Zm-B73-REFERENCE-GRAMENE-4.0 genome assembly
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The Zea mays ssp mays cv B73 Reference Genome


B73 Representative Reference Genome Assembly Status
B73 Representative Reference Genome Assembly Details
Change History
B73 Representative Reference Gene Models and Nomenclature
Gramene Versions
Genome Assembly and Gene Model Issues
B73 Stock Information
Chromosome names - Genbank accessions
Downloads
Genome Assembly Manifesto
The Nomenclature Standards
Genome Tools
Publications
FAQs
Coming Soon
Historic information


The Maize B73 Representative Reference Genome

The maize B73 reference genome has been revised four times since its initial release as a BAC-by-BAC assembly in 2009. As of 2016, the maize nomenclature committee has adopted naming standards to accommodate multiple Zea species, multiple accessions, and multiple versions. This recommendation is available here. The B73 reference assemblies have been known by these names:
assembly assembly aka annotation annotation aka Gramene/
EnsemblPlant
version
Zm-B73-REFERENCE-NAM-5.0 B73 RefGen_v5 Zm00001e.1
Zm-B73-REFERENCE-GRAMENE-4.0 B73 RefGen_v4, AGPv4 Zm00001d.2 AGPv4 32/50 - 40/58
B73 RefGen_v3 B73 RefGen_v3, AGPv3 5b+ AGPv3 18/36 - 31/49
B73 RefGen_v2 B73 RefGen_v2, AGPv2 5b 5b.60, AGPv2 7/25 - 17/37
B73 RefGen_v1 B73 RefGen_v1, AGPv1 4a 4a.53, AGPv1


B73 Representative Reference Genome Assembly Status

The current representative reference genome for Maize is B73 RefGen_v5 (also known as Zm-B73-REFERENCE-NAM-5.0).


The current B73 assembly version, RefGen_v5, released in January 2020, was sequenced and assembled along with a core set of 25 inbreds known as the NAM founder lines by the NAM Consortium using PacBio long reads and mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA.


The first three assemblies, B73 RefGen_v1, B73 RefGen_v2, and B73 RefGen_v3 were all based on a BAC (bacterial artificial chromosome) sequencing strategy. B73 RefGen_v4 assembly utilized a new approach that relied on PacBio Single Molecule Real Time (SMRT) sequencing at Cold Spring Harbor to a depth of 60X coverage with scaffolds created via the assistance of whole genome restriction mapping (aka Optical Mapping). Error correction of PacBio sequences was facilitated by Illumina short read DNA sequencing performed at Washington University. Annotation was accomplished in the Ware laboratory at Cold Spring Harbor using the Maker pipeline (Campbell, 2014) and ~111,000 long read PacBio transcipts from six maize tissues. More complete details in the B73 RefGen_v4 assembly can be found at Gramene or by reading the paper.


See the Assembly Manifesto for more information.




B73 Representative Reference Genome Assembly Details

The current version is Zm-B73-REFERENCE-NAM-5.0, also known as "B73 RefGen_v5".

Chromosomes
The assembly sequence includes all 10 chromosomes.
The sequence can be downloaded here. from ENA or from GenBank

Gaps
Gaps within BACs are indicated by runs of 100 N's. Gaps between contigs are indicated by runs of 1000 N's.



Zm-B73-REFERENCE-NAM-5.0/Zm00001e.1 Information

In-depth metadata for Zm-B73-REFERENCE-NAM-5.0 is available here.
See the paper for B73 RefGen_v1 here, and for Zm-B73-REFERENCE-GRAMENE-4.0 here.

Gene model counts are preliminary.
Counts for each chromosome.
Chromosome Accession Protein Coding miRNA Transposable Element Low Confidence
Chromosome 1 LR618874.1 5905 14 2209
Chromosome 2 LR618875.1 4737 22 2209
Chromosome 3 LR618876.1 4737 16 1571
Chromosome 4 LR618877.1 4115 20 1826
Chromosome 5 LR618878.1 4480 24 1681
Chromosome 6 LR618879.1 3290 11 1223
Chromosome 7 LR618880.1 3108 10 1193
Chromosome 8 LR618881.1 3561 13 1288
Chromosome 9 LR618882.1 2973 7 1191
Chromosome 10 LR618883.1 2684 17 1034
Unmapped 319 0 357
Nuclear Total 39,324 154 15,516
Annotations: Zm00001e.1


Zm-B73-REFERENCE-GRAMENE-4.0/Zm00001d Stats


Gene Feature Value
Average protein-coding transcript size 7638 bp
Average low confidence transcript size 6981 bp
Average transposable element size unavailable
Average Exon size 156 bp
Average Number of exons per gene 4 exons
Maximum exons per gene 81 exons (Zm00001d040166)
Average Intron size 578 bp
Average Coding region size 207 bp


Previous reference genome assemblies

Information and stats for B73 RefGen_v4 (Zm-B73-REFERENCE-GRAMENE-4.0)
Information and stats for B73 RefGen_v3.
Information and stats for B73 RefGen_v2.
Information and stats for B73 RefGen_v1.

Change history

B73 RefGen_v1

First complete assembly of the B73 genome.

B73 RefGen_v2

Improvements to order and orientation of within-BAC contigs using the minimum tiling path (MPT). Improvements to gene models.

B73 RefGen_v3

Captured missing gene space using WGS reads. 213 new gene models were introduced, 251 gene models were improved, and 10 gene models were merged to create new models:
GRMZM2G000964, GRMZM2G103315 -> GRMZM2G000964
GRMZM2G045892, GRMZM2G452386 -> GRMZM2G045892
GRMZM2G119720, GRMZM2G518717 -> GRMZM2G119720
GRMZM2G142383, GRMZM2G020429 -> GRMZM2G142383
GRMZM2G319465, GRMZM2G439578 -> GRMZM2G319465
GRMZM2G338693, GRMZM2G117517 -> GRMZM2G338693
GRMZM5G861997, GRMZM5G864178 -> GRMZM5G861997
GRMZM5G872800, GRMZM2G143862 -> GRMZM5G872800
GRMZM5G891969, GRMZM5G823855 -> GRMZM5G891969

Zm-B73-REFERENCE-GRAMENE-4.0

A de novo assembly using PacBio technologies. New annotation analysis with gene models linked to v3 gene models.

Zm-B73-REFERENCE-NAM-5.0

De novo Pac-Bio SEQUEL sequencing technology. Scaffolds validated by improved BioNano optical mapping. New annotation analysis.

Note that there is no converter yet available for translating between v4 and v5 positions, but chain files are available here, which can be used with LiftOver or CrossMap to convert sets of coordinates. Be aware that features on the unplaced scaffolds in the v4 assembly will not be correctly translated to the v5 assembly.


B73 Reference Gene Models and Nomenclature


Note: The current B73 gene model annotation is part of a two-set release process. The first set of models were generated using accession-specific RNA-seq from 10 tissues and the models obtained from these tissues were refined using evidence from B73 full-length cDNAs and EST data. These represent high-quality gene models expressed in the 10 tissues. This annotation will be augmented with a second set of gene models combining both ab-initio prediction and evidence. The second set of gene models are targeted for release in March 2020 or upon publication of the data manuscript.


With increasing numbers of full reference genomes with structural annotation becoming available, it has become necessary to establish naming standards that span genomes and versions. The recommendation is available here.

Important note: Sequential gene ids do not imply relative position. Although the Zm00001e.1 gene models were called and numbered sequentially, they may move as the assembly is improved.

The current reference gene model set is named Zm00001e.1. Gene models within this set are prefixed with "Zm00001e". Associations between the v4 gene models (Zm0001d.2) and the 5b+ gene models are available here.


Gene model sets (annotations) by reference assembly version:

gene model set   description assembly version Gramene version cross reference
Zm00001e.1 Filtered Gene Set Zm-B73-GRAMENE-NAM-5.0
Zm00001d.2 Filtered Gene Set Zm-B73-GRAMENE-REFERENCE-4.0 36 xref
Zm00001d.1 Filtered Gene Set Zm-B73-GRAMENE-REFERENCE-4.0 32-33 xref
5b+ Filtered Gene Set, mostly projections of 5b RefGen_v3 18-31 xref
5a Working Gene Set (WGS) RefGen_v2 7-17
5b Filtered Gene Set (FGS) - subset of WGS RefGen_v2 7-17
4a.53 Filtered and Working gene sets RefGen_v1

The Zm00001d.2 gene model set is the recommended gene model set for Zm-B73-GRAMENE-REFERENCE-4.0.

