Title:Complete Chloroplast Genomes of Pterodon emarginatus Vogel and
Pterodon pubescens Benth: Comparative and Phylogenetic Analyses
Volume: 24
Issue: 4
Author(s): Juliana Borges Pereira Brito*, Adriana Maria Antunes, Ramilla dos Santos Braga Ferreira, Mariana Pires de Campos Telles, Cíntia Pelegrineti Targueta and Thannya Nascimento Soares
Affiliation:
- Laboratory of Genetics and Biodiversity, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás,
CEP: 74001-970 Brazil
- Postgraduate Program in Genetics and Plant Breeding, School of Agronomy, Federal
University of Goiás, Goiânia, Goiás, Brazil
Keywords:
Comparative genomics, gene annotation, molecular markers, pterodon, semi-independent organelle, chloroplast genomes.
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%.
