The Cathaya argyrophylla Genome Reveals the Evolutionary Trade-offs of a Living Fossil

TL;DR

This study presents a high-quality genome assembly of Cathaya argyrophylla, revealing its evolutionary history, genomic adaptations, and trade-offs related to its status as a living fossil and endangered species.

Contribution

The paper provides the first chromosome-level genome assembly of C. argyrophylla, uncovering its unique genomic features and evolutionary divergence from Pinus.

Findings

Genome size of 22.73 Gb with high repeat content and intron expansion.

Identification of gene family expansions in lipid metabolism and transport.

Massive contraction in defense-related gene networks correlating with weak immunity.

Abstract

Cathaya argyrophylla is an endangered paleoendemic gymnosperm characterized by restricted ecological adaptability and high pathogen susceptibility. To elucidate its genomic architecture and evolutionary history, a de novo chromosome-level genome assembly was constructed using PacBio High-Fidelity long reads and Hi-C scaffolding. The resulting 22.73 Gb assembly resolves into 12 pseudochromosomes, demonstrating genome gigantism driven primarily by a 72.92 percent repeat sequence content and extensive intron expansion. Phylogenomic analysis using single-copy orthologs identifies C. argyrophylla as a sister lineage to the Pinus clade, with an estimated divergence time of 102.8 million years ago. Analysis of gene family dynamics reveals significant expansions in pathways related to membrane lipid metabolism, transmembrane transport, and translation machinery, indicating specific molecular adaptations for cellular homeostasis in resource-limited environments. Conversely, the genome exhibits massive contractions in endogenous defense networks, including plant-pathogen interactions, brassinosteroid signaling, and DNA repair mechanisms. This distinct genomic reduction correlates directly with the slow growth rate and weak innate immunity observed in the species, while the expanded transmembrane transport networks suggest an obligate physiological reliance on symbiotic microbiomes for survival. Ultimately, this reference genome establishes a critical molecular resource for future conservation and breeding programs.