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Overview of the Genome Assemblies for Maize
Assembly Name Identifier Line Quality Toronto
Agreement
Status
Zm-B104-DRAFT-ISU_USDA-0.1 Zm00007a B104   Draft genome yes Beta version released on October 4th 2016 under Toronto Agreement. Draft pseudomolecule release in December 2016. Full reference genome release Fall 2017.
Zm-B73-REFERENCE-GRAMENE-4.0 Zm00001d B73   Full reference genome no Assembly completed and annotation is nearly complete
Zm-CML247-DRAFT-PANZEA-1.0 Zm00006a CML247   Draft genome Assembly and annotation completed
Zm-EP1-REFERENCE-TUM-1.0 Zm00010a EP1   Reference genome yes Assembly completed and annotation in progress
Zm-F7-REFERENCE-TUM-1.0 Zm00011a F7   Reference genome yes Assembly completed and annotation in progress
Zm-Ki11-REFERENCE-GRAMENE-1.0 Zm00012a Ki11   Reference genome In progress
Zm-Mo17-REFERENCE-NRGENE-1.0 Zm00005a Mo17   Reference genome Completed
Zm-Mo17---1.0 Zm00009a Mo17   unknown Near completion
Zm-NC350-REFERENCE-GRAMENE-1.0 Zm00013a NC350   Reference genome In progress
Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0 Zm00008a PH207   Reference genome Assembly and annotation completed
Zm-W22-REFERENCE-NRGENE-2.0 Zm00004b W22   Reference genome yes Assembly and annotation completed
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Project name Sequencing, Assembly and Annotation of B104 , A Maize Transformation Resource.
Under Toronto Agreement? 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
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.
Project name B73 Genome Assembly
Under Toronto Agreement? 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
Project name De novo genome assembly of tropical maize inbred line CML247
Under Toronto Agreement? 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
Project name EP1 Genome Assembly - Technical University of Munich
Under Toronto Agreement? 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.
Project name F7 Genome Assembly - Technical University of Munich
Under Toronto Agreement? 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.
Project name Ki11 Genome Assembly
Under Toronto Agreement? 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
Project name Mo17 Genome Assembly - Yan Lab
Under Toronto Agreement? 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
Project name Mo17 Genome Assembly - Lai Lab
Under Toronto Agreement? 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
Project name NC350 Genome Assembly
Under Toronto Agreement? 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
Project name PH207 Genome Assembly
Under Toronto Agreement? 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
Project name W22 (C1:R-r:std - PI 674445) Sequence and Assembly
Under Toronto Agreement? 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