Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene

Abstract

Plastomes are very informative structures for comparative phylogenetic and evolutionary analyses. We sequenced and analyzed the complete plastome of Campomanesia xanthocarpa and compared its gene order, structure, and evolutionary characteristics within Myrtaceae. Analyzing 48 species of Myrtaceae, we identified six genes representing`hotspots' of variability within the plastomes (ycf2, atpA, rpoC2, pcbE, ndhH and rps16), and performed phylogenetic analyses based on: (i) the ycf2 gene, (ii) all the six genes identified as`hotspots' of variability, and (iii) the genes identified as`hotspots' of variability, except the ycf2 gene. The structure, gene order, and gene content of the C. xanthocarpa plastome are similar to other Myrtaceae species. Phylogenetic analyses revealed the ycf2 gene as a promissing region for barcoding within this family, having also a robust phylogenetic signal. The synonymous and nonsynonymous substitution rates and the Ka/Ks ratio revealed low values for the ycf2 gene among C. xanthocarpa and the other 47 analyzed species of Myrtaceae, with moderate purifying selection acting on this gene. The average nucleotide identity (ANI) analysis of the whole plastomes produced phylogenetic trees supporting the monophyly of three Myrtaceae tribes. The findings of this study provide support for planning conservation, breeding, and biotechnological programs for this species.

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

“…The regions LSC, SSC, and IR presented 34.8%; 30.8%, and 42.7% of the GC content respectively. These sizes are similar to those already sequenced for other species of tribe Myrteae (Eguiluz et al, 2017a(Eguiluz et al, , 2017bMachado et al, 2017Machado et al, , 2020Rodrigues et al, 2020;Table S1). A total of 112 different genes were identified: 78 protein-coding, 30 tRNA genes, and four rRNA genes (Table 1).…”

“…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).…”

Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies

“…Although matK and ndhF individually support the grouping of Syzygieae and Myrteae, the concatenation of these regions with rpl16 and six plastid intergenic regions (psbA-trnH, trnL-trnF, trnQ-rps16, rpl32-trnL) show a wellsupported relationship between Eucalypteae and Syzygieae (Vasconcelos et al, 2017). Previous works based on limited sampling, focused mostly in the description of Myrtaceae and Lythraceae chloroplast genomes, also present phylogenies that support a closer relationship between Syzygieae and Eucalypteae (Eguiluz et al, 2017a,b;Gu et al, 2019;Liu et al, 2019;Liu et al, 2020;Machado et al, 2020), reinforcing our results with analyses based on protein-coding genes and whole chloroplast genomes. Yet, when S. jambos is included in our analysis, along with two species from the tribe Melaleuceae (Figure S8), the grouping of Syzygieae and Eucalypteae is recovered.…”

Comparative analysis of the structure of complete chloroplast genomes in genus Mangifera and accuracy verification about phylogenetic analysis based on gene ycf2 in genus level

“…It meant that it could be possible to use gene ycf 2 confirmed relationship when we could not obtain the complete chloroplast genome. In Dr. Machado’s study, they used the same method, which used the gene ycf 2 in phylogenetic analysis, to construct the phylogenetic tree among the family Myrtaceae and got the same result to the result based on the complete cp genome and protein-coding genes [45]. So, this result could support Dr. Machado’s study at the family level.…”