GC content variation in angiosperm genomes reveals GC-biased gene conversion.

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conclusionThis study reveals the diversity of GC content characteristics among major angiosperm groups, with Poaceae species exhibiting significantly higher GC content and more pronounced heterogeneity. These features are likely associated with GC-biased gene conversion. Genome nucleotide composition critically shapes plant genetic diversity, yet its variation across angiosperms remains poorly understood. Here, we conducted a multilevel GC analysis across 495 angiosperm genomes (spanning 109 families, 44 orders; 284 species with annotated coding genes). Using SeqKit, we quantified GC content at whole-genome, chromosomal, gene, and codon scales, while estimating recombination rates with mlRho v2.9. We found that angiosperm GC content approximates a normal distribution (mean 36.64%) but varies markedly among lineages: monocots (41.97%) > eudicots (35.43%), with Poaceae highest (44.64%). Coding-region GC (mean 46.38%) exceeded genomic levels, showing maximal variation at the third codon position (GC3; mean 46.22%; up to 63.63% in Poaceae). Gene-level GC distributions shifted from unimodal to distinctly bimodal patterns-evident in Poaceae-reflecting divergence between high- and low-GC genes. Notably, GC content correlated positively with both chromosome length and recombination rate. These patterns are consistent with GC-biased gene conversion (gBGC) as a key driver of GC diversity in angiosperms, operating neutrally and locally across genomic scales, independent of phylogeny.