The Cathaya argyrophylla Genome Reveals the Evolutionary Trade-offs of a Living Fossil
Yun Wang, Peng Xie, Shaogang Fan, Zhibo Zhou, Wenyan Zhao + 10 more
TLDR
A new 22.73 Gb genome for the endangered Cathaya argyrophylla reveals its gigantism, ancient divergence, and genomic trade-offs between resource adaptation and weak immunity.
Key contributions
- First chromosome-level genome (22.73 Gb) for Cathaya argyrophylla, resolving 12 pseudochromosomes.
- Genome gigantism driven by high repeat content and intron expansion, diverging from Pinus 102.8 MYA.
- Expansions in metabolic and transport genes suggest adaptation to resource-limited environments.
- Contractions in defense genes explain its slow growth and weak immunity, hinting at microbiome reliance.
Why it matters
This paper provides the first high-quality genome for the endangered 'living fossil' Cathaya argyrophylla. It elucidates the genomic basis for its unique evolutionary trade-offs, linking specific gene family dynamics to its ecological vulnerabilities and adaptations. This resource is crucial for future conservation and breeding efforts.
Original 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.
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