Genome sequence and analysis of the tuber crop potato

Potato ( Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and as...

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Vydáno v:	Nature (London) Ročník 475; číslo 7355; s. 189 - 195
Hlavní autoři:	Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Zhang, Bo, Mu, Desheng, Ni, Peixiang, Zhang, Gengyun, Yang, Shuang, Li, Ruiqiang, Wang, Jun, Orjeda, Gisella, Guzman, Frank, Torres, Michael, Lozano, Roberto, Ponce, Olga, Martinez, Diana, De la Cruz, Germán, Chakrabarti, S K, Patil, Virupaksh U, Skryabin, Konstantin G, Kuznetsov, Boris B, Ravin, Nikolai V, Kolganova, Tatjana V, Beletsky, Alexey V, Mardanov, Andrei V, Di Genova, Alex, Bolser, Daniel M, Martin, David M A, Li, Guangcun, Yang, Yu, Kuang, Hanhui, Hu, Qun, Xiong, Xingyao, Bishop, Gerard J, Sagredo, Boris, Mejía, Nilo, Zagorski, Wlodzimierz, Gromadka, Robert, Gawor, Jan, Szczesny, Pawel, Huang, Sanwen, Zhang, Zhonghua, Liang, Chunbo, He, Jun, Li, Ying, He, Ying, Xu, Jianfei, Zhang, Youjun, Xie, Binyan, Du, Yongchen, Qu, Dongyu, Bonierbale, Merideth, Ghislain, Marc, Herrera, Maria del Rosario, Giuliano, Giovanni, Pietrella, Marco, Perrotta, Gaetano, Facella, Paolo, O'Brien, Kimberly, Feingold, Sergio E, Barreiro, Leandro E, Massa, Gabriela A, Diambra, Luis, Whitty, Brett R, Vaillancourt, Brieanne, Lin, Haining, Massa, Alicia N, Geoffroy, Michael, Lundback, Steven, DellaPenna, Dean, Buell, C Robin, Sharma, Sanjeev Kumar, Marshall, David F, Waugh, Robbie, Bryan, Glenn J, Destefanis, Marialaura, Nagy, Istvan, Milbourne, Dan, Thomson, Susan J, Fiers, Mark, Jacobs, Jeanne M E, Nielsen, Kåre L, Sønderkær, Mads, Iovene, Marina, Torres, Giovana A, Jiang, Jiming, Veilleux, Richard E, Bachem, Christian W B, de Boer, Jan, Borm, Theo, Kloosterman, Bjorn, van Eck, Herman, Datema, Erwin, Hekkert, Bas te Lintel, Goverse, Aska, van Ham, Roeland C H J, Visser, Richard G F
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London Nature Publishing Group UK 14.07.2011 Nature Publishing Group
Témata:	631/1647/2217 631/208/212/2304 631/449/2491 Agronomy. Soil science and plant productions Artificial chromosomes Biological and medical sciences Cloning Crops Cultivars elements eukaryotic genomes Evolution, Molecular Food security Fundamental and applied biological sciences. Psychology Gene Duplication Gene Expression Regulation, Plant Generalities. Genetics. Plant material Genes, Plant - genetics Genetic research Genetic Variation Genetics and breeding of economic plants Genome, Plant - genetics Genomes Genomics Haplotypes - genetics Heterozygote Homozygote Human physiology applied to population studies and life conditions. Human ecophysiology Humanities and Social Sciences identification Immunity, Innate in-vitro Inbreeding maize Medical sciences Molecular Sequence Annotation Molecular Sequence Data multidisciplinary Nutritional survey. Food supply and nutritional requirement Origin, evolution, domestication Plant Diseases - genetics Plant material Ploidies Potatoes resistance genes reveals rna-seq Science Science (multidisciplinary) solanum Solanum tuberosum Solanum tuberosum - genetics Solanum tuberosum - physiology Vegetables Inbreeding depression Nucleotide sequence Genome duplication Solanum tuberosum Homozygosity Protein Heterozygosity Tetraploidy Potato Autotetraploidy Monoploidy Non-food products Dicotyledones Food security Angiospermae Autoploidy Spermatophyta Tuber plant Solanaceae Genome Haplotype Food supply Clone
ISSN:	0028-0836, 1476-4687, 1476-4687
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Abstract	Potato ( Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. The potato genome The genome of the potato ( Solanum tuberosum L.), a staple crop vital to food security, has been sequenced. The Potato Genome Sequencing Consortium sequenced a homozygous doubled-monoploid potato clone as well as a heterozygous diploid clone. Genome analysis reveals traces of at least two genome duplication events and genes specific to Asterids, a large clade of flowering plants of which the potato is the first to be sequenced. Gene presence/absence variants and other potentially deleterious mutations are frequent and may be the cause of inbreeding depression. The genome sequence will facilitate genetic improvements in the potato with a view to improving yield and to increasing disease and stress resistance of this crop, which is a now a significant component of worldwide food production and is becoming increasingly important in the developing world.
