# Phylogeny, structural patterns, and polymorphisms in Dyckia spp. from the Espinhaço mountain range based on complete chloroplast genome

## TL;DR

This study analyzes the chloroplast genomes of six rare Dyckia bromeliad species to identify genetic markers for species identification and conservation.

## Contribution

The study identifies specific polymorphic regions and structural features in Dyckia chloroplast genomes that can serve as molecular markers.

## Key findings

- Three highly polymorphic regions (clpP1, psa1, and trnT-trnL spacer) were identified as potential molecular markers.
- Dyckia species showed high numbers of SSRs, repeats, SNPs, and indels compared to other bromeliads.
- Phylogenetic analysis revealed low genetic variability among species, linked to geographic distribution.

## Abstract

Dyckia spp. are xeromorphic bromeliads, with diversity centered in the ferruginous rocky outcrops of the Espinhaço mountain Range in Brazilian tropical savana. Due to their recent radiation – during the Pliocene – along with their vast phenotypic plasticity and the limited herbarium records, many species in the genus present challenges for correct identification and the development of robust conservation strategies. We sequenced the complete chloroplast genome of six rare Dyckia species in an effort to identify hotspots of diversity that could serve as molecular markers capable of distinguishing species and elucidating phylogenetic relationships within the genus. The plastome sizes of the species ranged from 159,689 bp to 159,264 bp, and the GC content was highly consistent across all species, varying narrowly between 37.2% to 37.3%. Despite the high structural similarity, polymorphism analyses identified three regions of high polymorphic diversity—the clpP1 and psa1 genes, and the intergenic spacer region between trnT and the trnL — that may serve as molecular markers within the genus. Additionally, we detected a high number of SSRs (637), dispersed repeats (208), SNPs (1035), and indels (823) among the species compared to other bromeliads. Phylogenetic analyses using whole plastid genomes showed low variability among species, associating them with their geographic distribution. These results not only highlight the structural variability of the Dyckia plastid genome but also provide new molecular tools for the identification of related species, enhancing the development of conservation protocols for these bromeliads.