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 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:

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

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 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

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+)?

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.

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.

Use the Ensembl assembly converter tool at Gramene.

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.

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.