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A Genomic Approach for Isolating Chloroplast Microsatellite Markers for Pachyptera kerere (Bignoniaceae)

Francisco, Jessica N. C., Nazareno, Alison G., Lohmann, Lúcia G.
Applications in plant sciences 2016 v.4 no.9
Bignoniaceae, alleles, chloroplast genome, chloroplasts, genetic markers, genetic variation, genomics, haploidy, intergenic DNA, loci, phylogeography, population structure
Premise of the study: In this study, we developed chloroplast microsatellite markers (cpSSRs) for Pachyptera kerere (Bignoniaceae) to investigate the population structure and genetic diversity of this species.Methods and Results: We used Illumina HiSeq data to reconstruct the chloroplast genome of P. kerere by a combination of de novo and reference-guided assembly. We then used the chloroplast genome to develop a set of cpSSRs from intergenic regions. Overall, 24 primer pairs were designed, 21 of which amplified successfully and were polymorphic, presenting three to nine alleles per locus. The unbiased haploid diversity per locus varied from 0.207 (Pac28) to 0.817 (Pac04). All but one locus amplified for all other taxa of Pachyptera.Conclusions: The markers reported here will serve as a basis for studies to assess the genetic structure and phylogeographic history of Pachyptera.