Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny.

The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%-37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein-coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69-78 tandem repeats, 45-60 SSRs (simple sequence repeats), and 8-22 repeat structures among 13 species. Four protein-coding genes were identified under positive site-specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.

Genetic diversity and genetic structure of Puya raimondii (Bromeliaceae) for its conservation in the Peruvian Andes

Resumen Puya raimondii es una especie endémica de los altos Andes de Perú y Bolivia. En el Perú se distribuye desde 8.068501°S, 16.170280°W hasta 16.180580° S, 70.658873° W, entre los 3600 y 4800 m de altitud, viviendo en condiciones climáticas extremas propias de la Puna, donde juega un papel ecológico importante. Pese a la amplia distribución de las poblaciones de P. raimondii en el Perú, aparentemente son bastante uniformes morfológicamente; por lo que surgen las siguientes preguntas: ¿Podrán las actuales herramientas moleculares mostrar diferencias entre las numerosas poblaciones? ¿Son suficientes las áreas de conservación establecidas para P. raimondii ya que albergan la variabilidad existente? Para responder a estas interrogantes, este trabajo tuvo como objetivo evaluar la diversidad genética y estructura genética en una población del norte del país, Pachapaqui (departamento de Ancash), una población del centro, Yanacancha (Junín), y una población del sur, Lampa - sector Choconchaca (Puno), utilizando marcadores microsatélites (SSR) específicos para la especie. Los parámetros de diversidad genética utilizados incluyeron número de alelos (A), alelos exclusivos (RA), heterocigosidad observada (Ho), heterocigosidad esperada (He) e índice de contenido polimórfico (PIC). Los resultados mostraron que el número total de A varió de 2 ‒ 13, los valores de He fueron 0 ‒ 0.723 y Ho 0 ‒ 0.929, con un He promedio de 0.217, indicando una diversidad genética moderada a alta, siendo la población de Lampa-sector Choconchaca, la que presentó mayor diversidad alélica y mayor diversidad genética. La prueba de Hardy-Weinberg mostró que las poblaciones se encuentran en desequilibrio HW, el análisis estadístico indica un 65% de variación genética a nivel poblacional y valores de FST (0.426) y RST (0.650) que indican alta diferenciación genética entre poblaciones, con dos grupos genéticos (K=2) que corresponden a las poblaciones del centro-norte y sur del Perú. Los resultados brindan información útil para establecer estrategias de conservación para P. raimondii, que conduzcan a la creación de una área de conservación adicional para proteger a las poblaciones del sur del Perú.

Abstract Puya raimondii is an endemic species from the high Andes of Peru and Bolivia. In Peru it is distributed from 8.068501°S, 16.170280°W to 16.180580°S, 70.658873°W, between 3600 and 4800 m, living in extreme climatic conditions typical of the Puna, where it plays an important ecological role. Despite the wide distribution of P. raimondii populations in Peru, they appear to be fairly uniform morphologically. The following questions arise: Will the current molecular tools be able to show differences between the numerous populations? Are the conservation areas established for P. raimondii sufficient since they harbor the existing variability? To answer these questions, this work aimed to evaluate the genetic diversity and genetic structure in a northern population, Pachapaqui (Ancash department), a central population, Yanacancha (Junin), and a southern population, Lampa - Choconchaca sector (Puno), using microsatellite markers (SSR) specific for the species. The genetic diversity parameters used included number of alleles (A), exclusive alleles (RA), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic content index (PIC). The results showed that the total number of A varied from 2 - 13, the He values were 0 ‒ 0.723 and Ho 0 ‒ 0.929, with an average He of 0.217, indicating a moderate to high genetic diversity, being the population of Lampa-Choconchaca sector, the one that presented the greatest allelic diversity and the greatest genetic diversity. The Hardy-Weinberg test showed that the populations are in HW disequilibrium, the statistical analysis indicates 65% of the genetic variation at the population level and values of FST (0.426) and RST (0.650) that indicate high genetic differentiation among populations, with two genetic groups (K=2) that correspond to the populations of northern-central and southern Peru. The results provide useful information to establish conservation strategies for P. raimondii, which lead to the creation of an additional conservation area to protect the populations in southern Peru.

Draft genome of Puya raimondii (Bromeliaceae), the Queen of the Andes.

Puya raimondii, the Queen of the Andes, is an endangered high Andean species in the Bromeliaceae family. Here, we report its first genome to promote its conservation and evolutionary study. Comparative genomics showed P. raimondii diverged from Ananas comosus about 14.8 million years ago, and the long terminal repeats were likely to contribute to the genus diversification in last 3.5 million years. The gene families related to plant reproductive development and stress responses significantly expanded in the genome. At the same time, gene families involved in disease defense, photosynthesis and carbohydrate metabolism significantly contracted, which may be an evolutionary strategy to adapt to the harsh conditions in high Andes. The demographic history analysis revealed the P. raimondii population size sharply declined in the Pleistocene and then increased in the Holocene. We also designed and tested 46 pairs of universal primers for amplifying orthologous single-copy nuclear genes in Puya species.

Microsatellite markers for the endangered Puya raimondii in Peru.

PREMISE: Microsatellite primers were developed for Puya raimondii (Bromeliaceae), an endangered species distributed in the Andean Mountains of Bolivia and Peru. METHODS AND RESULTS: Genome skimming of P. raimondii, P. macrura, and P. hutchisonii resulted in the selection of 46 pairs of cross-species microsatellite markers. Of these, 12 microsatellite primer pairs produced clear and polymorphic bands in P. raimondii. These primer sets were then used for the detection of potential polymorphisms in 84 P. raimondii individuals collected from four populations in Peru. The number of alleles per locus ranged from one to six, and the observed and expected levels of heterozygosity ranged from 0.000 to 0.8929 and from 0.000 to 0.7662, respectively. CONCLUSIONS: The microsatellite markers developed in this study will be useful for future population genetic analyses and breeding system studies in P. raimondii.