Structural and evolutive features of the Plinia phitrantha and P. cauliflora plastid genomes and evolutionary relationships within tribe Myrteae (Myrtaceae).

Lilian De Oliveira Machado,Leila Do Nascimento Vieira,Rubens Onofre Nodari,Valdir Marcos Stefenon

doi:10.1590/1678-4685-gmb-2021-0193

Lilian De Oliveira Machado, Leila Do Nascimento Vieira + Show 2 more

Open Access

https://doi.org/10.1590/1678-4685-gmb-2021-0193

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Abstract

Plinia phitrantha and P. cauliflora are Myrtaceae species with recognized horticultural and pharmacological potential. Nevertheless, studies on molecular genetics and the evolution of these species are absent in the literature. In this study, we report the complete plastid genome sequence of these species and an analysis of structural and evolutive features of the plastid genome within the tribe Myrteae. The two plastid genomes present the conserved quadripartite structure and are similar to already reported plastid genomes of Myrteae species concerning the size, number, and order of the genes. A total of 69-70 SSR loci, 353 single nucleotide polymorphisms, and 574 indels were identified in P. phitrantha and P. caulifora. Observed evolutive features of the plastid genomes support the development of programs for the conservation and breeding of Plinia. The phylogenomic analysis based on the complete plastid genome sequence of 15 Myrteae species presented a robust phylogenetic signal and evolutive traits of the tribe. Ten hotspots of nucleotide diversity were identified, evidence of purifying selection was observed in 27 genes, and relative conservation of the plastid genomes was confirmed for Myrteae. Altogether, the outcomes of the present study provide support for planning conservation, breeding, and biotechnological programs for Plinia species.

Highlights

Several studies have demonstrated that plastid genome sequences are quite useful tools for phylogenetic inferences (de Santana Lopes et al, 2018a; Machado et al, 2017, 2020; Nagel et al, 2020) and investigation of evolutionary events
Several studies have demonstrated that plastid genome sequences are quite useful tools for phylogenetic inferences and investigation of evolutionary events
The scarcity of genetic and genomic resources for species of minor economic importance but with high cultural and ecological value is one of the main struggles towards conserving genetic resources and evolutionary history understanding. This is true for Myrteae, which has a few species with significant genetic and genomic resources available

Summary

Introduction

Several studies have demonstrated that plastid genome sequences are quite useful tools for phylogenetic inferences (de Santana Lopes et al, 2018a; Machado et al, 2017, 2020; Nagel et al, 2020) and investigation of evolutionary events (de Santana Lopes et al, 2018b, 2019, Stefenon et al 2019). Plastid genomes of some species of tribe Myrteae (Myrtaceae) have been sequenced (Eguiluz et al, 2017a, 2017b; Machado et al, 2017, 2020; Rodrigues et al, 2020) and may assist in understanding the evolution and solving taxonomic uncertainties within this tribe. The plastid genomes of P. phitrantha and P. cauliflora were compared based on structural features, gene content, single nucleotide polymorphisms (SNPs), insertionsdeletions (indels), synonymous (Ks) and nonsynonymous (Ka) substitution rates, and the Ka/Ks ratio.

Results

Conclusion