The bracteatus pineapple genome and domestication of clonally propagated crops
Li-Yu Chen
(1)
,
Robert Vanburen
(2, 3)
,
Margot Paris
(4)
,
Hongye Zhou
(5)
,
Xingtan Zhang
(1)
,
Ching Man Wai
(2)
,
Hansong Yan
(1)
,
Shuai Chen
(1)
,
Michael Alonge
(6)
,
Srividya Ramakrishnan
(6)
,
Zhenyang Liao
(1)
,
Juan Liu
(1)
,
Jishan Lin
(1)
,
Jingjing Yue
(1)
,
Mahpara Fatima
(1)
,
Zhicong Lin
(1)
,
Jisen Zhang
(1)
,
Lixian Huang
(1)
,
Hao Wang
(5)
,
Teh-Yang Hwa
(7)
,
Shu-Min Kao
(7)
,
Jae Young Choi
(8)
,
Anupma Sharma
(9)
,
Jian Song
(10)
,
Lulu Wang
(1)
,
Won C. Yim
(11)
,
John C. Cushman
(11)
,
Robert E. Paull
(12)
,
Tracie Matsumoto
(13)
,
Yuan Qin
(1, 9)
,
Qingsong Wu
(14)
,
Jianping Wang
(1, 10)
,
Qingyi Yu
(1, 9)
,
Jun Wu
(15)
,
Shaoling Zhang
(15)
,
Peter Boches
(13)
,
Chih-Wei Tung
(7)
,
Ming-Li Wang
(16)
,
Garth M. Sanewski
(17)
,
Michael D. Purugganan
(8)
,
Michael C. Schatz
(6)
,
Jeffrey L. Bennetzen
(5)
,
Christian Lexer
(18)
,
Ray Ming
(1, 2)
1
FAFU -
Fujian Agriculture and Forestry University
2 UIUC - University of Illinois at Urbana-Champaign [Urbana]
3 Department of Horticulture
4 Department of Biology
5 Department of Genetics
6 JHU - Johns Hopkins University
7 National Taiwan University
8 NYU - New York University [New York]
9 Texas A&M University System
10 Department of agronomy
11 Department of Biochemistry and Molecular Biology
12 University of Hawaii at Manoa
13 USDA-ARS : Agricultural Research Service
14 South Subtropical Crops Research Institute, CATAS
15 NAU - Nanjing Agricultural University
16 Hawaii Agriculture Research Center
17 Queensland Department of Agriculture and Fisheries
18 Department of Botany and Biodiversity Research
2 UIUC - University of Illinois at Urbana-Champaign [Urbana]
3 Department of Horticulture
4 Department of Biology
5 Department of Genetics
6 JHU - Johns Hopkins University
7 National Taiwan University
8 NYU - New York University [New York]
9 Texas A&M University System
10 Department of agronomy
11 Department of Biochemistry and Molecular Biology
12 University of Hawaii at Manoa
13 USDA-ARS : Agricultural Research Service
14 South Subtropical Crops Research Institute, CATAS
15 NAU - Nanjing Agricultural University
16 Hawaii Agriculture Research Center
17 Queensland Department of Agriculture and Fisheries
18 Department of Botany and Biodiversity Research
Résumé
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.
Domaines
Biologie végétale| Origine | Fichiers éditeurs autorisés sur une archive ouverte |
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