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Aims of the study: Phreatophyte species of the Prosopis genus are very important to natural ecosystems in Africa, South America and Asia due to their uses as food and seed sources and in agroforestry. In this research, through next-generation sequencing, we sought to search for and develop SSR markers in Prosopis tamarugo, in addition to assessing their transferability to other species in the Strombocarpa section.Area of study: The study was carried out in species of the Strombocarpa section collected in the “Pampa del Tamarugal”, located in the Atacama Desert (Chile); which is considered the driest and oldest desert on Earth.Materials and methods: The next-generation sequencing for the development of simple sequence repeat (SSR) or microsatellite loci for genetic research in P. tamarugo and their transferability in Prosopis burkartii and Prosopis strombulifera was used.Main results: A total of ~90.000 microsatellite loci in P. tamarugo were found, and a set of 43 primer pairs was used for validating SSR locus amplification. We found a large difference in the percentage of amplified SSR markers between species of the Strombocarpa and Algarobia sections.Research highlights: The present study provides for the first time 24 polymorphic SSR markers for species in the Strombocarpa section, which could be a useful tool for estimating genetic structure, developing breeding programs, quantifying genetic diversity and performing population studies.Keywords: Strombocarpa section; Prosopis tamarugo; Atacama Desert; microsatellites; NGS.

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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.

Sporadic rains in the Atacama Desert reveal a high biodiversity of plant species that only occur there. One of these rare species is the “Red añañuca” ( Zephyranthes phycelloides ), formerly known as Rhodophiala phycelloides . Many species of Zephyranthes in the Atacama Desert are dangerously threatened, due to massive extraction of bulbs and cutting of flowers. Therefore, studies of the biodiversity of these endemic species, which are essential for their conservation, should be conducted sooner rather than later. There are some chloroplast genomes available for Amaryllidaceae species, however there is no complete chloroplast genome available for any of the species of Zephyranthes subgenus Myostemma . The aim of the present work was to characterize and analyze the chloroplast of Z. phycelloides by NGS sequencing. The chloroplast genome of the Z. phycelloides consists of 158,107 bp, with typical quadripartite structures: a large single copy (LSC, 86,129 bp), a small single copy (SSC, 18,352 bp), and two inverted repeats (IR, 26,813 bp). One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. The number of SSRs was 64 in Z. phycelloides and a total of 43 repeats were detected. The phylogenetic analysis of Z. phycelloides shows a distinct subclade with respect to Z. mesochloa . The average nucleotide variability ( Pi ) between Z. phycelloides and Z. mesochloa was of 0.02000, and seven loci with high variability were identified: psbA , trnS GCU -trnG UCC , trnD GUC -trnY GUA , trnL UAA -trnF GAA , rbcL, psbE-petL and ndhG-ndhI . The differences between the species are furthermore confirmed by the high amount of SNPs between these two species. Here, we report for the first time the complete cp genome of one species of the Zephyranthes subgenus Myostemma , which can be used for phylogenetic and population genomic studies.

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Bomarea ovallei (Phil.) Ravenna (2n=2x=18) is an endangered endemic species that inhabits only a small part of the coast of the Atacama region. We describe the structure, gene composition and phylogeny of the complete chloroplast sequence of this elusive species. The chloroplast genome consists of 155,018 bp, with typical quadripartite structures: a large single copy region (LSC) of 84,132 bp, a small single copy region (SSC) of 17,794 bp, and two inverted repeat regions (IRs) contain 26,546 bp. One hundred and thirty-four genes were identified out of which 84 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. B. ovallei chloroplast resembles chloroplasts from seven species of the order Liliales in length and structure and is most similar to Bomarea edulis (BP=100). The average nucleotide variability (Pi) of 0.00254 between these two Bomarea species is moderate. Nine loci with increased variability were identified: rps16-trnQ, atpF, trnL, ndhC-trnV, rbcL, psbJ, rpl32-trnL, ndhD and ycf1. These loci could be used as DNA markers for classification and evaluation studies in Bomarea populations.