Difference between revisions of "Classical Maize Genes"

Latest revision as of 16:27, 21 January 2021

An updated version of the classical maize gene dataset has just been released using version 2 gene models. While it's not included in the table below yet, you can download it as an excel sheet.

The B73_refgen2 version of the classical maize gene list has been peer reviewed and is now published. Check it out!

Schnable JC, Freeling M. "Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize." PLoS One DOI:10.1371/journal.pone.0017855

Do not lose all hope if your favorite gene or genes are not currently included on the table. With limited time we couldn't manually connect all the known maize genes to maizesequence.org gene models. If you are willing to identify a GenBank sequence for a gene and figure out the ID of the corresponding gene model from the B73 reference genome, we'd be happy to add it to this table (we'd identify syntenic orthologs in the other sequenced grass genomes and generate the comparison panels.) Contact James Schnable.

Maizesequence.org provides a list of named maize genes created using an independent methodology.

About the Dataset

This table contains 464 studied maize genes where the sequence was readily identifiable from the maizeGDB locus page, and the locus page listed at least three unique publications that dealt with the gene. Each of these genes was located on the reference B73 genome assembly (B73 RefGen_v1), tying a named maize gene (for example: liguleless3 ) to a maizesequence.org gene model (for example: GRMZM2G087741).

Be aware that maizesequence.org will doubtless release revised version of the maize genome assembly and maize gene models (in fact the v2 assembly is already available although the gene models for it are not). The links currently included in this table will always take you to comparisons using the version 1 assembly, but we plan to release updated versions if substantial changes are made in future revisions of the maize genome.

The table also includes data on the homeologous region of maize and syntenic orthologs (or syntenic regions if no orthologous gene was identified) in other sequenced grass genomes (Sorghum bicolor, Setaria italica, Oryza sativa(rice), and Brachypodium distachyon).

The mapping of maize gene names to maizesequence.org gene models and the identification of orthologous syntenic regions was done by James Schnable of the Freeling lab at UC-Berkeley, the contact person for any questions about the data.

Please let us know if you come across errors in the table or spreadsheet!

Table Key

1. Gene Symbol
2. Citation Count: The number of unique citations for this gene listed on the MaizeGDB locus page.
3. MaizeSequence.org Gene ID: The name of the gene model assigned by maizesequence.org in the B73 RefGen_v1 release.
4. Gene Name: Links to the maizeGDB locus page for this gene with up to a century of maize research (publications, phenotypes, alleles, sequences, mapping data etc).
5. GenBank ID: The GenBank ID of the sequence used to tie the named maize gene to a maizesequence.org gene model. Links to the NCBI page for that sequence.
6. GEvo Comparison: A GEvo link to compare the GenBank maize gene sequence and the region of the maize genome it was manually matched to. Good for catching problems with gene models and viewing the region around the maize gene.
7. Sorghum Ortholog: Syntenic Sorghum Ortholog (or the region where a syntenic ortholog would be predicted, if no ortholog was found)
8. Maize1: Maize region 1. This can either be the maize gene itself, the homeologous gene, or the homeologous region if no actual homeolog was found.
9. Maize2: Maize region 2. This can either be the maize gene itself, the homeologous gene, or the homeologous gene, or the homeologous region if no actual homeolog was found.
10. Rice Ortholog: Syntenic Rice Ortholog (or the region where a syntenic ortholog would be predicted, if no ortholog was identified)
11. Brachypodium Ortholog: Syntenic Brachypodium Ortholog (or the region where a syntenic ortholog would be predicted, if no ortholog was identified)
12. Syntenic Ortholog Panel: A GEvo link to compare up to five syntenic regions in the four sequenced grasses. (Two in maize and one each from rice, sorghum, and brachypodium.) Syntenic regions are displayed when a orthologous or homeologous gene could not be identified, but we could a syntenic orthologous/homeologous region of less than one megabase.

You can also download the whole table as a comma delimited spreadsheet here.

Maize region 1 and maize region 2 are reconstructions of the two copies of the maize genome created by the maize whole genome duplication 4-12 million years ago. More details on this process here.

Gotchas

• The maize gene of interest could be in either the Maize1 or Maize2 region. You can tell by checking the maizesequence.org assigned gene names.
• When linking to a region that contains a number of local duplicates of a gene it's difficult to determine exact orthologous relationships. The region will be centered on a gene from within the cluster of local dups, but the studied maize mutant may be one of the other nearby copies of the gene.

Help

Examples of interpreting data from the syntenic orthologs panels.

A video introduction to the links in this spreadsheet for people who have never used GEvo.

If you need to do more advanced comparisons, the place to go is our documentation of GEvo.

You can also check out the index of all the tutorials we've written for CoGe.

The Table