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Overview of the Genome Assemblies for Maize
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| Project name |
Version 1 of the maize B73 reference genome |
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Under Toronto Agreement?
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no |
| Project detail page |
B73 RefGen_v1 |
| Importance |
B73 is a key founder line to stiff stalk germplasm and has been extensively used for breeding and genetics for decades. Due to its importance to researchers and breeders, it became the first maize genome to be sequenced. |
| Assembly name |
B73 RefGen_v1 |
| Also known as |
AGPv1, B73 RefGen_v1 |
| Assembly identifier |
Zm00001a |
| Project accession |
PRJNA10769 |
| Quality |
Representative |
| Cultivar |
B73 |
| Current annotation |
not yet provided |
| Sequencing group |
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| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
Sanger |
| Status |
Completed |
| Changes since previous version |
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| Release date (may be an estimate) |
2011 |
| Publication |
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, Kai Ying, Cheng-Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, W. Brad Barbazuk, Regina S. Baucom, Thomas P. Brutnell, Nicholas C. Carpita, Cristian Chaparro, Jer-Ming Chia, Jean-Marc Deragon, James C. Estill, Yan Fu, Jeffrey A. Jeddeloh, Yujun Han, Hyeran Lee, Pinghua Li, Damon R. Lisch, Sanzhen Liu, Zhijie Liu, Dawn Holligan Nagel, Maureen C. McCann, Phillip SanMiguel, Alan M. Myers, Dan Nettleton, John Nguyen, Bryan W. Penning, Lalit Ponnala, Kevin L. Schneider, David C. Schwartz, Anupma Sharma, Carol Soderlund, Nathan M. Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K. Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L. Bennetzen, R. Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G. Presting, Susan R. Wessler, Srinivas Aluru, Robert A. Martienssen, Sandra W. Clifton, W. Richard McCombie, Rod A. Wing, Richard K. Wilson |
| Download |
http://ftp.maizesequence.org/ |
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| Project name |
Version 2 of the maize B73 reference genome |
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Under Toronto Agreement?
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no |
| Project detail page |
B73 RefGen_v2 |
| Importance |
B73 is a key founder line to stiff stalk germplasm and has been extensively used for breeding and genetics for decades. Due to its importance to researchers and breeders, it became the first maize genome to be sequenced. |
| Assembly name |
B73 RefGen_v2 |
| Also known as |
AGPv2, B73 RefGen_v2 |
| Assembly identifier |
Zm00001b |
| Project accession |
PRJNA10769 |
| Quality |
Representative |
| Cultivar |
B73 |
| Current annotation |
not yet provided |
| Sequencing group |
Doreen Ware |
| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
Sanger |
| Status |
Completed |
| Changes since previous version |
Improvements to order and orientation of within-BAC contigs using the minimum tiling path (MPT). |
| Release date (may be an estimate) |
2010 |
| Publication |
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| Download |
ftp://ftp.ensemblgenomes.org/pub/plants/release-7/fasta/zea_mays/dna/ |
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| Project name |
Version 3 of the maize B73 reference genome |
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Under Toronto Agreement?
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no |
| Project detail page |
B73 RefGen_v3 |
| Importance |
B73 is a key founder line to stiff stalk germplasm and has been extensively used for breeding and genetics for decades. Due to its importance to researchers and breeders, it became the first maize genome to be sequenced. |
| Assembly name |
B73 RefGen_v3 |
| Also known as |
AGPv3, B73 RefGen_v3 |
| Assembly identifier |
Zm00001c |
| Project accession |
PRJNA72137 |
| Quality |
Representative |
| Cultivar |
B73 |
| Current annotation |
5b+ |
| Sequencing group |
Doreen Ware |
| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
Sanger and 454 |
| Status |
Completed |
| Changes since previous version |
500 fosmid clones were sequenced and finished and an 8x shotgun sequence was generated via 454 sequencing. BAC assemblies were improved for BACs in the tiling path, and gaps in v2 were filled with resultant sequence contigs. |
| Release date (may be an estimate) |
2013 |
| Publication |
A panoply of genomics techniques to update the Zea mays B73 reference sequence and annotations. Andrew J. Olson, Joshua C. Stein, Shiran Pasternak, Jeffrey C. Glaubitz, Edward S. Buckler, Fusheng Wei, Jianwei Zhang, Rod A. Wing, Robert S. Fulton, Richard K. Wilson, Ethalinda K.S. Cannon, Carson M. Andorf, Carolyn J. Lawrence |
| Download |
ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/zea_mays/dna |
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| Project name |
Zea mays strain: Palomero Toluqueno EDMX-2233 Genome sequencing and assembly |
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Under Toronto Agreement?
