Pineapple genome

Domestication of clonally propagated crops such as pineapple from South America washypothesized as' one-step operation", We sequenced the genome of Ananas comosus var.bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 31,745 genes. Comparison ofthe genomes of CB5 and fruit pineapple 'F153' revealed genomic bases of fiber production, colorformation, sugar accumulation, and fruit maturation. We re-sequenced 89 Ananas genomes.Cultivars' Smooth Cayenne and 'Queen exhibited ancient and recent admixture, while'Singapore Spanish'supported one-step operation or domestication. We identified 24 selectivesweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors.Two candidate genes for self- incompatibility were linked in 'F153', but not functional in theself-compatible CB5. Our findings support co-existence of sexual recombination and one-stepoperation in domestication of clonally propagated crops. This investigation offers novelapproaches and perspectives to explore sexual and asexual domestication trajectories in otherclonally propagated crops. Updated supplementary file that contains two versions of gene IDs of Ananas comosus var. bracteatus can be downloaded from BioStudies (https://www.ebi.ac.uk/biostudies/studies/S-BSST687).