Genomic Analysis of <i>Laccaria</i> Genomes at High Altitude.

The Qinghai-Tibet Plateau (QTP) harbors extreme environmental conditions (e.g., low temperature, intense UV radiation, and hypoxia), presenting unique challenges for biological adaptation. However, the genetic mechanisms underlying the adaptation of macrofungi to high-altitude environments on the QTP remain poorly understood. In this study, we de novo sequenced and assembled the genomes of three <i>Laccaria</i> species collected from the QTP, aiming to unravel the genomic basis of their adaptation to high altitudes. The genomic data indicates that the genome of high-altitude species is slightly larger than that of their low-altitude relatives, particularly due to LTR retrotransposons, which also show a negative correlation with altitude. The expanded and positively selected gene families in high-altitude species were enriched in pathways related to DNA damage repair, maintenance of cell membrane stability, signal transduction, enzyme activity, stress response, and reproduction. In contrast, contracted gene families in high-altitude species were primarily associated with disease and immune responses, likely due to the reduced pathogen pressure in extreme high-altitude environments. Additionally, species-specific genes of high-altitude <i>Laccaria</i> were enriched in functions related to enzyme activity, membrane stability, and signal transduction, further supporting their adaptive roles. Analysis of carbohydrate-active enzymes (CAZymes) showed distinct gene family distributions between high- and low-altitude species, with several families absent in the low-altitude species, suggesting their potential involvement in environmental adaptation. Overall, our findings indicate that genome size expansion driven by LTR retrotransposons, coordinated evolution of gene families, positive selection, and divergence in CAZymes collectively may contribute to the adaptation of <i>Laccaria</i> to extreme high-altitude environments. This study provides basic data into the genetic mechanisms of fungal adaptation to harsh plateau environments and lays a foundation for further research on extremophilic fungi.