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no |
| Project detail page |
unavailable |
| Importance |
Palomero toluqueno is a Mexican landrace (heterogenous), and was chosen for having the smallest genome of the Mexican Land Races. |
| Assembly name |
ZeaMays_PT_EDMX2233_1.0 |
| Also known as |
Palomero |
| Assembly identifier |
Zm00002a |
| Project accession |
PRJNA51041 |
| Quality |
Scaffolds |
| Cultivar |
Palomero Toluqueno |
| Current annotation |
not yet provided |
| Sequencing group |
Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO) CINVESTAV Irapuato |
| Contact |
() |
| Sequencing platform(s) |
unknown |
| Status |
Completed |
| Changes since previous version |
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| Release date (may be an estimate) |
2011 |
| Publication |
The Palomero genome suggests metal effects on domestication.. Vielle-Calzada JP1, Martínez de la Vega O, Hernández-Guzmán G, Ibarra-Laclette E, Alvarez-Mejía C, Vega-Arreguín JC, Jiménez-Moraila B, Fernández-Cortés A, Corona-Armenta G, Herrera-Estrella L, Herrera-Estrella A. |
| Download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/all_assembly_versions/GCA_000223545.1_ZeaMays_PT_EDMX2233_1.0 |
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| Project name |
Sequencing, Assembly and Annotation of B104 , A Maize Transformation Resource. |
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Under Toronto Agreement?
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YES |
| Project detail page |
Zm-B104-DRAFT-ISU_USDA-0.1 |
| Importance |
The B104 inbreed was derived from the same BSSS breeding population as B73. The genomes are very similar (93% similar as defined by Romay et al. Genome Biology 2013), but B104 is readily transformed whereas B73 is not. Having the genome of a transformable maize line is therefore very valuable to the maize community. This B104 maize line is used in the Iowa State Transformation Facility. |
| Assembly name |
Zm-B104-DRAFT-ISU_USDA-0.1 |
| Also known as |
B104 |
| Assembly identifier |
Zm00007a |
| Project accession |
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| Quality |
Draft |
| Cultivar |
B104 |
| Current annotation |
Zm00007a.1 |
| Sequencing group |
Carolyn Dill, Carson Andorf, Nick Lauter, Kan Wang- ISU |
| Contact |
Carson Andorf (Carson.Andorf@ARS.USDA.GOV) |
| Sequencing platform(s) |
Illumina paired end sequencing |
| Status |
Draft pseudomolecules. Full reference genome release expected fall 2017. |
| Changes since previous version |
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| Release date (may be an estimate) |
fall 2017 |
| Publication |
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| Download |
https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-B104-DRAFT-ISU_USDA-0.1/ |
| Comments |
In the interest of the maize research community, the Iowa State Transformation Facility and Lawrence-Dill Plant Informatics and Computation Lab in collaboration with MaizeGDB has released a beta-version of the B104 maize genome and structural annotations prior to scientific publication in accordance with guidelines set forth by the Toronto Agreement for prepublication data sharing (Nature. 2009 461:168). The above groups reserve the first right to publish on the available B104 data including but not limited to whole-genome comparisons, genes, structural annotations, functional annotations, and genome-wide association studies. The group also reserves the right to the first opportunity to improve this sequence and its annotations for a full official genome release (version 1; anticipated release December 2017). Under the Toronto agreement, researchers can use the B104 sequence and annotation to study individual or small sets of genes and localized regions of the genome. Any redistribution of these data should include the full text of the data use policy. |
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| Project name |
B73 Genome Assembly |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-B73-REFERENCE-GRAMENE-4.0 |
| Importance |
B73 is a key founder line to stiff stalk germplasm and has been extensively used for breeding and genetics for decades. Due to its importance to researchers and breeders, it became the first maize genome to be sequenced. |
| Assembly name |
Zm-B73-REFERENCE-GRAMENE-4.0 |
| Also known as |
AGPv4, B73 RefGen_v4 |
| Assembly identifier |
Zm00001d |
| Project accession |
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| Quality |
Representative |
| Cultivar |
B73 |
| Current annotation |
Zm00001d.1 |
| Sequencing group |
Doreen Ware |
| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
PacBio SMRT |
| Status |
Assembly and annotation released in spring, 2017 |
| Changes since previous version |
De novo assembly of this representative maize genome using PacBio sequencing technologies. |
| Release date (may be an estimate) |
2016-09-16 |
| Publication |
Improved maize reference genome with single-molecule technologies. Yinping Jiao; Paul Peluso; Jinghua Shi; Tiffany Liang; Michelle C. Stitzer; Bo Wang; Michael Campbell; Joshua C. Stein; Xuehong Wei; Chen-Shan Chin; Katherine Guill; Michael Regulski; Sunita Kumari; Andrew Olson; Jonathan Gent; Kevin L. Schneider; Thomas K. Wolfgruber; Michael R. May; Nathan M. Springer; Eric Antoniou; Richard McCombie; Gernot G. Presting; Michael McMullen; Jeffrey Ross-Ibarra; Kelly Dawe; Alex Hastie; David R. Rank; Doreen Ware |
| Download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_000005005.6_B73_RefGen_v4 |
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| Project name |
B73 Genome Assembly |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-B73-REFERENCE-GRAMENE-4.0 |
| Importance |
B73 is a key founder line to stiff stalk germplasm and has been extensively used for breeding and genetics for decades. Due to its importance to researchers and breeders, it became the first maize genome to be sequenced. |
| Assembly name |
Zm-B73-REFERENCE-GRAMENE-4.0 |
| Also known as |
AGPv4, B73 RefGen_v4 |
| Assembly identifier |
Zm00001d |
| Project accession |
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| Quality |
Representative |
| Cultivar |
B73 |
| Current annotation |
Zm00001d.2 |
| Sequencing group |
Doreen Ware |
| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
PacBio SMRT |
| Status |
Assembly and annotation released in spring, 2017 |
| Changes since previous version |
De novo assembly of this representative maize genome using PacBio sequencing technologies. |
| Release date (may be an estimate) |
2016-09-16 |
| Publication |
Improved maize reference genome with single-molecule technologies. Yinping Jiao; Paul Peluso; Jinghua Shi; Tiffany Liang; Michelle C. Stitzer; Bo Wang; Michael Campbell; Joshua C. Stein; Xuehong Wei; Chen-Shan Chin; Katherine Guill; Michael Regulski; Sunita Kumari; Andrew Olson; Jonathan Gent; Kevin L. Schneider; Thomas K. Wolfgruber; Michael R. May; Nathan M. Springer; Eric Antoniou; Richard McCombie; Gernot G. Presting; Michael McMullen; Jeffrey Ross-Ibarra; Kelly Dawe; Alex Hastie; David R. Rank; Doreen Ware |
| Download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_000005005.6_B73_RefGen_v4 |
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| Project name |
De novo genome assembly of tropical maize inbred line CML247 |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-CML247-DRAFT-PANZEA-1.0 |
| Importance |
A topical line that is valuable line for maize breeding because of its high disease resistance, and is a maize NAM line parent. CML247 is also one of the CIMMYT maize inbred lines (CMLs). |
| Assembly name |
Zm-CML247-DRAFT-PANZEA-1.0 |
| Also known as |
CML247 |
| Assembly identifier |
Zm00006a |
| Project accession |
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| Quality |
Draft |
| Cultivar |
CML247 |
| Current annotation |
not yet provided |
| Sequencing group |
Ed Buckler |
| Contact |
Ed Buckler (esb33@cornell.edu) |
| Sequencing platform(s) |
Illumina HiSeq2500, Illumina MiSeq |
| Status |
Assembly and annotation released |
| Changes since previous version |
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| Release date (may be an estimate) |
5/30/2016 |
| Publication |
High-resolution genetic mapping of maize pan-genome sequence anchors. Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y, Li Y, Semagn K, Zhang X, Hernandez AG, Mikel MA, Soifer I, Barad O, Buckler ES |
| Download |
https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-CML247-DRAFT-PANZEA-1.0/ |
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| Project name |
De novo genome assembly of tropical maize inbred line CML247 by NRGene |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-CML247-REFERENCE-PANZEA-1.1 |
| Importance |
A valuable line for maize breeding because of its high disease resistance, and part of the maize pan-genome consortium. CML247 is a tropical line that is part of the CIMMYT maize inbred lines (CMLs). |
| Assembly name |
Zm-CML247-REFERENCE-PANZEA-1.1 |
| Also known as |
CML247 |
| Assembly identifier |
Zm00006b |
| Project accession |
PRJNA396542 |
| Quality |
Reference |
| Cultivar |
CML247 |
| Current annotation |
not yet provided |
| Sequencing group |
Ed Buckler |
| Contact |
Ed Buckler (esb33@cornell.edu) |
| Sequencing platform(s) |
Illumina HiSeq2500, Illumina MiSeq |
| Status |
Assembly released, annotation in progress |
| Changes since previous version |
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| Release date (may be an estimate) |
10/24/2017 |
| Publication |
High-resolution genetic mapping of maize pan-genome sequence anchors. Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y, Li Y, Semagn K, Zhang X, Hernandez AG, Mikel MA, Soifer I, Barad O, Buckler ES |
| Download |
https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-CML247-REFERENCE-PANZEA-1.1/ |
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| Project name |
DK105 Genome Assembly - Technical University of Munich |
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Under Toronto Agreement?
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n/a |
| Project detail page |
Zm-DK105-REFERENCE-TUM-1.0 |
| Importance |
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| Assembly name |
Zm-DK105-REFERENCE-TUM-1.0 |
| Also known as |
DK105 |
| Assembly identifier |
Zm00016a |
| Project accession |
PRJNA360923 |
| Quality |
Reference |
| Cultivar |
DK105 |
| Current annotation |
not yet provided |
| Sequencing group |
Bauer Lab |
| Contact |
Eva Bauer (e.bauer@tum.de) |
| Sequencing platform(s) |
Illumina technologies |
| Status |
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| Changes since previous version |
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| Release date (may be an estimate) |
2018-10-01 |
| Publication |
Flint sequences complement the maize pan-genome. E. Bauer, G. Haberer, M.A. Seidel, K. Baruch, M. Spannagl, K.F.X. Mayer, C.-C. Schön |
| Download |
none available |
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| Project name |
EP1 Genome Assembly - Technical University of Munich |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-EP1-REFERENCE-TUM-1.0 |
| Importance |
EP1 is an important Flint breeding line in Europe and trace back to the Spanish landrace Lizargarate. Many US lines derive from Dent germplasm. The EP1 reference sequence complements the maize pan-genome with European Flint diversity. |
| Assembly name |
Zm-EP1-REFERENCE-TUM-1.0 |
| Also known as |
EP1 |
| Assembly identifier |
Zm00010a |
| Project accession |
PRJNA360920 |
| Quality |
Reference |
| Cultivar |
EP1 |
| Current annotation |
Zm00010a.1 |
| Sequencing group |
Chris-Carolin Schön (Plant Breeding, Technical University of Munich) |
| Contact |
Eva Bauer (e.bauer@tum.de) |
| Sequencing platform(s) |
Illumina technologies |
| Status |
Assembly and annotation released |
| Changes since previous version |
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| Release date (may be an estimate) |
1st of February 2017 (pre-release) |
| Publication |
European Flint reference sequences complement the maize pan-genome. Unterseer, Sandra*; Seidel, Michael A.*; Bauer, Eva; Haberer, Georg; Hochholdinger, Frank; Opitz, Nina, Marcon, Caroline; Baruch, Kobi; Manuel Spannagl; Mayer, Klaus F.X.; Schön, Chris-Carolin
* These authors contributed equally. |
| Download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_001984235.2_Zm-EP1-REFERENCE-TUM-1.0 |
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| Project name |
F7 Genome Assembly - Technical University of Munich |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-F7-REFERENCE-TUM-1.0 |
| Importance |
F7 is an important Flint breeding line in Europe, and trace back to the French landrace Lacaune. Many US lines derive from Dent germplasm. The F7 reference sequence complements the maize pan-genome with European Flint diversity. |
| Assembly name |
Zm-F7-REFERENCE-TUM-1.0 |
| Also known as |
F7 |
| Assembly identifier |
Zm00011a |
| Project accession |
PRJNA360923 |
| Quality |
Reference |
| Cultivar |
F7 |
| Current annotation |
Zm00011a.1 |
| Sequencing group |
Chris-Carolin Schön (Plant Breeding, Technical University of Munich) |
| Contact |
Eva Bauer (e.bauer@tum.de) |
| Sequencing platform(s) |
Illumina technologies |
| Status |
Assembly and annotation released |
| Changes since previous version |
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| Release date (may be an estimate) |
1st of February 2017 (pre-release) |
| Publication |
European Flint reference sequences complement the maize pan-genome. Unterseer, Sandra*; Seidel, Michael A.*; Bauer, Eva; Haberer, Georg; Hochholdinger, Frank; Opitz, Nina, Marcon, Caroline; Baruch, Kobi; Manuel Spannagl; Mayer, Klaus F.X.; Schön, Chris-Carolin * These authors contributed equally. |
| Download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_001990705.1_Zm-F7-REFERENCE-TUM-1.0 |
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| Project name |
Mo17 Genome Assembly from CAU |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-Mo17-REFERENCE-CAU-1.0 |
| Importance |
Mo17 is a maize lineage used in breeding and genetics research. Many varients of Mo17 exist, and this line likely differs from the Mo17 that is available from the Plant Introduction Station in Ames, IA |
| Assembly name |
Zm-Mo17-REFERENCE-CAU-1.0 |
| Also known as |
Mo17 |
| Assembly identifier |
Zm00014a |
| Project accession |
PRJNA358298 |
| Quality |
Reference |
| Cultivar |
Mo17 |
| Current annotation |
Zm00014a.1 |
| Sequencing group |
Lai lab |
| Contact |
Jinsheng Lai (jlai@cau.edu.cn) |
| Sequencing platform(s) |
PacBio+Illumina+Bionano |
| Status |
Assembly and annotation completed. |
| Changes since previous version |
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| Release date (may be an estimate) |
full release 2018 |
| Publication |
Exceptional intra-specific gene order and gene structural variations between maize B73 and Mo17 genome. Silong Sun, Yingsi Zhou, Jian Chen, Junpeng Shi, Haiming Zhao, Hainan Zhao, Weibin Song, Mei Zhang, Yang Cui, Xiaomei Dong, Han Liu, Xuxu Ma, Yinping Jiao, Xuehong Wei, Joshua C. Stein, Jeff C. Glaubitz, Fei Lu, Guoliang Yu, Chengzhi Liang, Kevin Fengler, Bailin Li, Antoni Rafalski, Patrick S. Schnable, Doreen H. Ware, Edward S. Buckler, Jinsheng Lai |
| Download |
https://ftp.maizegdb.org/MaizeGDB/FTP/Zm-Mo17-REFERENCE-CAU-1.0ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/185/045/GCA_003185045.1_Zm-Mo17-REFERENCE-CAU-1.0 |
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| Project name |
Mo17 Genome Assembly - Lai Lab |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-Mo17-REFERENCE-NRGENE-1.0 |
| Importance |
Mo17 is a maize lineage used in breeding and genetics research. Many varients of Mo17 exist, and this line likely differs from the Mo17 that is available from the Plant Introduction Station in Ames, IA. |
| Assembly name |
Zm-Mo17-REFERENCE-NRGENE-1.0 |
| Also known as |
Mo17 |
| Assembly identifier |
Zm00005a |
| Project accession |
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| Quality |
Reference |
| Cultivar |
Mo17 |
| Current annotation |
Zm00005a.1 |
| Sequencing group |
Lai lab |
| Contact |
Jinsheng Lai (jlai@cau.edu.cn) |
| Sequencing platform(s) |
Illumina sequencing of 50x coverage reads with assembly by NRGene |
| Status |
Not released. Replaced by Zm-Mo17-REFERENCE-CAU-1.0 |
| Changes since previous version |
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| Release date (may be an estimate) |
n/a |
| Publication |
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| Download |
none available |
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| Project name |
Mo17 Genome Assembly - Yan Lab |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-Mo17-REFERENCE-YAN-1.0 |
| Importance |
Mo17 is a maize lineage used in breeding and genetics research. Many varients of Mo17 exist, and this line likely differs from the Mo17 that is available from the Plant Introduction Station in Ames, IA |
| Assembly name |
Zm-Mo17-REFERENCE-YAN-1.0 |
| Also known as |
Mo17 |
| Assembly identifier |
Zm00009a |
| Project accession |
PRJNA299869 |
| Quality |
Reference |
| Cultivar |
Mo17 |
| Current annotation |
Zm00009a.1 |
| Sequencing group |
Jianbing Yan |
| Contact |
Jianbing Yan (yjianbing@mail.hzau.edu.cn) |
| Sequencing platform(s) |
Illumina, Pacific Biosciences |
| Status |
Assembly and annotation completed |
| Changes since previous version |
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| Release date (may be an estimate) |
'Nov, 2017 |
| Publication |
Contributions of Zea mays subspecies mexicana haplotypes to modern maize.. Ning Yang, Xi-Wen Xu, Rui-Ru Wang, Wen-Lei Peng, Lichun Cai, Jia-Ming Song, Wenqiang Li, Xin Luo, Luyao Niu, Yuebin Wang, Min Jin, Lu Chen, Jingyun Luo, Min Deng, Long Wang, Qingchun Pan, Feng Liu, David Jackson, Xiaohong Yang, Ling-Ling Chen, Jianbing Yan |
| Download |
none available |
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| Project name |
PE0075 Genome Assembly - Technical University of Munich |
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Under Toronto Agreement?
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n/a |
| Project detail page |
Zm-PE0075-REFERENCE-TUM-1.0 |
| Importance |
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| Assembly name |
Zm-PE0075-REFERENCE-TUM-1.0 |
| Also known as |
PE0075 |
| Assembly identifier |
Zm00017a |
| Project accession |
PRJNA360923 |
| Quality |
Reference |
| Cultivar |
PE0075 |
| Current annotation |
not yet provided |
| Sequencing group |
Bauer Lab |
| Contact |
Eva Bauer (e.bauer@tum.de) |
| Sequencing platform(s) |
Illumina technologies |
| Status |
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| Changes since previous version |
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| Release date (may be an estimate) |
2018-10-01 |
| Publication |
Flint sequences complement the maize pan-genome. E. Bauer, G. Haberer, M.A. Seidel, K. Baruch, M. Spannagl, K.F.X. Mayer, C.-C. Schön |
| Download |
none available |
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| Project name |
PH207 Genome Assembly |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0 |
| Importance |
PH207 is a key founder line to Iodent germplasm and represents an alternative to B73 (stiff stalk germplasm). For more information, se the poster. |
| Assembly name |
Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0 |
| Also known as |
PH207 |
| Assembly identifier |
Zm00008a |
| Project accession |
PRJNA389728 |
| Quality |
Reference |
| Cultivar |
PH207 |
| Current annotation |
Zm00008a.1 |
| Sequencing group |
Candy Hirsch |
| Contact |
Candy Hirsch (cnhirsch@umn.edu) |
| Sequencing platform(s) |
Whole-genome shotgun sequencing using paired-end, mate-pair, and TruSeq synthetic long-reads |
| Status |
Assembly and annotation completed |
| Changes since previous version |
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| Release date (may be an estimate) |
Nov, 2016 |
| Publication |
De novo assembly of elite inbred line PH207 provides insights into genomic and transcriptomic diversity in maize (Zea mays L.). Candice N. Hirscha, Cory D. Hirsch, Alex B. Brohammer, Megan J. Bowman, Ilya Soifer, Omer Barad, Doron Shem-Tov, Kobi Baruch, Fei Lu, Alvaro G. Hernandez, Christopher J. Fields, Chris L. Wright, Klaus Koehler, Nathan M. Springer, Edward Buckler, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler, Kevin L. Childs, Mark A. Mikel |
| Download |
http://dx.doi.org/10.5061/dryad.8vj84 https://phytozome.jgi.doe.gov/pz/portal.html#!bulk?org=Org_ZmaysPH207 |
| Comments |
De novo genomic assembly of the Iodent PH207 through extensive (~220x) Illumina short read sequencing of multiple insert size libraries coupled with light (~1.3x) coverage from Illumina Moleculo Long Read Technology |
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| Project name |
W22 (C1:R-r:std - PI 674445) Sequence and Assembly |
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Under Toronto Agreement?
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no |
| Project detail page |
Zm-W22-REFERENCE-NRGENE-2.0 |
| Importance |
W22 has been heavily used in genetic and crop breeding experiments for decades. Its sequence is especially valuable to maize researchers using sequence-indexed Mutator insertion lines. |
| Assembly name |
Zm-W22-REFERENCE-NRGENE-2.0 |
| Also known as |
W22 |
| Assembly identifier |
Zm00004b |
| Project accession |
PRJNA311133 |
| Quality |
Reference |
| Cultivar |
W22 |
| Current annotation |
Zm00004b.1 |
| Sequencing group |
Tom Brutnell, Erik Vollbrecht, Charles Du, Hugo Dooner, Don McCarty |
| Contact |
Tom Brutnell (tbrutnell@danforthcenter.org) |
| Sequencing platform(s) |
NRGene de novo assembly |
| Status |
Assembly and annotation completed |
| Changes since previous version |
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| Release date (may be an estimate) |
December, 2016 |
| Publication |
The maize W22 genome provides a foundation for functional genomics and transposon biology.. Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong, Brutnell TP. |
| Download |
ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_001644905.2_Zm-W22-REFERENCE-NRGENE-2.0 |
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| Project name |
Zea mays ssp. mexicana Genome Assembly - PI 566673 |
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Under Toronto Agreement?
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no |
| Project detail page |
Zx-PI566673-REFERENCE-YAN-1.0 |
| Importance |
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| Assembly name |
Zx-PI566673-REFERENCE-YAN-1.0 |
| Also known as |
Zea mexicana |
| Assembly identifier |
Zx00001a |
| Project accession |
PRJNA299874 |
| Quality |
Reference |
| Cultivar |
PI 566673 |
| Current annotation |
Zx00001a.1 |
| Sequencing group |
Yan lab |
| Contact |
Jianbing Yan (yjianbing@mail.hzau.edu.cn) |
| Sequencing platform(s) |
Illumina, Pacific Biosciences |
| Status |
Assembly and annotation completed |
| Changes since previous version |
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| Release date (may be an estimate) |
'Nov, 2017 |
| Publication |
Contributions of Zea mays subspecies mexicana haplotypes to modern maize.. Ning Yang, Xi-Wen Xu, Rui-Ru Wang, Wen-Lei Peng, Lichun Cai, Jia-Ming Song, Wenqiang Li, Xin Luo, Luyao Niu, Yuebin Wang, Min Jin, Lu Chen, Jingyun Luo, Min Deng, Long Wang, Qingchun Pan, Feng Liu, David Jackson, Xiaohong Yang, Ling-Ling Chen, Jianbing Yan |
| Download |
none available |
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