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

Peer reviewed

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

20/11/2009

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

PMID: 19965430

Abstract

Base Sequence

Biochemistry

Biochemistry, Molecular Biology

Biodiversity

Bioinformatics

Cellular Biology

Centromere

Chromosome Mapping

Chromosomes, Plant

Computer Science

Crops, Agricultural

DNA Copy Number Variations

DNA Methylation

DNA Transposable Elements

DNA, Plant

Genes, Plant

Genetic Variation

Genetics

Genome, Plant

Genomics

Inbreeding

Life Sciences

MicroRNAs

Molecular biology

Molecular Networks

Molecular Sequence Data

Plant breeding

Plants genetics

Ploidies

Populations and Evolution

Quantitative Methods

Recombination, Genetic

Retroelements

RNA, Plant

Sequence Analysis, DNA

Structural Biology

Systematics, Phylogenetics and taxonomy

Vegetal Biology

Zea mays

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 - without role: Patrick S Schnable - Iowa State University
Doreen Ware - Cold Spring Harbor Laboratory
Robert S Fulton - Washington University in St. Louis
Joshua C Stein - Cold Spring Harbor Laboratory
Fusheng Wei - University of Arizona
Shiran Pasternak - Cold Spring Harbor Laboratory
Chengzhi Liang - Cold Spring Harbor Laboratory
Jianwei Zhang - University of Arizona
Lucinda Fulton - Washington University in St. Louis
Tina A Graves - Washington University in St. Louis
Patrick Minx - Washington University in St. Louis
Amy Denise Reily - Washington University in St. Louis
Laura Courtney - Washington University in St. Louis
Scott S Kruchowski - Washington University in St. Louis
Chad Tomlinson - Washington University in St. Louis
Cindy Strong - Washington University in St. Louis
Kim Delehaunty - Washington University in St. Louis
Catrina Fronick - Washington University in St. Louis
Bill Courtney - Department of Genetics [Saint-Louis]
Susan M Rock - Washington University in St. Louis
Eddie Belter - Washington University in St. Louis
Feiyu Du - Washington University in St. Louis
Kyung Kim - Washington University in St. Louis
Rachel M Abbott - Washington University in St. Louis
Marc Cotton - Washington University in St. Louis
Andy Levy - Washington University in St. Louis
Pamela Marchetto - Washington University in St. Louis
Kerri Ochoa - Washington University in St. Louis
Stephanie M Jackson - Washington University in St. Louis
Barbara Gillam - Washington University in St. Louis
Weizu Chen - Washington University in St. Louis
Le Yan - Washington University in St. Louis
Jamey Higginbotham - Washington University in St. Louis
Marco Cardenas - Washington University in St. Louis
Jason Waligorski - Washington University in St. Louis
Elizabeth Applebaum - Washington University in St. Louis
Lindsey Phelps - Washington University in St. Louis
Jason Falcone - Washington University in St. Louis
Krishna Kanchi - Washington University in St. Louis
Thynn Thane - Washington University in St. Louis
Adam Scimone - Washington University in St. Louis
Nay Thane - Washington University in St. Louis
Jessica Henke - Washington University in St. Louis
Tom Wang - Washington University in St. Louis
Jessica Ruppert - Washington University in St. Louis
Neha Shah - Washington University in St. Louis
Kelsi Rotter - Washington University in St. Louis
Jennifer Hodges - Washington University in St. Louis
Elizabeth Ingenthron - Washington University in St. Louis
Matt Cordes - Washington University in St. Louis
Sara Kohlberg - Washington University in St. Louis
Jennifer Sgro - Washington University in St. Louis
Brandon Delgado - Washington University in St. Louis
Kelly Mead - Washington University in St. Louis
Asif Chinwalla - Washington University in St. Louis
Shawn Leonard - Washington University in St. Louis
Kevin Crouse - Washington University in St. Louis
Kristi Collura - University of Arizona
Dave Kudrna - University of Arizona
Jennifer Currie - University of Arizona
Ruifeng He - Ecology and Evolutionary Biology [Tucson]
Angelina Angelova - University of Arizona
Shanmugam Rajasekar - University of Arizona
Teri Mueller - University of Arizona
Rene Lomeli - University of Arizona
Gabriel Scara - University of Arizona
Ara Ko - University of Arizona
Krista Delaney - University of Arizona
Marina Wissotski - University of Arizona
Georgina Lopez - University of Arizona
David Campos - University of Arizona
Michele Braidotti - University of Arizona
Elizabeth Ashley - University of Arizona
Wolfgang Golser - University of Arizona
Hyeran Kim - Ecology and Evolutionary Biology [Tucson]
Seunghee Lee - Ecology and Evolutionary Biology [Tucson]
Jinke Lin - Ecology and Evolutionary Biology [Tucson]
Zeljko Dujmic - University of Arizona
Woojin Kim - University of Arizona
Jayson Talag - University of Arizona
Andrea Zuccolo - University of Arizona
Chuanzhu Fan - University of Arizona
Aswathy Sebastian - University of Arizona
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
Publisher: American Association for the Advancement of Science (AAAS)
Identifiers: 9943607208331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article