Location: Tropical Plant Genetic Resources and Disease Research
Title: The bracteatus pineapple genome and domestication of clonally propagated cropsAuthor
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LI-YU, CHEN - University Of Illinois |
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VANBUREN, ROBERT - University Of Illinois |
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PARIS, MARGOT - University Of Fribourg |
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ZHOU, HONGYE - University Of Georgia |
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ZHANG, XINGTAN - University Of Illinois |
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WAI, CHING MAN - University Of Illinois |
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YAN, HANSONG - University Of Illinois |
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CHEN, SHUAI - University Of Illinois |
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ALONGE, MICHAEL - Johns Hopkins University |
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RAMAKRISHNAN, SRIVIDYA - Johns Hopkins University |
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LIAO, ZHENYANG - University Of Illinois |
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LIU, JUAN - University Of Illinois |
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LIN, JISHAN - University Of Illinois |
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YUE, JINGJING - University Of Illinois |
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FATIMA, MAHPARA - University Of Illinois |
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LIN, ZHICONG - University Of Illinois |
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ZHANG, JISEN - University Of Illinois |
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HUANG, LIXIAN - University Of Illinois |
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WANG, HAO - University Of Georgia |
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HWA, TEH-YANG - National Taiwan University |
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KAO, SHU-MIN - National Taiwan University |
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CHOI, JAE - New York University |
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SHARMA, ANUPMA - Texas A&M University |
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SONG, JIAN - University Of Florida |
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WANG, LULU - University Of Illinois |
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YIM, WON - University Of Nevada |
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CUSHMAN, JOHN - University Of Nevada |
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PAULL, ROBERT - University Of Hawaii |
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Matsumoto Brower, Tracie |
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QIN, YUAN - University Of Illinois |
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WU, QINGSONG - Chinese Academy Of Agricultural Sciences |
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WANG, JIANPING - University Of Illinois |
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YU, QINGYI - University Of Illinois |
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WU, JUN - Nanjing Agricultural University |
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ZHANG, SHAOLING - Nanjing Agricultural University |
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BOCHES, PETER - Retired ARS Employee |
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TUNG, CHIH-WEI - National Taiwan University |
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WANG, MING-LI - Hawaii Agricultural Research Center |
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COPPENSD'EECKENBRUGE, GEO - University Of Montpellier |
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SANEWSKI, GARTH - Queensland University - Australia |
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PURUGGANAN, MICHAEL - New York University |
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SCHATZ, MICHAEL - Texas A&M Agrilife |
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BENNETZEN, JEFFREY - University Of Georgia |
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LEXER, CHRISTIAN - University Of Vienna |
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MING, RAY - University Of Illinois |
Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 8/28/2019 Publication Date: N/A Citation: N/A Interpretive Summary: Domestically grown plants can be produced either sexually through seed propagation or asexually through cuttings, grafting, air layering, divisions, or tissue culture. Sexually reproducing species undergo hundreds to thousands of generations of recombination during domestication which can be tracked in the plants genome. In contrast, domestication of clonally propagated crops depends on both vegetative and sexual reproduction. It can even be a one-step operation, where selection is completed once a clone is selected. Using pineapple as a model we sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. We compared the genome of Ananas comosus var. bracteatus CB5 with other pineapple cultivars for genomic traits responsible for fiber production, color formation, sugar accumulation and fruit maturation. Pineapple cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixtures, while ‘Singapore Spanish’ represents a one-step operation in the domestication. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops. Technical 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 24 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. |