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Zm-P39-REFERENCE-NAM-1.0 genome assembly
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The NAM parents sequencing project
NAM Consortium website:
https://nam-genomes.github.io/
Currently, many or most forms of sequence analyses are referenced to the single
B73 inbred. Beyond B73, some of the most extensively researched maize lines are
the core set of 25 inbreds known as the NAM founder lines, which represent a broad
cross-section of modern maize diversity. Prior data show that gene content can
differ by more than 5% across lines and that as much as half of the functional
genetic information lies outside of genes in highly variable intergenic spaces.
To capture and utilize this variation, B73 and the NAM founder inbreds have been sequenced
and assembled by the NAM Consortium using PacBio long reads a 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. These data will help the maize community assess the role of structural
variation such as presence-absence variation and copy number variation in the
determination of agronomic traits.
Learn more about maize genome sequencing here.
Explore the NAM assemblies at the whole genome level
here.
Important note: The NAM founders genome assemblies were released
with a preliminary annotation. The official annotations are sufficiently
different from the preliminary annotations that they have been given new names
and gene models were given new identifiers. For example, the preliminary
annotation for B97, Zm00018a.1 was replaced with annotation Zm00018ab.1.
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 and are linked
in the table below.
The publication is available here:
De novo assembly,
annotation, and comparative analysis of 26 diverse maize genomes. Hufford et
al., 2021
Data hosted at MaizeGDB:
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FASTA for all genome assemblies and the official
annotations are available in the
MaizeGDB downloads
section.
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JBrowse instances for all assemblies are available
here. All genomes
are listed in the "Genome" menu on the top bar.
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BLAST targets for all genome assemblies and annotations
are available in the MaizeGDB
BLAST tool
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Genome assembly pages available for all NAM founders. See
the list under "+ NAM founders" here.
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Gene model pages available for all NAM founders. See the
Gene/Gene Model data center.
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NAM genetic maps:
1
2
3
4
5
6
7
8
9
10
Additional data is available
here.
B73 v5 assembly and stock
All NAM founder assemblies and stock:
FAQs
General Information about Nested Association Mapping (first developed in
Maize!):
https://en.wikipedia.org/wiki/Nested_association_mapping
First report of the maize NAM population:
https://science.sciencemag.org/content/325/5941/737
Genetic Design and Statistical Power of NAM in Maize:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206100/
How to Order NAM lines:
http://maizecoop.cropsci.uiuc.edu/nam-rils.php
Coming soon to MaizeGDB
Updated September 28th, 2021
Tracks
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Ab initio gene models for v5 and NAM assemblies
- completed
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TE annotations - completed
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Structural Variations
- completed (based on B73v5 coordinates)
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Align SNPs from MaizeSNP50 chip
- completed
- Core Bin Markers
- available on browsers, but not yet elsewhere
- HapMap5 → replaced with WGS mapping, in progress
B73v5 methylome
- completed
- HiC data
Page updates
- Core Bin Marker Pages
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Additional functional annotations for NAM gene models
- completed
JBrowse snapshots within gene model pages
- completed
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Pan-gene information on gene pages - completed
- Add physical coordinates for each NAM line to NAM genetic map page
Tools
- MaizeMine update to include v5 annotations
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qTeller update to include NAM RNA-seq data
- completed
Features
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Pan-genome and syntenic ortholog information - completed
- External links to Apollo instances for manual structural annotations
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V5 gene models linked to gene data - completed
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Current v5 gene models are evidence-based. Ab initio gene models
will be added when available. - completed
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Create JBrowse instances for non-NAM assemblies
- done for W22 and Mo17 CAU
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Deploy JBrowse plugins to combine bigWig tracks
- completed
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Project details
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Metadata
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Browser
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