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		Zm00001eb.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 Zm-B73-REFERENCE-NAM-5.0 (also known as RefGen_v5).

The current B73 assembly version, Zm-B73-REFERENCE-NAM-5.0, released in January 2020, was sequenced and assembled along with a 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 used 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 History of Maize Genome Assemblies and Annotations 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-GRAMENE-4.0/Zm00001d.2 Information

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

Counts for each chromosome.

Chromosome	Accession	Protein Coding	miRNA	Transposable Element	Low Confidence
Chromosome 1	NC_024459.2	5905	14		2209
Chromosome 2	NC_024460.2	4737	22		2209
Chromosome 3	NC_024461.2	4737	16		1571
Chromosome 4	NC_024462.2	4115	20		1826
Chromosome 5	NC_024463.2	4480	24		1681
Chromosome 6	NC_024464.2	3290	11		1223
Chromosome 7	NC_024465.2	3108	10		1193
Chromosome 8	NC_024466.2	3561	13		1288
Chromosome 9	NC_024467.2	2973	7		1191
Chromosome 10	NC_024468.2	2684	17		1034
Unmapped		319	0		357
Nuclear Total		39,324	154		15,516

Annotations: Zm00001d.2

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

Assembly process: In-depth metadata for B73 RefGen_v3 is available here.
Detailed information about the V3 assembly process is available at .

B73 RefGen_v3 Information

Counts for each chromosome.

Chromosome	Accession	Protein Coding	miRNA	Transposable Element	Low Confidence
Chromosome 1	NC_024459.1	6007	15	4296	6044
Chromosome 2	NC_024460.1	4742	23	3582	4997
Chromosome 3	NC_024461.1	4174	16	3093	4352
Chromosome 4	NC_024462.1	4182	21	3668	4688
Chromosome 5	NC_024463.1	4473	22	3103	4249
Chromosome 6	NC_024464.1	3278	10	2502	3430
Chromosome 7	NC_024465.1	3115	10	2424	3274
Chromosome 8	NC_024466.1	3505	13	2593	3508
Chromosome 9	NC_024467.1	2991	8	2404	3288
Chromosome 10	NC_024468.1	2688	18	2268	2734
Unmapped		146	0	51	59
Nuclear Total		39,475	156	29,996	40,680

Annotation: B73 RefGen_v3 gene model set 5b+

B73 RefGen_v3 Stats

Gene Feature	Value
Average protein-coding transcript size	4255 bp
Average low confidence transcript size	959 bp
Average transposable element size	1694 bp
Average Exon size	287 bp
Average Number of exons per gene	3.6 exons
Maximum exons per gene	35 exons (GRMZM2G068755_T01)
Average Intron size	630 bp
Average Coding region size	213 bp

Change history

B73 RefGen_v1

B73 RefGen_v2

B73 RefGen_v3

Zm-B73-REFERENCE-GRAMENE-4.0

Zm-B73-REFERENCE-NAM-5.0

B73 Reference Gene Models and Nomenclature

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: The B73 v5 and NAM founders genome assemblies were released with a preliminary annotation, named "Zm00001e.1". The official annotation was sufficiently different from the preliminary annotation that it was given a new name, "Zm00001eb.1" and the gene models were given new identifiers. Unlike previous annotations, the new identifiers are numbered in sequential order.

Cross-reference files that translate between the preliminary and official annotations can be found in the MaizeGDB downloads. The cross-reference for Zm00001e.1 to Zm00001eb.1 is here.

The current reference gene model set is named Zm00001eb.1. Gene models within this set are prefixed with "Zm00001eb". Associations between the v4 gene models (Zm0001d.2) and the 5b+ gene models are available here.

Gene model sets (annotations) by reference assembly version:

The Zm00001eb.1 gene model set is the recommended gene model set for Zm-B73-GRAMENE-REFERENCE-5.0 and is the representative gene model set for maize.

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

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 contact MaizeGDB 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

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

Publications

FAQs

What is a Reference Genome?
What is a Representative Genome?
What are the main changes between the v4 and v5 assemblies?
What are the main changes between the v3 and v4 assemblies?
What are the main changes between the v2 and v3 assemblies?
Why was a preliminary v5 annotation released?
How can I map positions between the v2 and v3 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+)?

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.

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

Zm-B73-REFERENCE-NAM-5.0 is a de novo assembly using improved PacBio long-read technology and BioNano optical maps, using the same tissue sourc as RefGen_v4 (Zm-B73-REFERENCE-GRAMENE-4.0).

Zm-B73-REFERENCE-GRAMENE-4.0 was a complete de novo assembly using PacBio technology on DNA extracted from a descendant of the accession used for the v1 - v3 assemblies.

Changes to the assembly include:

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

A preliminary annotation, Zm00001e.1, was release alongside the v5 genome assembly to put tools into the hands of researchers as soon as possible, but with warnings to not rely on any specific gene models until the formal annotation, Zm00001eb.1 was released.

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.

Use the Ensembl assembly converter tool at Gramene.

At the Gramene ftp archive.

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

From the Gramene 5b+ ftp folder.