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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.
Hufford, Matthew B; Seetharam, Arun S; Woodhouse, Margaret R; Chougule, Kapeel M; Ou, Shujun; Liu, Jianing; Ricci, William A; Guo, Tingting; Olson, Andrew; Qiu, Yinjie; Della Coletta, Rafael; Tittes, Silas; Hudson, Asher I; Marand, Alexandre P; Wei, Sharon; Lu, Zhenyuan; Wang, Bo; Tello-Ruiz, Marcela K; Piri, Rebecca D; Wang, Na; Kim, Dong Won; Zeng, Yibing; O'Connor, Christine H; Li, Xianran; Gilbert, Amanda M; Baggs, Erin; Krasileva, Ksenia V; Portwood, John L; Cannon, Ethalinda K S; Andorf, Carson M; Manchanda, Nancy; Snodgrass, Samantha J; Hufnagel, David E; Jiang, Qiuhan; Pedersen, Sarah; Syring, Michael L; Kudrna, David A; Llaca, Victor; Fengler, Kevin; Schmitz, Robert J; Ross-Ibarra, Jeffrey; Yu, Jianming; Gent, Jonathan I; Hirsch, Candice N; Ware, Doreen; Dawe, R Kelly.
Afiliação
  • Hufford MB; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Seetharam AS; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Woodhouse MR; Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA.
  • Chougule KM; USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.
  • Ou S; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Liu J; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Ricci WA; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
  • Guo T; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
  • Olson A; Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
  • Qiu Y; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Della Coletta R; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
  • Tittes S; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
  • Hudson AI; Center for Population Biology, University of California, Davis, CA 95616, USA.
  • Marand AP; Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
  • Wei S; Center for Population Biology, University of California, Davis, CA 95616, USA.
  • Lu Z; Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
  • Wang B; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
  • Tello-Ruiz MK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Piri RD; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Wang N; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Kim DW; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Zeng Y; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
  • O'Connor CH; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
  • Li X; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
  • Gilbert AM; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
  • Baggs E; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
  • Krasileva KV; Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA.
  • Portwood JL; Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
  • Cannon EKS; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
  • Andorf CM; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
  • Manchanda N; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
  • Snodgrass SJ; USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.
  • Hufnagel DE; USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.
  • Jiang Q; USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA.
  • Pedersen S; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Syring ML; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Kudrna DA; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Llaca V; Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA.
  • Fengler K; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Schmitz RJ; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Ross-Ibarra J; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
  • Yu J; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
  • Gent JI; Corteva Agriscience, Johnston, IA 50131, USA.
  • Hirsch CN; Corteva Agriscience, Johnston, IA 50131, USA.
  • Ware D; Department of Genetics, University of Georgia, Athens, GA 30602, USA.
  • Dawe RK; Center for Population Biology, University of California, Davis, CA 95616, USA.
Science ; 373(6555): 655-662, 2021 08 06.
Article em En | MEDLINE | ID: mdl-34353948
ABSTRACT
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genoma de Planta / Zea mays / Anotação de Sequência Molecular Idioma: En Ano de publicação: 2021 Tipo de documento: Article
Texto completo
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PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genoma de Planta / Zea mays / Anotação de Sequência Molecular Idioma: En Ano de publicação: 2021 Tipo de documento: Article