instance, the A. thaliana ecotype Ale-Stenar-44-4 (strain 992)
seems to have non-synonymous single nucleotide polymorphism in ABI3 that causes a proline to leucine change at
amino acid 556 of ABI3, which is near the DNA-binding site
(based on information we could see at Araport), a change that
might cause ABI3 to bind differently to DNA in that ecotype.
5. You can also look for small insertions in ABI3 other strains.
Switch the “Variant Type” to “Insertions.” Keep “Impact” and
“Effect Type” at “All.”
6. To search for small deletions, switch the “Variant Type” to
“Deletions.” Keep “Impact” and “Effect Type” at “All.”
3.2 Precomputed
Gene Trees
The recent explosion in the number of available sequenced genomes, a resource once reserved only for a handful of model species,
has boosted the value of phylogenomic approaches in understanding gene function. Investigating the evolutionary history of a gene
can provide valuable insight into its potential role. As an example,
imagine we had identified a mutation of a gene, but its annotation
revealed little about its biological function. We could investigate its
evolutionary relationships and use the annotations of its homologs
to help guide us toward a function. Alternatively, this approach
would also reveal additional relevant information such as gene
duplication events that might help us refine our subsequent reverse
genetic strategies (e.g., generating a double knockout mutant) or
generate hypotheses about sub-functionalization events. Finally, if
we wished to determine the function of a given Arabidopsis gene in
another species, we could identify the homolog most likely to be
the ortholog. For these purposes, we can take advantage of precomputed phylogenetic trees, available from online platforms such
as Ensembl Plants or PLAZA.
3.2.1 Ensembl Plants
Ensembl Plants is a scientific project aimed to provide genome-scale
data from plant species, as part of the Ensembl Genomes initiative
[12]. Ensembl Plants was created as joint effort between the
European Bioinformatics Institute and the teams at Gramene. It
is maintained by the EBI and is based on the Ensembl annotation
framework [13].
1. Go to https://plants.ensembl.org/index.html. In the search
box, search for “ABI3” and select “Arabidopsis thaliana” as
the species. Click on the first result (labeled “ABI3”).
2. Find the display menu, located on the left sidebar. Also note
that Ensembl Plants has many built-in search tools, like BLAST
and HMMER, linked in the top navigation bar.
3. Click on the “Gene tree” link on the left sidebar (under “Plant
Compara”). You will see some information at the top, and then
a graphic similar to Fig. 1, but interactive.
30
G. Alex Mason et al.
seems to have non-synonymous single nucleotide polymorphism in ABI3 that causes a proline to leucine change at
amino acid 556 of ABI3, which is near the DNA-binding site
(based on information we could see at Araport), a change that
might cause ABI3 to bind differently to DNA in that ecotype.
5. You can also look for small insertions in ABI3 other strains.
Switch the “Variant Type” to “Insertions.” Keep “Impact” and
“Effect Type” at “All.”
6. To search for small deletions, switch the “Variant Type” to
“Deletions.” Keep “Impact” and “Effect Type” at “All.”
3.2 Precomputed
Gene Trees
The recent explosion in the number of available sequenced genomes, a resource once reserved only for a handful of model species,
has boosted the value of phylogenomic approaches in understanding gene function. Investigating the evolutionary history of a gene
can provide valuable insight into its potential role. As an example,
imagine we had identified a mutation of a gene, but its annotation
revealed little about its biological function. We could investigate its
evolutionary relationships and use the annotations of its homologs
to help guide us toward a function. Alternatively, this approach
would also reveal additional relevant information such as gene
duplication events that might help us refine our subsequent reverse
genetic strategies (e.g., generating a double knockout mutant) or
generate hypotheses about sub-functionalization events. Finally, if
we wished to determine the function of a given Arabidopsis gene in
another species, we could identify the homolog most likely to be
the ortholog. For these purposes, we can take advantage of precomputed phylogenetic trees, available from online platforms such
as Ensembl Plants or PLAZA.
3.2.1 Ensembl Plants
Ensembl Plants is a scientific project aimed to provide genome-scale
data from plant species, as part of the Ensembl Genomes initiative
[12]. Ensembl Plants was created as joint effort between the
European Bioinformatics Institute and the teams at Gramene. It
is maintained by the EBI and is based on the Ensembl annotation
framework [13].
1. Go to https://plants.ensembl.org/index.html. In the search
box, search for “ABI3” and select “Arabidopsis thaliana” as
the species. Click on the first result (labeled “ABI3”).
2. Find the display menu, located on the left sidebar. Also note
that Ensembl Plants has many built-in search tools, like BLAST
and HMMER, linked in the top navigation bar.
3. Click on the “Gene tree” link on the left sidebar (under “Plant
Compara”). You will see some information at the top, and then
a graphic similar to Fig. 1, but interactive.
30
G. Alex Mason et al.