The complete chloroplast genome sequences of three Spondias species reveal close relationship among the species

Abstract

This study reports the complete chloroplast sequences of three Spondias species. The genome sequences were obtained for Spondias tuberosa, Spondias bahienses, and Spondias mombin using the Illumina sequencing technology by a combination of de novo methods and a reference-guided assembly using Sapindus mukorossi as reference. The genomes of S. tuberosa, S. bahiensis, and S. mombin had 162,036, 162,218, and 162,302 bp, respectively. The coding regions exhibited 130 genes, including 34–35 tRNAs and 4 rRNAs. The results revealed synteny among the genomes, with high conservation in the gene order and content and CG content. The inverted repeat regions (IRA and IRB) and the large and small single copies were very similar among the three genomes. The phylogenomic analysis reported similar topologies as that of previous studies, which used partial chloroplast, wherein S. mombin was the first diverging lineage, while S. tuberosa and S. bahiensis were derived, indicating that the phylogenetic analysis using partial or complete genome produces similar results. In summary, (1) we presented the first complete chloroplast genome for the genus Spondias, (2) phylogenies analyzed using the complete chloroplast genomes revealed a robust phylogenetic topology for Spondias, and (3) gene order, content, and orientation in Spondias are highly conserved.

The chloroplast genome sequence of Dipteryx alata Vog. (Fabaceae: Papilionoideae): genomic features and comparative analysis with other legume genomes

“…Sequences of cp genomes have been widely used in the development of molecular markers (Liu et al 2019). Therefore, choroplast genes sequences, intergenic spacer fragments and microsatellites are useful in phylogenetic studies, population genetics, phylogeography and species identification (Santos and Almeida 2019;Song et al 2019;Yang et al 2019). Comparative analysis of the complete genome of different species is, also, useful to understand the evolution of the structure of the genomes (Yang et al 2019).…”

Biometry in Umbu fruits from the semi-arid region of Paraiba

“…From this perspective, the characterization of umbu accessions with regard to their fruits and endocarps contributes to subsidizing the identification of genotypes and their genetic variability, in addition to determining cultivars with the potential for immediate use by producers and defining which genotypes have desirable characteristics for the genetic improvement of the species and associated studies (FRANÇA et al, 2019;SANTOS;ALMEIDA, 2019;BARROS, 2020;SANTOS et al, 2020).…”

The Spondias mombin (Anarcadiaceae): molecular characterization and conservation

“…Recently, some studies have contributed to the characterization of the Spondias genus through molecular phylogeny (Silva et al, 2015;Machado et al, 2015), and much information is now available in GenBank. For S. mombin, the assembly of the complete chloroplast genome (Santos & Almeida, 2019) and its mitochondria (Martins et al, 2019) has already been obtained. The genetic diversity of S. mombin has been evaluated by means of isoenzymes (Gois et al, 2009), morphological traits of the fruits (Silva et al, 2017a), molecular markers, RAPD (Lima et al, 2011) and ISSR (Silva et al, 2017b).…”