Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses

Juliana Borges Pereira Brito; Adriana Maria Antunes; Ramilla Dos Santos Braga Ferreira; Mariana Pires de Campos Telles; Cintia Pelegrineti Targueta; Thannya Nascimento Soares

doi:10.2174/0113892029244147231016050434

Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses

Curr Genomics. 2023 Dec 12;24(4):236-249. doi: 10.2174/0113892029244147231016050434.

Authors

Juliana Borges Pereira Brito^{1

2}, Adriana Maria Antunes^{1

2}, Ramilla Dos Santos Braga Ferreira¹, Mariana Pires de Campos Telles^{1

3}, Cintia Pelegrineti Targueta¹, Thannya Nascimento Soares^{1

2}

Affiliations

¹ Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, CEP: 74001-970 Brazil.
² Postgraduate Program in Genetics and Plant Breeding, School of Agronomy, Federal University of Goiás, Goiânia, Goiás , Brazil.
³ School of Medical and Life Sciences, Pontifical Catholic University of Goiás, Goiânia, Goiás, CEP: 74605-010 Brazil.

PMID: 38169762
PMCID: PMC10758126 (available on 2024-06-12)
DOI: 10.2174/0113892029244147231016050434

Abstract

Background: The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity.

Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.

Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.

Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens. The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.

Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.

Keywords: Comparative genomics; chloroplast genomes; gene annotation; molecular markers; pterodon; semi-independent organelle.