The At-Cp-Vv-Pt-Pt gene list with GEvo links
Brent Pedersen in the Freeling group prepared a spreadsheet of potential At syntenic gene sets by comparing the gene sequences of At to Vv, Cp, and Pt. This spreadsheet has a list of every At gene listed in order by chromosome and chromosome position in the first column, followed by the locations of candidate syntelogs in Vv, Cp, Pt, and then a link to GEvo using those positions as genomic anchors for comparative genomics. You can read about how this list was generated at the bottom of this page. Since At is best annotated, this list uses annotations from At only.
How The At-Cp-Vv-Pt-Pt gene list with GEvo links was generated
At was blasted against Cp and Vv using blastn with an e-value filter of 0.001. The top hit to each was taken as a potential syntelog. To generate syntelogs to Pt, which has had a relatively recent genome duplication event, DAGchainer (Haas et al., 2004) was used. If a single matching syntenic region was found, a single Pt gene was included (if one matched the At query sequence). If two matching syntenic regions were found, a gene from each region was used (if there were matches to the At query sequence). These sets of genes were then used to generate links to GEvo with appropriate anchors for each matching genome.
** By scanning down a column of chromosomal positions, it is usually easy to identify the expected chromosomal segment that "should" contain the syntelog to the At query sequence.
At gene
Vv position
Cp position
Pt1 position
Pt2 position
GEvo
Link
Interpreting the list:
Above is a screen shot of the 5 potentially syntenous chromosomal positions list with one row highlighted in green that you will be analyzing. Colored boxes have been drawn to show a series of genomic locations for each organism compared to At. If you look at the genomic locations of regions within the colored boxes, you will note that they are collinear in order. Finding a series of putatively homologous genes with conservation of genomic order (e.g. collinearity) is the watermark of synteny, and these regions are likely to be syntenic with this region of At.
However, there are several inconsistencies to note:
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1.Not every At gene has a potential ortholog (syntelog) in the other genomes. This is to be expected. Genes evolve at different rates in different lineages, genes may have been lost in some lineages, genes may have been inserted in At's lineage, etc.
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2.Some genes violate synteny. This too is to be expected. The method used to identify syntelogs in Cp and Vv rely on "best blast hits" which does not take into account synteny and may misidentify syntelogs. Also, some genes may have been duplicated or transposed in some lineages.**
In this example, these regions are likely to be syntenic and you can use GEvo to evaluate whether they are indeed syntenic.
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