For RefGen_v3, the 5b+ gene model set is recommended. Other gene model sets for RefGen_v3 are provided for comparison. Due to the difficulty of determining when two gene models are the same (or when one represents an alternative splicing of the same genomic material), there are no plans to merge the sets.


For more information see the Nomenclature Standards



Alternative annotations

Additional annotations for the B73 genome assemblies have been generated by groups outside the genome sequencing project. The outside annotations listed below are shown as tracks on the assembly browsers.
Assembly Name Source link
Zm-B73-REFERENCE-GRAMENE-4.0 NCBI 102 NCBI https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Zea_mays/102/
B73 RefGen_v3 NCBI 100 NCBI/th> https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Zea_mays/100/
B73 RefGen_v3 EvidentialGene Don Gilbert, Indiana University http://arthropods.eugenes.org/EvidentialGene/plants/corn/evg5corn/

Description of Gramene/Ensembl versions of B73 genome download files

Versions supported by MaizeGDB is in bold

No changes were made to unmasked or masked assembly downloads unless noted.


Ensembl Gramene Assembly Gene Model Set Date Changes
7-17 25-35 B73 RefGen_v2 5b 11/30/10 - 03/10/13  not calculated
18 36 B73 RefGen_v3 5b+ 04/29/13 Initial B73 v3 downloads
19 37 B73 RefGen_v3 5b+ 07/08/13 GFF downloads available
20 38 B73 RefGen_v3 5b+ 09/10/13 17625 additional gene models [more]
21 39 B73 RefGen_v3 5b+ 01/16/14 2830 gene models removed, additional repeated masked files [more]
22 40 B73 RefGen_v3 5b+ 04/09/14 70676 models removed (WGS) [more]
23 41 B73 RefGen_v3 5b+ 09/01/14 166 gene models removed [more]
24 42 B73 RefGen_v3 5b+ 11/24/14 None
25 43 B73 RefGen_v3 5b+ 02/03/15 None
26 44 B73 RefGen_v3 5b+ 04/06/15 No repeat masked sequence in downloads
27 45 B73 RefGen_v3 5b+ 06/18/15 Repeat masked sequence returned to downloads
28 46 B73 RefGen_v3 5b+ 08/18/15 None
29 47 B73 RefGen_v3 5b+ 10/27/15 None
30 48 B73 RefGen_v3 5b+ 01/14/16 None
31 49 B73 RefGen_v3 5b+ 07/23/17 Repeat-masked gene model downloads
32 50 Zm-B73-REFERENCE-GRAMENE-4.0 Zm00001d.1 08/04/16 Initial B73 v4 downloads
33 51 Zm-B73-REFERENCE-GRAMENE-4.0 07/14/17 174 additional gene models (organelle), changes in 5825 gene models [more], Mt and Pt sequence added to assembly downloads, new repeat masked assembly FASTA files (%Ns changed from 85.12% to 6.69%).
34 52 Zm-B73-REFERENCE-GRAMENE-4.0 12/18/16 Changes in 154 gene models [more], no changes to assembly FASTA files.
35 53 Zm-B73-REFERENCE-GRAMENE-4.0 04/26/17 Changes in 787 gene models [more], no changes to assembly FASTA files.
36 54 Zm-B73-REFERENCE-GRAMENE-4.0 Zm00001d.2 06/27/17 Changes in 154 gene models [more], no changes to assembly FASTA files.
37 55 Zm-B73-REFERENCE-GRAMENE-4.0 10/05/17 1861 additional gene models including Rfam predictions, changes to 154 gene models [more], no changes to assembly FASTA files
38 56 Zm-B73-REFERENCE-GRAMENE-4.0 02/07/18 70 gene models removed, 7 added, changes to 1945 gene models [more], new repeat masked assembly FASTA files (%Ns chaged to 90.22)
39 57 Zm-B73-REFERENCE-GRAMENE-4.0 05/15/18 New repeat masked assembly FASTA files (%Ns chaged to 90.01)
40 58 Zm-B73-REFERENCE-GRAMENE-4.0 05/15/18 New repeat masked assembly FASTA files (%Ns chaged to 90.22)
41 59 Zm-B73-REFERENCE-GRAMENE-4.0 09/20/18 174 GRMZM ids for organelle gene models removed, 364 organelle gene models added.