AbstractList	Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop Potato ( Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. The potato genome The genome of the potato ( Solanum tuberosum L.), a staple crop vital to food security, has been sequenced. The Potato Genome Sequencing Consortium sequenced a homozygous doubled-monoploid potato clone as well as a heterozygous diploid clone. Genome analysis reveals traces of at least two genome duplication events and genes specific to Asterids, a large clade of flowering plants of which the potato is the first to be sequenced. Gene presence/absence variants and other potentially deleterious mutations are frequent and may be the cause of inbreeding depression. The genome sequence will facilitate genetic improvements in the potato with a view to improving yield and to increasing disease and stress resistance of this crop, which is a now a significant component of worldwide food production and is becoming increasingly important in the developing world. Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. [PUBLICATION ABSTRACT]
Author	Yang, Shuang Kloosterman, Bjorn Sønderkær, Mads Visser, Richard G F Bishop, Gerard J Torres, Giovana A Orjeda, Gisella Mejía, Nilo Cheng, Shifeng Milbourne, Dan Iovene, Marina Skryabin, Konstantin G Ni, Peixiang Whitty, Brett R Goverse, Aska Martinez, Diana Du, Yongchen Qu, Dongyu Massa, Gabriela A Bolser, Daniel M Bryan, Glenn J Destefanis, Marialaura Xu, Xun Li, Ruiqiang Hu, Qun Feingold, Sergio E Chakrabarti, S K Pan, Shengkai Bonierbale, Merideth Zhang, Gengyun Szczesny, Pawel Zhang, Zhonghua Marshall, David F de Boer, Jan Giuliano, Giovanni Ravin, Nikolai V Vaillancourt, Brieanne Gromadka, Robert Veilleux, Richard E Gawor, Jan Li, Ying Liang, Chunbo Buell, C Robin Lundback, Steven Ponce, Olga Datema, Erwin DellaPenna, Dean Martin, David M A Barreiro, Leandro E Kuznetsov, Boris B O'Brien, Kimberly Herrera, Maria del Rosario Fiers, Mark He, Ying Xu, Jianfei Zhang, Bo Xiong, Xingyao Lin, Haining Kolganova, Tatjana V Guzman, Frank Li, Guangcun Beletsky, Alexey V Di Genova, Alex Diambra, Luis Patil, Virupaksh U Mardanov, Andrei V Perrotta, Gaetano Nag
AuthorAffiliation	BGI-Shenzhen, Chinese Ministry of Agricultural, Key Lab of Genomics, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
AuthorAffiliation_xml	– name: BGI-Shenzhen, Chinese Ministry of Agricultural, Key Lab of Genomics, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
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Keywords	Inbreeding depression Nucleotide sequence Genome duplication Solanum tuberosum Homozygosity Protein Heterozygosity Tetraploidy Potato Autotetraploidy Monoploidy Non-food products Dicotyledones Food security Angiospermae Autoploidy Spermatophyta Tuber plant Solanaceae Genome Haplotype Food supply Clone
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Snippet	Potato ( Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly... Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly... Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly...
SourceID	wageningen proquest pubmed pascalfrancis crossref springer
SourceType	Open Access Repository Aggregation Database Index Database Enrichment Source Publisher
StartPage	189
SubjectTerms	631/1647/2217 631/208/212/2304 631/449/2491 Agronomy. Soil science and plant productions Artificial chromosomes Biological and medical sciences Cloning Crops Cultivars elements eukaryotic genomes Evolution, Molecular Food security Fundamental and applied biological sciences. Psychology Gene Duplication Gene Expression Regulation, Plant Generalities. Genetics. Plant material Genes, Plant - genetics Genetic research Genetic Variation Genetics and breeding of economic plants Genome, Plant - genetics Genomes Genomics Haplotypes - genetics Heterozygote Homozygote Human physiology applied to population studies and life conditions. Human ecophysiology Humanities and Social Sciences identification Immunity, Innate in-vitro Inbreeding maize Medical sciences Molecular Sequence Annotation Molecular Sequence Data multidisciplinary Nutritional survey. Food supply and nutritional requirement Origin, evolution, domestication Plant Diseases - genetics Plant material Ploidies Potatoes resistance genes reveals rna-seq Science Science (multidisciplinary) solanum Solanum tuberosum Solanum tuberosum - genetics Solanum tuberosum - physiology Vegetables
Title	Genome sequence and analysis of the tuber crop potato
URI	https://link.springer.com/article/10.1038/nature10158 https://www.ncbi.nlm.nih.gov/pubmed/21743474 https://www.proquest.com/docview/880396901 https://www.proquest.com/docview/1468340873 https://www.proquest.com/docview/877408385 http://www.narcis.nl/publication/RecordID/oai:library.wur.nl:wurpubs%2F407783
Volume	475
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