The B73 maize genome: complexity, diversity, and dynamics

Patrick S Schnable; Doreen Ware; Robert S Fulton; Joshua C Stein; Fusheng Wei; Shiran Pasternak; Chengzhi Liang; Jianwei Zhang; Lucinda Fulton; Tina A Graves; Patrick Minx; Amy Denise Reily; Laura Courtney; Scott S Kruchowski; Chad Tomlinson; Cindy Strong; Kim Delehaunty; Catrina Fronick; Bill Courtney; Susan M Rock; Eddie Belter; Feiyu Du; Kyung Kim; Rachel M Abbott; Marc Cotton; Andy Levy; Pamela Marchetto; Kerri Ochoa; Stephanie M Jackson; Barbara Gillam; Weizu Chen; Le Yan; Jamey Higginbotham; Marco Cardenas; Jason Waligorski; Elizabeth Applebaum; Lindsey Phelps; Jason Falcone; Krishna Kanchi; Thynn Thane; Adam Scimone; Nay Thane; Jessica Henke; Tom Wang; Jessica Ruppert; Neha Shah; Kelsi Rotter; Jennifer Hodges; Elizabeth Ingenthron; Matt Cordes; Sara Kohlberg; Jennifer Sgro; Brandon Delgado; Kelly Mead; Asif Chinwalla; Shawn Leonard; Kevin Crouse; Kristi Collura; Dave Kudrna; Jennifer Currie; Ruifeng He; Angelina Angelova; Shanmugam Rajasekar; Teri Mueller; Rene Lomeli; Gabriel Scara; Ara Ko; Krista Delaney; Marina Wissotski; Georgina Lopez; David Campos; Michele Braidotti; Elizabeth Ashley; Wolfgang Golser; Hyeran Kim; Seunghee Lee; Jinke Lin; Zeljko Dujmic; Woojin Kim; Jayson Talag; Andrea Zuccolo; Chuanzhu Fan; Aswathy Sebastian; Melissa Kramer; Lori Spiegel; Lidia Nascimento; Theresa Zutavern; Beth Miller; Claude Ambroise; Stephanie Muller; Will Spooner; Apurva Narechania; Liya Ren; Sharon Wei; Sunita Kumari; Ben Faga; Michael J Levy; Linda Mcmahan; Peter Van Buren; Matthew W Vaughn

doi:10.1126/science.1178534

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The B73 maize genome: complexity, diversity, and dynamics

Journal article

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The B73 maize genome: complexity, diversity, and dynamics

Patrick S Schnable, Doreen Ware, Robert S Fulton, Joshua C Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A Graves, …

Science (American Association for the Advancement of Science), Vol.326(5956), pp.1112-5

11/20/2009

DOI: https://doi.org/10.1126/science.1178534

Handle:

