The bracteatus pineapple genome and domestication of clonally propagated crops

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Chen, L.-Y., VanBuren, R., Paris, M., Zhou, H., Zhang, X., Wai, C. M., Yan, H., Chen, S., Alonge, M., Ramakrishnan, S., Liao, Z., Liu, J., Lin, J., Yue, J., Fatima, M., Lin, Z., Zhang, J., Huang, L., Wang, H., Hwa, T.-Y., Kao, S.-M., Choi, J. Y., Sharma, A., Song, J., Wang, L., Yim, W. C., Cushman, J. C., Paull, R. E., Matsumoto, T., Qin, Y., Wu, Q., Wang, J., Yu, Q., Wu, J., Zhang, S., Boches, P., Tung, C.-W., Wang, M.-L., Coppens d’Eeckenbrugge, G., Sanewski, G. M., Purugganan, M. D., Schatz, M. C., Bennetzen, J. L., Lexer, C. and Ming, R. (2019) The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics, 51 (10). pp. 1549-1558. ISSN 1546-1718

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Article Link: https://doi.org/10.1038/s41588-019-0506-8

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.

Item Type:	Article
Business groups:	Horticulture and Forestry Science
Additional Information:	Open access Code availability We developed a new algorithm, Pseudohaploid, that identifies and filters out heterozygous contigs based on whole-genome alignment. This method can be run stand-alone with any assembler and is available open-source at http://github.com/schatzlab/pseudohaploid. Other public available open-source and custom software/code used to analyze the data in this study are listed in the Nature Research Reporting Summary.
Keywords:	AgTech
Subjects:	Science > Botany > Genetics Plant culture > Propagation Plant culture > Horticulture. Horticultural crops Plant culture > Fruit and fruit culture > Culture of individual fruits or types of fruit > Pineapple
Live Archive:	12 Nov 2019 04:45
Last Modified:	03 Sep 2021 16:45

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