B73 Reference Genome Assembly and Gene Model Issues

We need your help! Please report any assembly or gene model structure problems. This includes misassembled regions, evidence for closing gaps, gene models that should be merged or split, evidence supporting low-confidence gene models, et cetera. All issues will be shared with the maize community and with the team charged with improving the B73 assembly and gene models.


Please for information about open gene model issues
All resolved gene model issues


All open assembly issues
All resolved assembly issues



B73 Stock Information

The seed source for both Zm-B73-REFERENCE-NAM-5.0 and Zm-B73-REFERENCE-GRAMENE-4.0 descended from PI 550473, but was maintained for several generations prior to being used as the source seed. The seeds closest to those used for sequencing v4 were deposited at the NCRPIS (accession number: PI 677128).

The B73 source for the BAC libraries (BACs with prefix "b" prepared in Rod Wing's lab; BACs with prefix "c" prepared in Peter deJong's lab) was PI 550473. When requesting seed from the North Central Regional Plant Introduction Station, ask for any lot descended from the Coe PI 550473 lines.

The stock was received directly by the North Central Regional Plant Intoduction Station from Arnel Hallauer and has been maintained by the quality-maintenance procedures at the PI Station. Ed Coe reports that, "The results of QC lab checks for constancy in PI 550473 have been excellent."

The same source was used for the IBM mapping population. Maps produced at Missouri used 302 lines of this population, providing unmatched precision (resolution is at the intra-BAC level). These maps anchor the fingerprint-based contig assemblies to chromosome location.

High-Molecular-Weight DNA was prepared by Jack Gardiner in the lab at Missouri and shipped to Clemson (Wing's lab at the time) and to deJong's lab (just at the time his lab was moving to California) for BAC preparation.

NSF grant reports have documented the details, and specifics for the materials, preparation, characterization, and final assembly of the contig framework can be found in Coe E, Schaeffer ML (2005) Genetic, physical, maps, and database resources for maize. Maydica 50:285-303. Ed Coe has made a copy of that paper available here



B73 Assembly and Gene Model Downloads

Gramene files currently hosted at MaizeGDB correspond to Gramene version 36. See the summary of Gramene versions above.

assembly datasest Gramene version(s)
Zm-B73-REFERENCE-NAM-5.0 assembly and annotations
Zm-B73-REFERENCE-GRAMENE-4.0 assembly 32-40
Zm-B73-REFERENCE-GRAMENE-4.0 gene model cDNA fasta 36
Zm-B73-REFERENCE-GRAMENE-4.0 gene model ncRNA fasta 36
Zm-B73-REFERENCE-GRAMENE-4.0 gene model CDS fasta 36
Zm-B73-REFERENCE-GRAMENE-4.0 gene model translations fasta 36
Zm-B73-REFERENCE-GRAMENE-4.0 gene model GFF3 36
B73 RefGen_v3 assembly 18-31
B73 RefGen_v3 gene model cDNA fasta 18-31
B73 RefGen_v3 gene model ncRNA fasta 18-31
B73 RefGen_v3 gene model translations fasta 18-31
B73 RefGen_v3 gene model GFF3 18-31
B73 RefGen_v3 MAKER-P gene models n/a
B73 RefGen_v2 assembly 7-17
B73 RefGen_v2 filtered gene models 7-17
B73 RefGen_v2 working gene set 7-17
B73 RefGen_v2 functional annotation from Gramene n/a
B73 RefGen_v1 assembly n/a
B73 RefGen_v1 filtered gene models n/a
B73 RefGen_v1 working gene set n/a

WGS (Whole Genome Shotgun) records at GenBank:
Zm-B73-REFERENCE-GRAMENE-4.0
Zm-B73-REFERENCE-NAM-5.0


V4 Functional annotation from Phytozome 10 (log in required)


Cross reference for GRMZM and ZEAMMB73 IDs


Genome Tools for B73 Reference Assembly

BLAST
Genome browser
Map V3 data to V4



Publications

Jiao et al., 2017. Improved maize reference genome with single-molecule technologies.

