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Table of Contents: PLoS Genetics: 2009 Maize Genome Collection

The authors of the research presented in this special collection used the first description of the B73 maize genome to probe some of the most intriguing questions in genetics and plant biology. Read about maize centromeres, new insights into transposon types and distribution, the abundance of very short FLcDNAs encoding predicted peptides, and many other "genetic jewels" contained herein.

Collection Editors: Gregory S. Barsh (Stanford University School of Medicine), Gregory P. Copenhaver (The University of North Carolina at Chapel Hill), Joseph R. Ecker (The Salk Institute for Biological Studies), and Harmit S. Malik (Fred Hutchinson Cancer Research Center).

Download: Complete Collection (10 MB PDF).

Image Credit: Seneca Mini Indian variety (Jordan Seeds). Photo by David Cavagnaro with assistance from Lois Girton and Marianne Smith as part of NSF project DBI-0321711 to P. Schnable, D. Ashlock, and B. Buckner.

Editorial

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000723

Research Articles

The Physical and Genetic Framework of the Maize B73 Genome

Fusheng Wei, Jianwei Zhang, Shiguo Zhou, Ruifeng He, Mary Schaeffer, Kristi Collura, David Kudrna, Ben P. Faga, Marina Wissotski, Wolfgang Golser, Susan M. Rock, Tina A. Graves, Robert S. Fulton, Ed Coe, Patrick S. Schnable, David C. Schwartz, Doreen Ware, Sandra W. Clifton, Richard K. Wilson, Rod A. Wing

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000715

Abstract • Figures

A Genome-Wide Characterization of MicroRNA Genes in Maize

Lifang Zhang, Jer-Ming Chia, Sunita Kumari, Joshua C. Stein, Zhijie Liu, Apurva Narechania, Christopher A. Maher, Katherine Guill, Michael D. McMullen, Doreen Ware

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000716

Abstract • Figures

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Fusheng Wei, Joshua C. Stein, Chengzhi Liang, Jianwei Zhang, Robert S. Fulton, Regina S. Baucom, Emanuele De Paoli, Shiguo Zhou, Lixing Yang, Yujun Han, Shiran Pasternak, Apurva Narechania, Lifang Zhang, Cheng-Ting Yeh, Kai Ying, Dawn H. Nagel, Kristi Collura, David Kudrna, Jennifer Currie, Jinke Lin, HyeRan Kim, Angelina Angelova, Gabriel Scara, Marina Wissotski, Wolfgang Golser, Laura Courtney, Scott Kruchowski, Tina A. Graves, Susan M. Rock, Stephanie Adams, Lucinda A. Fulton, Catrina Fronick, William Courtney, Melissa Kramer, Lori Spiegel, Lydia Nascimento, Ananth Kalyanaraman, Cristian Chaparro, Jean-Marc Deragon, Phillip San Miguel, Ning Jiang, Susan R. Wessler, Pamela J. Green, Yeisoo Yu, David C. Schwartz, Blake C. Meyers, Jeffrey L. Bennetzen, Robert A. Martienssen, W. Richard McCombie, Srinivas Aluru, Sandra W. Clifton, Patrick S. Schnable, Doreen Ware, Richard K. Wilson, Rod A. Wing

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000728

Abstract • Figures

A Single Molecule Scaffold for the Maize Genome

Shiguo Zhou, Fusheng Wei, John Nguyen, Mike Bechner, Konstantinos Potamousis, Steve Goldstein, Louise Pape, Michael R. Mehan, Chris Churas, Shiran Pasternak, Dan K. Forrest, Roger Wise, Doreen Ware, Rod A. Wing, Michael S. Waterman, Miron Livny, David C. Schwartz

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000711

Abstract • Figures

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000734

Abstract • Figures

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

Carol Soderlund, Anne Descour, Dave Kudrna, Matthew Bomhoff, Lomax Boyd, Jennifer Currie, Angelina Angelova, Kristi Collura, Marina Wissotski, Elizabeth Ashley, Darren Morrow, John Fernandes, Virginia Walbot, Yeisoo Yu

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000740

Abstract • Figures

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000737

Abstract • Figures

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Dan Nettleton, Patrick S. Schnable

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000733

Abstract • Figures

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

Regina S. Baucom, James C. Estill, Cristian Chaparro, Naadira Upshaw, Ansuya Jogi, Jean-Marc Deragon, Richard P. Westerman, Phillip J. SanMiguel, Jeffrey L. Bennetzen

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000732

Abstract • Figures

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons

Thomas K. Wolfgruber, Anupma Sharma, Kevin L. Schneider, Patrice S. Albert, Dal-Hoe Koo, Jinghua Shi, Zhi Gao, Fangpu Han, Hyeran Lee, Ronghui Xu, Jamie Allison, James A. Birchler, Jiming Jiang, R. Kelly Dawe, Gernot G. Presting

PLOS Genetics: published 20 Nov 2009 | info:doi/10.1371/journal.pgen.1000743

Abstract • Figures

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Table of Contents: PLoS Genetics: 2009 Maize Genome Collection

Editorial

10 Reasons to be Tantalized by the B73 Maize Genome

Research Articles

The Physical and Genetic Framework of the Maize B73 Genome

A Genome-Wide Characterization of MicroRNA Genes in Maize

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

A Single Molecule Scaffold for the Maize Genome

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons