arXiv subjects

Haoliang Hu

Publications and source records attributed to Haoliang Hu.

3 recordsLinked to original sources

arXiv2026

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

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.

q-bio.GN↗

arXiv2026

Synonymous Codon Usage Bias Overrides Phylogeny to Reflect Convergent Frond Architecture in a Rapidly Radiating Fern Family Thelypteridaceae

Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon usage bias (CUB) to override phylogenetic history remains a fundamental question. Here, we investigate this within the rapidly radiating fern family Thelypteridaceae by establishing a comparative framework that integrates chloroplast phylogenomics with dimensionality reduction of codon usage, morphological data, and divergence time estimation. Our results reveal that chloroplast CUB patterns are strikingly incongruent with the phylogeny of this family. Instead, they partition species into distinct clusters that strongly correlate with a convergently evolved morphological trait, lamina base architecture, a key adaptation whose radiation we date to the early Neogene. This convergent molecular signal is driven by a specific subset of photosynthesis-related genes (ndhJ, psaA, and psbD), which exhibit a high density of type-specific, third-position codon substitutions. These findings demonstrate that CUB can serve as a powerful, quantifiable indicator of adaptive history, revealing a cryptic layer of molecular convergence linked to the regulation of protein synthesis. Our work providing a new framework for uncovering adaptive histories obscured by complex evolutionary processes.

q-bio.PE↗

arXiv2024

The Mitochondrial Genome of Cathaya argyrophylla Reaches 18.99 Mb: Analysis of Super-Large Mitochondrial Genomes in Pinaceae

Mitochondrial genomes in the Pinaceae family are notable for their large size and structural complexity. In this study, we sequenced and analyzed the mitochondrial genome of Cathaya argyrophylla, an endangered and endemic Pinaceae species, uncovering a genome size of 18.99 Mb, meaning the largest mitochondrial genome reported to date. To investigate the mechanisms behind this exceptional size, we conducted comparative analyses with other Pinaceae species possessing both large and small mitochondrial genomes, as well as with other gymnosperms. We focused on repeat sequences, transposable element activity, RNA editing events, chloroplast-derived sequence transfers (mtpts), and sequence homology with nuclear genomes. Our findings indicate that while Cathaya argyrophylla and other extremely large Pinaceae mitochondrial genomes contain substantial amounts of repeat sequences and show increased activity of LINEs and LTR retrotransposons, these factors alone do not fully account for the genome expansion. Notably, we observed a significant incorporation of chloroplast-derived sequences in Cathaya argyrophylla and other large mitochondrial genomes, suggesting that extensive plastid-to-mitochondrial DNA transfer may play a crucial role in genome enlargement. Additionally, large mitochondrial genomes exhibited distinct patterns of RNA editing and limited similarity with nuclear genomes compared to smaller genomes. These results suggest that the massive mitochondrial genomes in Pinaceae are likely the result of multiple contributing factors, including repeat sequences, transposon activity, and extensive plastid sequence incorporation. Our study enhances the understanding of mitochondrial genome evolution in plants and provides valuable genetic information for the conservation and study of Cathaya argyrophylla.

q-bio.GN↗