Law et al., 2015. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

Wei et al., 2009. The physical and genetic framework of the maize B73 genome.

Schnable et al., 2009. The B73 maize genome: complexity, diversity, and dynamics.

Wei et al., 2007. Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History.

Bi et al., 2006. Single Nucleotide Polymorphisms and Insertion–Deletions for Genetic Markers and Anchoring the Maize Fingerprint Contig Physical Map.

Gardiner et al., 2004. Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization.

Coe et al., 2002. Access to the Maize Genome: An Integrated Physical and Genetic Map.

Yim et al., 2002. Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter Hybridization.

FAQs

What is a Reference Genome?
What is a Representative Genome?
What are the main changes between RefGen_v2 and RefGen_v3?
How can I map positions between the v2 and v3 assemblies?
How can I map positions between the v4 and v5 assemblies?
Where can I find legacy resources from MaizeSequence.Org?
How can I identify the Filtered Gene Set (FGS) in RefGen_v3?
Where can I download a GFF dump of the FGS for maize genes in v3 (5b+)?


What is a Reference Genome?

A Reference Genome is a haploid representation of a genome as DNA sequence with a defined coordinate system, and accession and version identification. A Reference genome is usually assembled de novo, rather than relying on related genomes for assembly of small DNA fragments (which would be a reference guided assembly). A Reference Genome usually includes the structural annotations, or gene models, derived from the sequence assembly. A Reference Genome is almost always a work in progress that gets better with the additional new data over time. Data for improvement is collected continually, and at certain times, new Reference Genome versions come out that incorporate this data. B73 RefGen_v3 is such an updated version.


What is a Representative Genome?

A Representative Genome is a reference-quality genome which is considered to be representative for a species. B73 is the representative maize genome.


What are the main changes between RefGen_v2 and RefGen_v3?

Changes to the assembly include:

  • v3 captured missing gene space in v2 using WGS reads (v2 improved initial BAC assembly using MTP)
  • X contigs were moved or flipped.


How can I map positions between the v2 and v3 assemblies?

Use the Ensembl assembly converter tool at Gramene.


How can I map positions between the v4 and v5 assemblies?

There is no converter yet available for translating between v4 and v5 positions, but chain files are available here (CyVerse login required), which can be used with LiftOver or CrossMap to convert sets of coordinates. Be aware that features on the unplaced scaffolds in the v4 assembly will not be correctly translated to the v5 assembly.


Where can I find legacy resources from MaizeSequence.Org?

At the Gramene ftp archive.


How can I identify the Filtered Gene Set (FGS) in RefGen_v3?

In the 5b+ gene build, the former FGS gene models are indicated as protein-coding.


Where can I download a GFF dump of the FGS for maize genes in v3 (5b+)?

From the Gramene 5b+ ftp folder.



Coming soon to MaizeGDB

Updated August 4, 2020

Tracks

  • Ab initio gene models for v5 and NAM assemblies
  • TE annotations
  • Structural Variations
  • SNPs used with the NAM RILs
  • SNPs used for IBM and LHRF RILs
  • Core Bin Markers - available on browsers, but not yet elsewhere
  • Insertion data
  • HapMap5
  • B73v5 methylome
  • HiC data

Page updates

  • Core Bin Marker Pages
  • Additional functional annotations for NAM gene models
  • JBrowse snapshots within gene model pages - completed
  • Pan-gene information on gene pages
  • Add physical coordinates for each NAM line to NAM genetic map page

Tools

  • MaizeMine update to include v5 annotations
  • qTeller update to include NAM RNA-seq data

Features

  • Pan-genome and syntenic ortholog information
  • External links to Apollo instances for manual structural annotations
  • V5 gene models linked to gene data
  • Current v5 gene models are evidence-based. Ab initio gene models will be added when available
  • Create links between GBrowse and JBrowse instances at MaizeGDB
  • Deploy JBrowse plugins to combine bigWig tracks