The bracteatus pineapple genome and domestication of clonally propagated crops
Journal
Nature Genetics
Journal Volume
51
Journal Issue
10
Pages
1549-1558
Date Issued
2019
Author(s)
Chen, Li-Yu
VanBuren, Robert
Paris, Margot
Zhou, Hongye
Zhang, Xingtan
Wai, Ching Man
Yan, Hansong
Chen, Shuai
Alonge, Michael
Ramakrishnan, Srividya
Liao, Zhenyang
Liu, Juan
Lin, Jishan
Yue, Jingjing
Fatima, Mahpara
Lin, Zhicong
Zhang, Jisen
Huang, Lixian
Wang, Hao
Hwa, Teh-Yang
Kao, Shu-Min
Choi, Jae Young
Sharma, Anupma
Song, Jian
Wang, Lulu
Yim, Won C.
Cushman, John C.
Paull, Robert E.
Matsumoto, Tracie
Qin, Yuan
Wu, Qingsong
Wang, Jianping
Yu, Qingyi
Wu, Jun
Zhang, Shaoling
Boches, Peter
Wang, Ming-Li
Coppens d’Eeckenbrugge, Geo
Sanewski, Garth M.
Purugganan, Michael D.
Schatz, Michael C.
Bennetzen, Jeffrey L.
Lexer, Christian
Ming, Ray
Abstract
Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.
Type
journal article