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Background  The Orchidaceae family is one of the most diverse among flowering plants and serves as an important research model for plant evolution, especially “evo-devo” study on floral organs. Recently, sequencing of several orchid genomes has greatly improved our understanding of the genetic basis of orchid biology. To date, however, most sequenced genomes are from the Epidendroideae subfamily. To better elucidate orchid evolution, greater attention should be paid to other orchid lineages, especially basal lineages such as Apostasioideae.    Results  Here, we present a genome sequence of  Apostasia ramifera , a terrestrial orchid species from the Apostasioideae subfamily. The genomes of  A. ramifera  and other orchids were compared to explore the genetic basis underlying orchid species richness. Genome-based population dynamics revealed a continuous decrease in population size over the last 100 000 years in all studied orchids, although the epiphytic orchids generally showed larger effective population size than the terrestrial orchids over most of that period. We also found more genes of the terpene synthase gene family, resistant gene family, and  LOX1 / LOX5  homologs in the epiphytic orchids.    Conclusions  This study provides new insights into the adaptive evolution of orchids. The  A. ramifera  genome sequence reported here should be a helpful resource for future research on orchid biology.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07852-3.

Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids