jéssica da Silva Oliveira
  • Andre Marques
  • Cícero AlmeidaEmail author
Original Article
  • 27 Downloads

Abstract

The chloroplast genomes have been utilized in many studies of evolution, population structure and molecular identification. The aim of this study was to assemble the chloroplast genome of Hancornia speciosa Gomes, an economically important fruit species from Brazil, using next-generation sequencing data in order to reconstruct the phylogenetic analysis of Rauvolfioideae. Twenty-four million Illumina short paired-end reads were used for de novo assembly, and the chloroplast contig was identified by BLAST. The chloroplast genome of H. speciosa contains 155,357 bp, with 25,755 bp of inverted repeat A, 25,654 bp of inverted repeat B, 85,702 bp of large single copy and 18,229 bp of small single copy. The coding regions contained 83 genes, eight rRNAs and 36 tRNAs. The phylogenomic analysis reported similar topologies as in previous studies, which used partial chloroplast genomes, and demonstrated that Rauvolfioideae is paraphyletic. In summary, we demonstrated: (1) the first complete chloroplast genome of H. speciosa; (2) phylogenies analyzed using the complete chloroplast genomes revealed a robust phylogenetic topology for Rauvolfioideae; and (3) the phylogenetic analysis showed that the subfamily Rauvolfioideae is paraphyletic.

Keywords

Evolution Mangaba Plastome 

Notes

Acknowledgements

We would like to thank the Federal University of Alagoas for the laboratories and scientific support, the Fundação de Apoio à Pesquisa de Alagoas (FAPEAL) for funding this Project, and the National Council for the Improvement of Higher Education (CAPES).

Author contributions

EJSO performed the DNA library, de novo assembles. AM and CA analyzed data and wrote the manuscript.

Compliance with ethical standards

Conflicts of interest

The authors declare that they have no conflicts of interest.

Supplementary material

40415_2019_549_MOESM1_ESM.tiff (33 mb)
Fig. S1 Molecular phylogenetic analysis by the maximum likelihood method, with supported values estimated by bootstrap. (A) Phylogenetic tree using complete chloroplast genome and rcbL gene; (B) Phylogenetic tree using complete chloroplast genome and rcbL + matK genes; (C) Phylogenetic tree using complete chloroplast genome and rcbL + matK + trnH-psbA (TIFF 33,752 kb)

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Copyright information

© Botanical Society of Sao Paulo 2019

Authors and Affiliations

  1. 1.Laboratory of Genetics Resources, Campus de ArapiracaUniversidade Federal de AlagoasArapiracaBrazil

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