Syntenic gene sets

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.

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.

Papaya, Poplar, and Grape: CoGe with Rosids. Plant Physiol. 148: 1772 Lyons et al.:

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.