Syntenic gene sets
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Syntenic gene sets are sets of genes located in syntenic regions (genomic regions derived from the same ancestral genomic region) within and across genomes. These genes are usually in a collinear gene order and are used as evidence that the regions are syntenic. These data are made available for download for use in any publication. However, we ask that you reference CoGe or the publication from which the data was derived.
Contents
Non-published Syntenic Gene Sets
Sorghum and Maize
Since maize and sorghum divered ~10-15 million years ago, maize underwent an additional tetraploidy event. For more information see this page on their genomes' evolutionary history.
This dataset contains:
- sorghum-maize1-maize2 syntelogs (or missing one of the maize homeologs due to post-tetraploidy genome fractionation.
- tandem gene duplication data.
- Links to GEvo for multi-genomic region comparisons
- Where one of the maize homeologs is missing, a place-holder is added so the region is still shown in GEvo.
- Links to FeatList to extract information about the set of syntelogs including getting their sequences and sending them to other tools in CoGe for further analysis.
Uses these genome versions:
Pan-grass synteny
Among the four sequenced grass genomes of maize, sorghum, rice, and brachypodium, there are three large-scale genomic evolution events:
- a pre-grass whole genome duplication event shared among all grass genomes
- the radiation of the grasses
- a maize lineage specific whole genome duplication event that happened after the divergence of maize and sorghum
These data are organized into two sets (Note: not finalized!):
- Set 1: Syntenic sets for the radiation of the grasses (#2) and the maize specific whole genome duplication event (#3). This would result in up to 5 syntenic regions (2x maize, 1x sorghum, 1x rice, 1x brachypodium).
- Set 2:Syntenic sets derived from the pre-grass whole genome duplication event (#1). This would result in up to 10 syntenic regions (4x maize, 1x sorghum, 1x rice, 1x brachypodium).
Published Syntenic Gene Sets
These lists are usually from publications in MS Excel format and provide links to populate the sequence submission form in GEvo, CoGe's tool for analyzing multiple genomic regions. These links allow you to quickly start comparing syntenic regions of interest.
Arabidopsis Papaya, Poplar, and Grape: CoGe with Rosids.
Arabidopsis thaliana - Carica papaya: Since their divergence, Arabidopsis thaliana has had two tetraploidies while papaya has had none. Prepared by the Paterson lab at the Plant Center at the University of Georgia and modified by the Freeling lab to include GEvo links. From: Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups.
Arabidopsis thaliana - Carica papaya - Vitis vinifera - Populus trichocarpa(2x): This list contains both syntenic regions for poplar from its most recent genome duplication event, but only a single for Arabidopsis. From: Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups.
How to generate syntenic gene sets with links to GEvo
SynMap allows you to compare any two genomes. Its output includes a text file of all identified syntenic gene pairs and links to GEvo.
Want a syntelog gene set?
We are happy to help. Just e-mail Eric Lyons.