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

Lilian De Oliveira Machado,Miguel Pedro Guerra,Fábio De Oliveira Pedrosa,Valdir Marcos Stefenon,Helisson Faoro,Rubens Onofre Nodari,Leila Do Nascimento Vieira

doi:10.1590/1678-4685-gmb-2018-0377

Lilian De Oliveira Machado, Miguel Pedro Guerra + Show 5 more

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https://doi.org/10.1590/1678-4685-gmb-2018-0377

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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.

Highlights

Plastidial genomes are useful tools to perform comparative analyses associated with phylogenetic and evolutionary studies
After trimming a total of 3,228,689 reads were mapped in aligned pairs with mean length of 147.52 bp, generating a total of 58,815,423 bp, which were used for the de novo assembly
The difference between the C. xanthocarpa plastome and the plastomes of the other species included in this study, which ranged from 314 bp to 2,940 bp, was due to indels occurring in intergenic regions of both, inverted repeat regions (IRs) and LSC regions of all species, except for P. dioica (Table 1)

Summary

Introduction

Plastidial genomes (plastomes) are useful tools to perform comparative analyses associated with phylogenetic and evolutionary studies. The relatively small size, mostly uniparental inheritance, high gene synteny, and elevated copy number in green plant cells are the main characteristics that make plastids useful for such studies. Plastome sizes range from 70 to 218 Kbp (Xiao-Ming et al, 2017) and typically present a quadripartite structure with two inverted repeat regions (IRs) divided between the large (LSC) and the small (SSC) single-copy regions (Bock, 2007). The plastome contains essential genes in conserved open reading frames (ORFs). Some plastidial ORFs have unknown function and are called hypothetical chloroplast open reading frame (ycf). The largest plastome coding sequence (ORF2280 or ycf2) encodes a plastidial protein (Glick and Sears, 1993) whose function has been hypothesized to exhibit similarities with fstH, such as ATPase-related activities, chaperone function, and activity associated with cell division (Wolfe, 1994)

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