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B73 Reference Genome Assembly Status
The current representative 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 2018) Release dates will be posted
here and elsewhere at MaizeGDB as they become available.
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B73 Representative Reference Genome Assembly Details
The current version is
Zm-B73-REFERENCE-GRAMENE-4.0,
also known as "B73 RefGen_v4" and "AGPv4".
Chromosomes
The assembly sequence includes all 10 chromosomes, along with
the mitochondrial and plastid genomes.
The sequence can be downloaded
from Gramene
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 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_v3.
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 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 |
Information and stats for B73 RefGen_v2.
B73 RefGen_v2 Stats
Gene Feature |
Value |
Average WGS transcript size |
2646 bp |
Average FGS transcript size |
4237 bp |
Average Exon size |
287 bp |
Average Number of exons per gene |
3.6 exons |
Maximum exons per gene |
53 exons (GRMZM2G068755_T01) |
Average Intron size |
629 bp |
Average Coding region size |
210 bp |
Average 5' UTR average length |
280 bp |
Average 3' UTR average length |
336 bp |
Information and stats for B73 RefGen_v1.
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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:
gene model set |
description |
assembly version |
Gramene version |
cross reference |
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
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5b+
|
Filtered Gene Set, mostly projections of 5b |
RefGen_v3 |
18-31 |
xref
|
5a
|
Working Gene Set (WGS) |
RefGen_v2 |
7-17 |
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5b
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Filtered Gene Set (FGS) - subset of WGS |
RefGen_v2 |
7-17 |
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4a.53 |
Filtered and Working gene sets |
RefGen_v1 |
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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
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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.
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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]
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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 |
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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%).
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34 |
52 |
Zm-B73-REFERENCE-GRAMENE-4.0 |
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12/18/16 |
Changes in 154 gene models [more],
no changes to assembly FASTA files.
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35 |
53 |
Zm-B73-REFERENCE-GRAMENE-4.0 |
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04/26/17 |
Changes in 787 gene models [more],
no changes to assembly FASTA files.
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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.
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37 |
55 |
Zm-B73-REFERENCE-GRAMENE-4.0 |
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10/05/17 |
1861 additional gene models including Rfam predictions, changes to 154 gene models
[more],
no changes to assembly FASTA files
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38 |
56 |
Zm-B73-REFERENCE-GRAMENE-4.0 |
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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)
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39 |
57 |
Zm-B73-REFERENCE-GRAMENE-4.0 |
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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 |
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09/20/18 |
174 GRMZM ids for organelle gene models removed, 364 organelle gene models added. |
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B73 Stock Information
The B73 seed source for B73-REF-REFERENCE-4.0 was also 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
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Chromosome - Genbank accessions reference |
Chromosome |
B73 RefGen_v1 |
B73 RefGen_v2 |
B73 RefGen_v3 |
B73 RefGen_v4 |
Publication |
Chromosome 1 |
GK000031.1
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GK000031.2
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GK000031.3
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CM007647.1
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PubMed,
MaizeGDB
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Chromosome 2 |
GK000032.1
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GK000032.2
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GK000032.3
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CM007648.1
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PubMed,
MaizeGDB
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Chromosome 3 |
GK000033.1
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GK000033.2
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GK000033.3
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CM007649.1
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PubMed,
MaizeGDB
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Chromosome 4 |
CM000780.1
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CM000780.2
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CM000780.3
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CM000780.4
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PubMed,
MaizeGDB
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Chromosome 5 |
CM000781.1
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CM000781.2
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CM000781.4
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CM000781.4
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PubMed,
MaizeGDB
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Chromosome 6 |
CM000782.1
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CM000782.2
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CM000782.3
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CM000782.4
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PubMed,
MaizeGDB
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Chromosome 7 |
GK000034.1
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GK000034.2
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GK000034.3
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CM007650.1
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PubMed,
MaizeGDB
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Chromosome 8 |
CM000784.1
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CM000784.2
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CM000784.3
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CM000784.4
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PubMed,
MaizeGDB
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Chromosome 9 |
CM000785.1
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CM000785.2
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CM000785.3
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CM000785.4
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PubMed,
MaizeGDB
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Chromosome 10 |
CM000786.1
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CM000786.2
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CM000786.3
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CM000786.4
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PubMed,
MaizeGDB
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WGS (Whole Genome Shotgun) record at GenBank
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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?
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 reference-quality genome
which is considered to be representative for a species. For maize, the
representative genome is the Gramene B73 genome assembly.
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.
Changes to the v3 gene models include:
-
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)
How can I map positions between the v2 and v3 assemblies?
Use the Ensembl assembly converter tool
at Gramene.
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.
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