Generating a Robust Genome and Transcriptome for Prickly Pear Cactus

Prickly pear cactus (Opuntia ficus-indica) is an agriculturally significant crassulacean acid metabolism (CAM) species grown for human food, animal feed, fodder, and a multitude of other uses including biofuel production that requires significantly lower water inputs than C₃ and C₄ crops. The large octoploid genome (4 Gbp) of O. ficus-indica makes comprehensive and accurate de novo genome assembly difficult. Multiple ‘omics resources are in development for O. ficus-indica­ to enable the identification of key genetic determinants for adaptations including CAM, tissue succulence, fruit development, and epicuticular wax synthesis. Major project goals include 1) utilize single-molecule sequencing to de novo sequence the genome of the reference species Opuntia cochenillifera, 2) leverage the O. cochenillifera genome as a scaffold to assemble the O. ficus-indica genome, and 3) assemble and analyze sequence reads from an 84-sample transcriptomic study of circadian clock regulation, water-deficit stress responses, and tissue types. The O. cochenillifera  genome is currently undergoing PacBio SMRT sequencing and will augment the assembly of an existing Illumina data set from O. ficus-indica. A pooled RNA sample from O. ficus-indica fruit and pads at multiple stages of development has been sequenced using PacBio IsoSeq cDNA sequencing to create a scaffold for further refinement of an Illumina-based RNA-Seq transcriptome assembly and to conduct read mapping for digital mRNA expression analysis. Metabolomic data generated using cognate transcriptomic tissue samples will also be discussed. Taken together, these data will offer a platform for CAM Biodesign efforts and assist in improvement of agronomic traits in prickly pear cactus.