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Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant  Ranunculus bungei , and two terrestrial relatives  R. cantoniensis  and  R. brotherusii , followed by comparative evolutionary analyses to determine candidate genes for adaption to aquatic habitats. We obtained 126,037, 140,218 and 114,753 contigs for  R. bungei ,  R. cantoniensis  and  R. brotherusii  respectively. Bidirectional Best Hit method and OrthoMCL method identified 11,362 and 8,174 1:1:1 orthologous genes (one ortholog is represented in each of the three species) respectively. Non-synonymous/synonymous ( d  N / d  S ) analyses were performed with a maximum likelihood method and an approximate method for the three species-pairs. In total, 14 genes of  R. bungei  potentially involved in the adaptive transition from terrestrial to aquatic habitats were identified. Some of the homologs to these genes in model plants are involved in vacuole protein formation, regulating ‘water transport process’ and ‘microtubule cytoskeleton organization’. Our study opens the door to understand the molecular mechanism of plant adaptation from terrestrial to aquatic habitats.

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats