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Overview of the Genome Assemblies for Maize
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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 |
B104 was derived from the same populations as the B73 reference. 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 |
| Quality |
Draft genome |
| Cultivar |
B104 |
| Current annotation |
not yet provided |
| 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 |
Beta version released on October 4th 2016 under Toronto Agreement. Draft pseudomolecule release in December 2016. Full reference genome release Fall 2017. |
| Release date (may be an estimate) |
Fall 2017 |
| Publication |
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| 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 |
The maize inbred line B73 has been extensively used for corn breeding and for maize 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 |
| Quality |
Full reference genome |
| Cultivar |
B73 |
| Current annotation |
not yet provided |
| Sequencing group |
Doreen Ware |
| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
PacBio Single Molecule Real-Time sequencing |
| Status |
Assembly completed and annotation is nearly complete |
| Release date (may be an estimate) |
2016-09-16 |
| Publication |
The complex sequence landscape of maize revealed by 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 |
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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 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-DRAFT-PANZEA-1.0 |
| Also known as |
CML247 |
| Assembly identifier |
Zm00006a |
| Quality |
Draft genome |
| 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 completed |
| Release date (may be an estimate) |
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 |
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| Project name |
EP1 Genome Assembly - Technical University of Munich |
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Under Toronto Agreement?
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YES |
| Project detail page |
Zm-EP1-REFERENCE-TUM-1.0 |
| Importance |
To remedy the scarcity of sequence resources for the Flint pool, a reference sequence was generated de novo from inbred line EP1. 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 |
| Quality |
Reference genome |
| Cultivar |
EP1 |
| Current annotation |
not yet provided |
| 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 completed and annotation in progress |
| Release date (may be an estimate) |
February, 2017 (under Toronto agreement) |
| 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. |
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| Project name |
F7 Genome Assembly - Technical University of Munich |
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Under Toronto Agreement?
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YES |
| Project detail page |
Zm-F7-REFERENCE-TUM-1.0 |
| Importance |
To remedy the scarcity of sequence resources for the Flint pool, a reference sequence was generated de novo from inbred line F7. 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 |
| Quality |
Reference genome |
| Cultivar |
F7 |
| Current annotation |
not yet provided |
| 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 completed and annotation in progress |
| Release date (may be an estimate) |
February, 2017 (under Toronto agreement) |
| 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. |
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| Project name |
Ki11 Genome Assembly |
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Under Toronto Agreement?
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N/A |
| Project detail page |
unavailable |
| Importance |
Drought-tolerant inbred line eveloped in 1982 Thailand by Kasetsart University. |
| Assembly name |
Zm-Ki11-REFERENCE-GRAMENE-1.0 |
| Also known as |
Ki11 |
| Assembly identifier |
Zm00012a |
| Quality |
Reference genome |
| Cultivar |
Ki11 |
| Current annotation |
not yet provided |
| Sequencing group |
Doreen Ware |
| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
unknown |
| Status |
In progress |
| Release date (may be an estimate) |
2017 |
| Publication |
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| Project name |
Mo17 Genome Assembly - Yan Lab |
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Under Toronto Agreement?
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N/A |
| Project detail page |
unavailable |
| Importance |
Mo17 is a maize lineage used in crop breeding and in maize genetics research. |
| Assembly name |
Zm-Mo17---1.0 |
| Also known as |
Mo17 |
| Assembly identifier |
Zm00009a |
| Quality |
unknown |
| Cultivar |
Mo17 |
| Current annotation |
not yet provided |
| Sequencing group |
Jianbing Yan |
| Contact |
Jianbing Yan (yjianbing@mail.hzau.edu.cn) |
| Sequencing platform(s) |
Combination of Illumina and PacBio |
| Status |
Near completion |
| Release date (may be an estimate) |
2017 |
| Publication |
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| Project name |
Mo17 Genome Assembly - Lai Lab |
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Under Toronto Agreement?
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N/A |
| Project detail page |
Zm-Mo17-REFERENCE-NRGENE-1.0 |
| Importance |
Mo17 is a maize lineage used in crop breeding and in maize genetics research. While this says it is Mo17, it is likely, almost certain, that is differs quite substantially 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 |
| Quality |
Reference genome |
| Cultivar |
Mo17 |
| Current annotation |
not yet provided |
| 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 |
Completed |
| Release date (may be an estimate) |
Late 2016 |
| Publication |
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| Project name |
NC350 Genome Assembly |
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Under Toronto Agreement?
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N/A |
| Project detail page |
unavailable |
| Importance |
Inbred line derived from an experimental line sharing the same pedigree of NC296 with an experimental line from the hybrid H101 from El Salvador. Developed in 1998 North Carolina, United States by North Carolina Agricultural Research Service. |
| Assembly name |
Zm-NC350-REFERENCE-GRAMENE-1.0 |
| Also known as |
NC350 |
| Assembly identifier |
Zm00013a |
| Quality |
Reference genome |
| Cultivar |
NC350 |
| Current annotation |
not yet provided |
| Sequencing group |
Doreen Ware |
| Contact |
Doreen Ware (ware@cshl.edu) |
| Sequencing platform(s) |
unknown |
| Status |
In progress |
| Release date (may be an estimate) |
2017 |
| Publication |
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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 |
Maize lineage that has been crossed into numerous maize lines along with B73. (PDF: https://pag.confex.com/pag/xxii/webprogram/Handout/Paper12232/PH207%20Assembly.pdf) |
| Assembly name |
Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0 |
| Also known as |
PH207 |
| Assembly identifier |
Zm00008a |
| Quality |
Reference genome |
| Cultivar |
PH207 |
| Current annotation |
not yet provided |
| 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 |
| Release date (may be an estimate) |
November, 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 |
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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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YES |
| 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 |
| Quality |
Reference genome |
| Cultivar |
W22 |
| Current annotation |
not yet provided |
| 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 |
| Release date (may be an estimate) |
2017 |
| Publication |
The maize W22 genome: a foundation for gene discovery and functional genomics. Tom Brutnell, Omer Barad, Kobi Baruch, Gil Ben-Zvi, Ed Buckler, Ethalinda Cannon, Paul Chomet, Hugo Dooner, Chunguang Du, Georg Jander, Karen Koch, Don McCarty, Ilya Soifer, Doron Shem-Tov, Erik Vollbrect, Doreen Ware, Maggie Woodhouse |
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