The pineapple genome and the evolution of CAM photosynthesis.
Ming R., VanBuren R., Wai CM., Tang H., Schatz MC., Bowers JE., Lyons E., Wang ML., Chen J., Biggers E., Zhang J., Huang L., Zhang L., Miao W., Zhang J., Ye Z., Miao C., Lin Z., Wang H., Zhou H., Yim WC., Priest HD., Zheng C., Woodhouse M., Edger PP., Guyot R., Guo HB., Guo H., Zheng G., Singh R., Sharma A., Min X., Zheng Y., Lee H., Gurtowski J., Sedlazeck FJ., Harkess A., McKain MR., Liao Z., Fang J., Liu J., Zhang X., Zhang Q., Hu W., Qin Y., Wang K., Chen LY., Shirley N., Lin YR., Liu LY., Hernandez AG., Wright CL., Bulone V., Tuskan GA., Heath K., Zee F., Moore PH., Sunkar R., Leebens-Mack JH., Mockler T., Bennetzen JL., Freeling M., Sankoff D., Paterson AH., Zhu X., Yang X., Smith JA., Cushman JC., Paull RE., Yu Q.
Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.