Genome compaction underlies the molecular adaptation of bay cedar (Suriana maritima) to the extreme habitat on the tropical coral islands

•The assembled genome of Bay cedar is 292.8 Mb, representing a small genome size within Fabales.•The compact genome was likely caused by remarkable reduction of long terminal repeat retrotransposons and gene losses.•The genes related to cold tolerance and pest/pathogen resistance were largely lost.•Expanded, positively selected, or retained genes after WGD may drive Bay cedar's adaptation to tropical coral islands.•Differentially expressed genes under salt and drought stresses were particularly identified in the abscisic acid pathway.