Genomic convergence underlying high‐altitude adaptation in alpine plants

Abstract

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein‐coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high‐altitude adaptation in alpine plants. Our results detected convergent contractions of disease‐resistance genes in alpine genomes, which might be an energy‐saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self‐incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high‐taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.

Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae)

“…In response to these environmental challenges, alpine plants generally develop distinctive morphological traits, such as a dwarf stature, a cushion form, and a reduction in leaf size, which could result from convergent adaptive evolution [ 3 , 4 ]. Recently, various omics technologies, such as genome sequencing, transcriptomics, and proteomics, have advanced research on the adaptation of alpine plants [ 5–8 ]. The molecular mechanisms of alpine adaptation have been gradually revealed via the detection of positively selected genes (PSGs), fast-evolving genes (FEGs), expanded gene families, and differentially expressed genes (DEGs) [ 5–8 ].…”

“…Recently, various omics technologies, such as genome sequencing, transcriptomics, and proteomics, have advanced research on the adaptation of alpine plants [ 5–8 ]. The molecular mechanisms of alpine adaptation have been gradually revealed via the detection of positively selected genes (PSGs), fast-evolving genes (FEGs), expanded gene families, and differentially expressed genes (DEGs) [ 5–8 ]. Candidate genes discovered to date for high-elevation adaptation are involved in different functional pathways, especially DNA repair, UV-B tolerance, and cold tolerance [ 5 , 9 ].…”

“…The molecular mechanisms of alpine adaptation have been gradually revealed via the detection of positively selected genes (PSGs), fast-evolving genes (FEGs), expanded gene families, and differentially expressed genes (DEGs) [ 5–8 ]. Candidate genes discovered to date for high-elevation adaptation are involved in different functional pathways, especially DNA repair, UV-B tolerance, and cold tolerance [ 5 , 9 ]. Approximately 100 flowering plant families have alpine representatives [ 3 ], and recent research into their adaptations has only revealed the tip of the iceberg.…”

“…Approximately 100 flowering plant families have alpine representatives [ 3 ], and recent research into their adaptations has only revealed the tip of the iceberg. Comparative genomics studies for high- vs low-elevation species that explore the underlying genomic convergence of alpine adaptation among different families are very rare [ 5 ].…”

Recurrent duplication and diversification of a vital DNA repair gene family across Drosophila

“…Despite the essentiality and deep conservation of eukaryotic DNA repair, many DNA repair proteins are unconserved. These repair proteins evolve rapidly under positive selection, resulting in highly divergent alleles between closely related species (Sawyer and Malik 2006; Demogines, et al 2010; Lou, et al 2014; Lee, et al 2016; Lou, et al 2016; Sun, et al 2018; Zhang, et al 2019; Kolora, et al 2021; Rowley, et al 2021; Zhang, et al 2023). This rapid evolution has been attributed largely to extreme environments and viral pathogens; however, a building literature implicates rapidly evolving DNA repeats as dynamic substrates that select for innovation of DNA repair proteins (Brand and Levine 2021).…”