Complete sequence and comparative analysis of the chloroplast genome of Plinia trunciflora

Abstract

Plinia trunciflora is a Brazilian native fruit tree from the Myrtaceae family, also known as jaboticaba. This species has great potential by its fruit production. Due to the high content of essential oils in their leaves and of anthocyanins in the fruits, there is also an increasing interest by the pharmaceutical industry. Nevertheless, there are few studies focusing on its molecular biology and genetic characterization. We herein report the complete chloroplast (cp) genome of P. trunciflora using high-throughput sequencing and compare it to other previously sequenced Myrtaceae genomes. The cp genome of P. trunciflora is 159,512 bp in size, comprising inverted repeats of 26,414 bp and single-copy regions of 88,097 bp (LSC) and 18,587 bp (SSC). The genome contains 111 single-copy genes (77 protein-coding, 30 tRNA and four rRNA genes). Phylogenetic analysis using 57 cp protein-coding genes demonstrated that P. trunciflora, Eugenia uniflora and Acca sellowiana form a cluster with closer relationship to Syzygium cumini than with Eucalyptus. The complete cp sequence reported here can be used in evolutionary and population genetics studies, contributing to resolve the complex taxonomy of this species and fill the gap in genetic characterization.

Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

“…These analyses also revealed that one-half of the codons were used more frequently than expected with an RSCU value > 1, of which all of them ended with A/U. These codon usage patterns were similar to those reported in other angiosperms, possibly due to the high proportion of A/T nucleotides present in chloroplast genomes 60 .…”

In silico analysis of Pinus L. chloroplast DNA to microsatellites regions

“…For Gymnosperm, the size of cpDNA the chloroplast genome is significantly lower than for Angiosperm (XIAO-MING et al, 2017) and, for Eucalyptus spp. and another superior genus, cpDNAs with around 160,000 bp are commonly observed (EGUILUZ et al, 2017;LI et al, 2017;PAIVA et al, 2011;SAINA et al, 2018;STEANE et al, 2005 Regarding the cpSSR regions identified, the majority were classified as mononucleotides. In 31 Eucalyptus species the total number of cpSSRs varied between 71 for Eucalyptus melliodora A. Cunn and 135 for Eucalyptus aromaphloia L.D.Pryor J.H.Willis, superior than we observed to Pinus spp.…”

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

“…Several studies have demonstrated that plastid genome sequences are quite useful tools for phylogenetic inferences (de Santana Lopes et al, 2018a;Machado et al, 2017Machado et al, , 2020Nagel et al, 2020) and investigation of evolutionary events (de Santana Lopes et al, 2018b, Stefenon et al 2019. Plastid genomes of some species of tribe Myrteae (Myrtaceae) have been sequenced (Eguiluz et al, 2017a(Eguiluz et al, , 2017bMachado et al, 2017Machado et al, , 2020Rodrigues et al, 2020) and may assist in understanding the evolution and solving taxonomic uncertainties within this tribe. The taxonomy of Myrteae has been considered particularly difficult (Vasconcelos et al, 2017) due to morphological conservatism, relatively homogeneous flowers, and the rarity of single diagnostic characters for individual clades (Lucas et al, 2019).…”