In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta-and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.

The Pinus genus covers a wide variety of widely cultivated species due to adaptability, high growth and wood quality. Molecular markers have been used for many genetic analyses, and among them, the microsatellite markers (SSR) have several applications and can be found in chloroplast genome (cpDNA) as well as in nuclear genomes (ntDNA). The chloroplast microsatellites markers (cpSSR) can be used for gene flow analysis, identification of hybrids,clones, paternity tests, genetic diversity studies, phylogenetic analysis, among others. The work aimed to characterize the cpSSRs of Pinus species with cpDNA sequenced and deposited in NCBI (National Center for Biotechnology Information). In the twenty species of Pinus spp. studied, 1.542 cpSSRs were identified, with 86,45% of mononucleotide type, and the less frequent the penta-(1.10%) and hexanucleotide (1.04%) types. Predominated cpSSRs in non-coding regions (intergenic). The results indicate presence of a wide range of cpSSR for Pinus spp., which can subsidize breeding programs of interesting species.