B73 Reference Genome Assembly Status

The current Reference Genome for Maize is B73 RefGen_v4 (also known as Zm-B73-REFERENCE-GRAMENE-4.0).

The three previous 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 B73RefGen_v4 assembly can be found at Gramene or by reading the paper.

See the Assembly Manifesto for more information.

Next assembly version: The release date of the next assembly update is not known at this time (October 2016) Release dates will be posted here and elsewhere at MaizeGDB as they become available.

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: Sequential gene ids do not imply relative position. Although the Zm00001d.2 gene models were called and numbered sequentially, they may move as the assembly is improved.

The current reference gene model set is named Zm00001d.2. Gene models within this set are prefixed with "Zm00001d". Associations between the new gene models and the 5b+ gene models is 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

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.

All 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-GRAMENE-4.0	assembly	32-36
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

Functional annotation from Phytozome 10 (log in required)


Cross reference for GRMZM and ZEAMMB73 IDs

FAQs

What is a Reference Genome?
What are the main changes between RefGen_v2 and RefGen_v3?
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.

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.

• 251 improved gene models
• Among the improved modes, the following Fgenesh models were improved and given GRMZM IDs:

  AC147602.5_FG004 -> GRMZM6G741210

  AC190882.3_FG003 -> GRMZM6G961377

  AC192244.3_FG001 -> GRMZM6G869379

  AC194389.3_FG001 -> GRMZM6G399977

  AC204604.3_FG008 -> GRMZM6G220418

  AC210529.3_FG004 -> GRMZM6G945840

  AC232289.2_FG005 -> GRMZM6G404540

  AC233893.1_FG001 -> GRMZM6G310687

  AC233910.1_FG005 -> GRMZM6G729818

  AC235534.1_FG001 -> GRMZM6G798998

• 213 novel gene models
• 10 gene models were merged into 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

• The 39,656 FGS gene models in 5b are now 39,475 protein-coding gene models in 5b+ (loss is due to merging; non-protein-coding gene models indicated as low confidence, and transposable elements)

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.