Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding

Chinese fir (Cunninghamia lanceolata) is a cornerstone timber species in China. It has been cultivated for millennia and introduced globally. Here, we present a high-quality chromosome-scale reference genome, revealing a recent burst of transposable elements during the Pliocene. While no whole-genome duplications are observed, tandem and proximal gene duplications expand families linked to environmental adaptation. Population resequencing of 87 provenance accessions and 15 ancient trees, including specimens planted in 1176 by the esteemed Neo-Confucianist Zhu Xi, reveals three principal phylogenetic groups corresponding to major geographic regions: the Yangtze River basin (group I), the Wuyi-Nanling region (group II; superior provenance), and regions along the Hakka migration route (group III). The Wuyi Mountains likely represent a historical hub of germplasm exchange and genetic connectivity. Analysis of 90 advanced-generation seed orchard progeny individuals and 13 elite clones reveals a marked bias in modern breeding practices toward specific lineages (primarily group II), whereas group I, which includes nearly all ancient trees, remains underutilized. These findings provide a genomic framework for understanding the domestication continuum, anthropogenic reshaping, and lineage-biased selection in C. lanceolata, offering insights for sustainable improvement and conservation. Chinese fir (Cunninghamia lanceolata) is a timber species that is native to China but cultivated globally. Here, the author report the genome assembly of this species and conduct population genomics analysis to reveal its domestication continuum, anthropogenic reshaping, and lineage-biased selection.