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. •First assembly of nuclear genome in the genus Puya.•A total of 26,696 genes were predicted in the nuclear genome of Puya raimondii.•The Puya raimondii genome revealed its adaptation to high Andes with the genes associated with reproductive development and stress responses significantly expanded.•Using the nuclear genome of Puya raimondii as reference, single-copy nuclear genes were tested and proved to be useful in improving phylogenetic reconstruction of Puya species