Overview
Genome Size
242.67 Mb
Date performed
2021
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Publication
Abstract
Background: The Great Himalayan Mountains and their foothills are believed to be centers of origin and genetic diversity for many cultivated plant species. However, the genetic basis of adaptation to extreme Himalayan climates in plants, especially perennials, remains largely unknown. Prunus L. includes economically important fruit crops, with some wild species like Tibetan peach (P. mira) endemic to middle- to high-altitude regions of the Himalayas, shaped by the harsh environments of the Tibetan Plateau. The genetic basis of their adaptation to such harsh conditions has been unexplored.
Results: We collected 377 Prunus accessions from the Himalayan region (2017-2019) and de novo assembled high-quality genomes of three Tibetan Prunus species: P. mira (242.67 Mb), P. mume "Tibet" (241.72 Mb), and P. armeniaca "Tibet" (266.25 Mb). Comparative analysis revealed a remarkable expansion of SINE retrotransposons in Tibetan Prunus genomes. Genetic differentiation was observed between high- and low-altitude Tibetan peach populations, with enrichment of genes related to light/UV stress signaling in differentiated regions. Metabolomic profiling identified 379 metabolites genetically correlated with altitude, particularly phenylpropanoids. Sixty-two Tibetan peach-specific SINEs colocalized with differentially accumulated metabolites; two SINE insertions (SINE1 specific to Tibetan peach, SINE2 predominant at high altitudes) were associated with 3-O-feruloyl quinic acid accumulation, with SINE2 altering nearby gene expression.
Conclusions: The expansion of SINE retrotransposons in Tibetan Prunus species promotes accumulation of beneficial metabolites (e.g., phenylpropanoids), aiding adaptation to the harsh Himalayan environment. This study provides genomic and metabolic resources, illustrating how focusing on SINEs and related genetic variations can advance understanding of high-altitude adaptation mechanisms in plants.
