ArticleNature genetics2019
The bracteatus pineapple genome and domestication of clonally propagated crops.
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Article in Nature genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45 citing papers in PubMed, 100 citations in OpenAlex.
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- Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- AcMYB266, a key regulator of the red coloration in pineapple peel: a case of subfunctionalization in tandem duplicated genes.Horticulture research · 2024Article
- Molecular insights into self-incompatibility systems: From evolution to breeding.Plant communications · 2024Review
- TCOD: an integrated resource for tropical crops.Nucleic acids research · 2024Article
- Identification of bromelain subfamily proteases encoded in the pineapple genome.Scientific reports · 2023Article
- Recent Advances in Assembly of Complex Plant Genomes.Genomics, proteomics & bioinformatics · 2023Review
- Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus.Genomics, proteomics & bioinformatics · 2023Article
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- Genome-Wide Identification and Characterization ofInternational journal of molecular sciences · 2023Article
- Chromosome-level genome and the identification of sex chromosomes in Uloborus diversus.GigaScience · 2022Article
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Authors and funding
45 authors at 17 institutions in 6 countries.
Li-Yu Chen *FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.ORCID http://orcid.org/0000-0002-5199-6237
Robert VanBuren *Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Margot Paris *Department of Biology, University of Fribourg, Fribourg, Switzerland.
Hongye Zhou *Department of Genetics, University of Georgia, Athens, GA, USA.ORCID http://orcid.org/0000-0003-4373-8083
Xingtan ZhangFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Ching Man WaiDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.ORCID http://orcid.org/0000-0002-2913-5721
Hansong YanFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Shuai ChenFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Michael AlongeDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Srividya RamakrishnanDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Zhenyang LiaoFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Juan LiuFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Jishan LinFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Jingjing YueFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Mahpara FatimaFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Zhicong LinFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Jisen ZhangFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Lixian HuangFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Hao WangDepartment of Genetics, University of Georgia, Athens, GA, USA.
Teh-Yang HwaDepartment of Agronomy, National Taiwan University, Taipei, ROC.
Shu-Min KaoDepartment of Agronomy, National Taiwan University, Taipei, ROC.
Jae Young ChoiDepartment of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA.ORCID http://orcid.org/0000-0002-0238-8980
Anupma SharmaTexas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA.
Jian SongDepartment of Agronomy, University of Florida, Gainesville, FL, USA.
Lulu WangFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Won C YimDepartment of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA.ORCID http://orcid.org/0000-0002-7489-0435
John C CushmanDepartment of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA.
Robert E PaullDepartment of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
Tracie MatsumotoUSDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA.
Yuan QinFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
Qingsong WuSouth Subtropical Crops Research Institute, CATAS, Zhanjiang, China.
Jianping WangFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.ORCID http://orcid.org/0000-0002-0259-1508
Qingyi YuFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.ORCID http://orcid.org/0000-0001-5393-5764
Jun WuCentre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
Shaoling ZhangCentre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
Peter BochesUSDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA.
Chih-Wei TungDepartment of Agronomy, National Taiwan University, Taipei, ROC.
Ming-Li WangHawaii Agriculture Research Center, Kunia, HI, USA.
Geo Coppens d'EeckenbruggeCentre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France.
Garth M SanewskiQueensland Department of Agriculture and Fisheries, Nambour, Queensland, Australia.
Michael D PuruggananDepartment of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA.ORCID http://orcid.org/0000-0002-9197-4112
Michael C SchatzDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Jeffrey L BennetzenDepartment of Genetics, University of Georgia, Athens, GA, USA. maize@uga.edu.
Christian LexerDepartment of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. christian.lexer@univie.ac.at.ORCID http://orcid.org/0000-0002-7221-7482
Ray MingFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. rayming@illinois.edu.ORCID http://orcid.org/0000-0002-9417-5789
Fujian Agriculture and Forestry University · CNJohns Hopkins University · USNational Taiwan University · TWUniversity of Georgia · USUniversity of Illinois Urbana-Champaign · USDaniel K. Inouye U.S. Pacific Basin Agricultural Research Center · USNanjing Agricultural University · CNNew York University · USTexas A&M University System · USUniversity of Florida · USUniversity of Nevada, Reno · USCentre de Coopération Internationale en Recherche Agronomique pour le Développement · FRChinese Academy of Tropical Agricultural Sciences · CNHawaii Agriculture Research Center · USUniversity of Fribourg · CHUniversity of Hawaiʻi at Mānoa · USUniversity of Vienna · AT
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
DomesticationGenome, PlantQuantitative Trait, HeritableAnanasBromelainsCrops, AgriculturalGene Expression Regulation, PlantPhenotypePlant ProteinsPlants, Genetically ModifiedPopulation DynamicsSugarsBromelainsPlant ProteinsSugars
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