Characterization of the complete chloroplast genome of Prosopis tamarugo (Prosopis, Leguminosae), an endangered endemic tree species from the Atacama Desert

Abstract

Prosopis tamarugo (Prosopis, Sect. Strombocarpa) is an important endangered tree species from the Atacama Desert (Chile). However, this species requires urgent conservation measures, for which it is necessary to evaluate their genetic diversity. Here, we present the characterization of the complete chloroplast genome of P. tamarugo; the first complete chloroplast of a species from the Strombocarpa section, obtained by next generation sequencing (NGS) methods. The complete chloroplast contains 161,575 bp and a total of 129 genes. A phylogenetic analysis of four Prosopis plastomes revealed that P. tamarugo is a sister species of the other Prosopis species albeit having smaller chloroplast sequence compared to those of other Prosopis species. Nine DNAcp markers were detected to distinguish between haplotypes. Therefore, the chloroplast sequence of P. tamarugo could be highly valuable for upcoming phylogenetic studies.

Comparative analysis of the complete plastid genomes of desert trees Neltuma and Strombocarpa genera

“…However, the Strombocarpa species presented slightly more GC content (36.0%-36.2%) compared to the Neltuma species (35.9%). These GC values fall within the limit of variation registered in others studies 25,57 . Furthermore, a study about several orchid species, showed that the species with a smallest chloroplast size (Pholidota cantonensis, 158,786 bp), had a highest GC content (37.47%) 59 , similar to our observations.…”

“…The chloroplast of N. alba and N. chilensis showed similar values for genome size and the number of genes compared to Neltuma juli ora and Neltuma glandulosa described by Asaf 57 , ~ 163.000 bp for both, while the number of genes varied between 131 and 128. The number of genes was similar between the Neltuma and Strombocarpa genera, although S. tamarugo lost the gene psbL (remaining with 127 genes only) 25 . The absence of the psbL gene has been observed in some other eudicots, magnoliids, and monocots as well 58 .…”

“…The absence of the psbL gene has been observed in some other eudicots, magnoliids, and monocots as well 58 . The genome sizes of S. strombulifera (160,569 bp) and S. tamarugo (161,575 bp) were smaller compared to the Neltuma species (~ 163.000 bp) 25 . However, the Strombocarpa species presented slightly more GC content (36.0%-36.2%) compared to the Neltuma species (35.9%).…”

“…Lately, the use of complete chloroplast genome as a "super-barcoding" method has become an excellent approach allowing for the increase of the phylogenetic resolution at lower taxonomic levels in plants 19,20 . However, in the Atacama Desert only a few plastomes of the native and endemic herbaceous plants 21,22 , shrubs 23,24 and leguminous trees 25,26 have been characterized so far.…”

Structure, gene composition, divergence time and phylogeny analysis of the woody desert species Neltuma alba, Neltuma chilensis and Strombocarpa strombulifera

“…The number of genes was similar between the Neltuma and Strombocarpa genera. Although S. tamarugo was thought to have lost the gene psbL (remaining with 127 genes only) 24 , we performed a new sequence annotation and finally found the reading frame of the gene. The genome sizes of S. strombulifera (160,569 bp) and S. tamarugo (161,575 bp) were smaller compared to the Neltuma species (~ 163.000 bp) 24 .…”