https://hdl.handle.net/2376/107375

PMID: 19965430

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Abstract

Populations and Evolution

Genes, Plant

Genomics

Molecular Sequence Data

Biodiversity

Cellular Biology

DNA Copy Number Variations

DNA, Plant

Genetic Variation

Life Sciences

DNA Methylation

Recombination, Genetic

Base Sequence

Computer Science

Inbreeding

Biomolecules

Genetics

Crops, Agricultural

Vegetal Biology

Bioinformatics

Plants genetics

RNA, Plant

Zea mays

Retroelements

Quantitative Methods

Biochemistry, Molecular Biology

Chromosome Mapping

Genome, Plant

Chromosomes, Plant

Systematics, Phylogenetics and taxonomy

Sequence Analysis, DNA

DNA Transposable Elements

Plant breeding

Centromere

MicroRNAs

Ploidies

Molecular biology

Molecular Networks

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

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Title: The B73 maize genome: complexity, diversity, and dynamics
Creators: Patrick S Schnable - Center for Plant Genomics
Doreen Ware - Cold Spring Harbor Laboratory
Robert S Fulton - Department of Genetics [Saint-Louis]
Joshua C Stein - Cold Spring Harbor Laboratory
Fusheng Wei - Ecology and Evolutionary Biology [Tucson]
Shiran Pasternak - Cold Spring Harbor Laboratory
Chengzhi Liang - Cold Spring Harbor Laboratory
Jianwei Zhang - Ecology and Evolutionary Biology [Tucson]
Lucinda Fulton - Department of Genetics [Saint-Louis]
Tina A Graves - Department of Genetics [Saint-Louis]
Patrick Minx - Department of Genetics [Saint-Louis]
Amy Denise Reily - Department of Genetics [Saint-Louis]
Laura Courtney - Department of Genetics [Saint-Louis]
Scott S Kruchowski - Department of Genetics [Saint-Louis]
Chad Tomlinson - Department of Genetics [Saint-Louis]
Cindy Strong - Department of Genetics [Saint-Louis]
Kim Delehaunty - Department of Genetics [Saint-Louis]
Catrina Fronick - Department of Genetics [Saint-Louis]
Bill Courtney - Department of Genetics [Saint-Louis]
Susan M Rock - Department of Genetics [Saint-Louis]
Eddie Belter - Department of Genetics [Saint-Louis]
Feiyu Du - Department of Genetics [Saint-Louis]
Kyung Kim - Department of Genetics [Saint-Louis]
Rachel M Abbott - Department of Genetics [Saint-Louis]
Marc Cotton - Department of Genetics [Saint-Louis]
Andy Levy - Department of Genetics [Saint-Louis]
Pamela Marchetto - Department of Genetics [Saint-Louis]
Kerri Ochoa - Department of Genetics [Saint-Louis]
Stephanie M Jackson - Department of Genetics [Saint-Louis]
Barbara Gillam - Department of Genetics [Saint-Louis]
Weizu Chen - Department of Genetics [Saint-Louis]
Le Yan - Department of Genetics [Saint-Louis]
Jamey Higginbotham - Department of Genetics [Saint-Louis]
Marco Cardenas - Department of Genetics [Saint-Louis]
Jason Waligorski - Department of Genetics [Saint-Louis]
Elizabeth Applebaum - Department of Genetics [Saint-Louis]
Lindsey Phelps - Department of Genetics [Saint-Louis]
Jason Falcone - Department of Genetics [Saint-Louis]
Krishna Kanchi - Department of Genetics [Saint-Louis]
Thynn Thane - Department of Genetics [Saint-Louis]
Adam Scimone - Department of Genetics [Saint-Louis]
Nay Thane - Department of Genetics [Saint-Louis]
Jessica Henke - Department of Genetics [Saint-Louis]
Tom Wang - Department of Genetics [Saint-Louis]
Jessica Ruppert - Department of Genetics [Saint-Louis]
Neha Shah - Department of Genetics [Saint-Louis]
Kelsi Rotter - Department of Genetics [Saint-Louis]
Jennifer Hodges - Department of Genetics [Saint-Louis]
Elizabeth Ingenthron - Department of Genetics [Saint-Louis]
Matt Cordes - Department of Genetics [Saint-Louis]
Sara Kohlberg - Department of Genetics [Saint-Louis]
Jennifer Sgro - Department of Genetics [Saint-Louis]
Brandon Delgado - Department of Genetics [Saint-Louis]
Kelly Mead - Department of Genetics [Saint-Louis]
Asif Chinwalla - Department of Genetics [Saint-Louis]
Shawn Leonard - Department of Genetics [Saint-Louis]
Kevin Crouse - Department of Genetics [Saint-Louis]
Kristi Collura - Ecology and Evolutionary Biology [Tucson]
Dave Kudrna - Ecology and Evolutionary Biology [Tucson]
Jennifer Currie - Ecology and Evolutionary Biology [Tucson]
Ruifeng He - Ecology and Evolutionary Biology [Tucson]
Angelina Angelova - Ecology and Evolutionary Biology [Tucson]
Shanmugam Rajasekar - Ecology and Evolutionary Biology [Tucson]
Teri Mueller - Ecology and Evolutionary Biology [Tucson]
Rene Lomeli - Ecology and Evolutionary Biology [Tucson]
Gabriel Scara - Ecology and Evolutionary Biology [Tucson]
Ara Ko - Ecology and Evolutionary Biology [Tucson]
Krista Delaney - Ecology and Evolutionary Biology [Tucson]
Marina Wissotski - Ecology and Evolutionary Biology [Tucson]
Georgina Lopez - Ecology and Evolutionary Biology [Tucson]
David Campos - Ecology and Evolutionary Biology [Tucson]
Michele Braidotti - Ecology and Evolutionary Biology [Tucson]
Elizabeth Ashley - Ecology and Evolutionary Biology [Tucson]
Wolfgang Golser - Ecology and Evolutionary Biology [Tucson]
Hyeran Kim - Ecology and Evolutionary Biology [Tucson]
Seunghee Lee - Ecology and Evolutionary Biology [Tucson]
Jinke Lin - Ecology and Evolutionary Biology [Tucson]
Zeljko Dujmic - Ecology and Evolutionary Biology [Tucson]
Woojin Kim - Ecology and Evolutionary Biology [Tucson]
Jayson Talag - Ecology and Evolutionary Biology [Tucson]
Andrea Zuccolo - Ecology and Evolutionary Biology [Tucson]
Chuanzhu Fan - Ecology and Evolutionary Biology [Tucson]
Aswathy Sebastian - Ecology and Evolutionary Biology [Tucson]
Melissa Kramer - Cold Spring Harbor Laboratory
Lori Spiegel - Cold Spring Harbor Laboratory
Lidia Nascimento - Cold Spring Harbor Laboratory
Theresa Zutavern - Cold Spring Harbor Laboratory
Beth Miller - Cold Spring Harbor Laboratory
Claude Ambroise - Cold Spring Harbor Laboratory
Stephanie Muller - Cold Spring Harbor Laboratory
Will Spooner - Cold Spring Harbor Laboratory
Apurva Narechania - Cold Spring Harbor Laboratory
Liya Ren - Cold Spring Harbor Laboratory
Sharon Wei - Cold Spring Harbor Laboratory
Sunita Kumari - Cold Spring Harbor Laboratory
Ben Faga - Cold Spring Harbor Laboratory
Michael J Levy - Cold Spring Harbor Laboratory
Linda Mcmahan - Cold Spring Harbor Laboratory
Peter Van Buren - Cold Spring Harbor Laboratory
Matthew W Vaughn - Cold Spring Harbor Laboratory
Publication Details: Science (American Association for the Advancement of Science), Vol.326(5956), pp.1112-5
Academic Unit: Plant Pathology, Department of; Biological Chemistry, Institute of
Publisher: American Association for the Advancement of Science
Identifiers: 99900547155701842
Language: English
Resource Type: Journal article