Difference between revisions of "Syntenic gene sets"

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(→‎Non-published Syntenic Gene Sets)
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##Where one of the maize homeologs is missing, a place-holder is added so the region is still shown in GEvo.
 
##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.
 
#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.
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Uses these genome versions:
 
Uses these genome versions:
 
#[http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?dsgid=8062 maize]
 
#[http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?dsgid=8062 maize]
 
#[http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?dsgid=93 sorghum]
 
#[http://synteny.cnr.berkeley.edu/CoGe/OrganismView.pl?dsgid=93 sorghum]
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===[[Pan-grass synteny]]===
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Among the four sequenced grass genomes of maize, sorghum, rice, and brachypodium, there are three large-scale genomic evolution events:
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# a pre-grass [[whole genome duplication event]] shared among all grass genomes
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# the radiation of the grasses
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# a [[Maize_Sorghum_Syntenic_dotplot | maize lineage specific]] [[whole genomic duplication event]] that happened after the divergence of maize and sorghum
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These data are organized into two sets:
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*[[http://synteny.cnr.berkeley.edu/CoGe/data/distrib/pan_grass/pan_grass_ortholog_panels_v1.csv 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).
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*[[http://synteny.cnr.berkeley.edu/CoGe/data/distrib/pan_grass/pan_grass_rho_panels_v0.1.csv 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==
 
==Published Syntenic Gene Sets==

Revision as of 14:39, 10 March 2010

Syntenic comparison of two regions from the genome of Arabidopsis thaliana using GEvo. This genome underwent a whole genome duplication event which created a copy of every genomic region. Over evolutionary time, many of the duplicated genes were lost by a process known as fractionation. However, many duplicated genes have been retained in duplicate and their collinear arrangement in the genome is evidence for synteny. Results can be regenerated at: http://tinyurl.com/noul6b

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.


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.

Here is the dataset!

This dataset contains:

  1. sorghum-maize1-maize2 syntelogs (or missing one of the maize homeologs due to post-tetraploidy genome fractionation.
  2. tandem gene duplication data.
  3. Links to GEvo for multi-genomic region comparisons
    1. Where one of the maize homeologs is missing, a place-holder is added so the region is still shown in GEvo.
  4. 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:

  1. maize
  2. sorghum

Pan-grass synteny

Among the four sequenced grass genomes of maize, sorghum, rice, and brachypodium, there are three large-scale genomic evolution events:

  1. a pre-grass whole genome duplication event shared among all grass genomes
  2. the radiation of the grasses
  3. a maize lineage specific whole genomic duplication event that happened after the divergence of maize and sorghum

These data are organized into two sets:

  • [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.

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