Integrated analysis uncovers the role of circadian rhythm genes in cold adaptation of Kandelia obovata using the multi-omics data.

Kandelia obovata and Kandelia candel, two sister mangrove species within the genus Kandelia (Rhizophoraceae), exhibit pronounced differences in cold tolerance. However, the genetic basis underlying this adaptive divergence remains unclear. In this study, we assembled a high-quality, chromosome-level genome of K. candel (~225 Mb) to facilitate comparative genomic analysis with K. obovata. Functional enrichment revealed that expanded gene families in K. candel and contracted families in K. obovata were both significantly associated with transcription factor (TF) activity, highlighting TFs as potential key drivers of adaptive evolution. Using whole-genome resequencing data from 53 accessions across representative geographic ranges, we investigated population structure and identified genomic loci associated with environmental adaptation in K. obovata. Notably, temperature-responsive TFs were found to be involved in the circadian rhythm pathway. Through integrated genomic and transcriptomic analysis, we prioritized 18 circadian rhythm-related TFs, including PIF3, CCA1, LHY, and MYB family members such as PAP1, as high-priority candidates linked to cold adaptation in K. obovata. Enrichment analysis of the target genes regulated by these TFs further underscored the importance of flavonoid and phenylpropanoid metabolism under cold stress. Our results suggest that circadian rhythm genes, through their regulation of specialized metabolism, represent promising candidate regulators that may contribute to cold adaptation of K. obovata. This study provides not only key insights into the evolutionary mechanisms of mangrove cold resilience but also a valuable genomic resource for guiding conservation and assisted migration strategies under climate change.