ABSTRACT

The Intron density Indicator Map is an interactive eukaryotic model designed to provide insight into the evolution of eukaryotes. The map serves as a comparative tool for intron density and the core components of the Exon Junction Complex in eukaryotes. The map also shows the distribution of the Exon Junction Complex amongst the six eukaryotic super-groups; the conservation of eIF4AIII in all eukaryotes, the presence of eIF4AIII, Magoh, and Y14 in the LECA, the selective loss of Magoh and Y14 in intron-poor species and the founder effect of Y14 within the trypanosome lineage. The interactive feature illustrates the correlation of the eIF4AIII, Magoh, Y14, MLN51, and intron density amongst both parasites and non-parasites.

This model can also be used to illustrate (1) the variation of intron densities in comparison to the presence of the different EJC core units amongst different eukaryotic species (2) Run an instantaneous display of the position of any newly sequenced genome of both parasitic and non-parasitic eukaryotes on the intron density scale. The interactive eukaryotic model, which can be found in [https://www.idimap.patmedb.org/] will continually be updated with new eukaryotic species.

Browsing the Database:

On the menu, at the top right corner of the screen, you can browse the distribution of the Exon Junction Complex and intron density by the eukaryotic supergroups: Amorphea, Excavata and Diaphoretickes Home Screen: This page gives an overview of the eukaryotic tree. Click on any area to direct you to the distribution of eIF4A3, Y15, Magoh and MLN51 in each eukaryotic supergroup.

Register and login:

To perform more elaborate queries, and analysis, you can register free of charge to receive login details from the panels situated at the top right-hand corner of the screen.

Querying the Database:

As a registered user, you can access the tables of the database, which can be queried by division, supergroup, subgroup, or specie.

References:

Bannerman BP, Kramer S, Dorrell RG, Carrington M. Multispecies reconstructions uncover widespread conservation, and lineage-specific elaborations in eukaryotic mRNA metabolism. PLoS One. 2018 Mar 21;13(3):e0192633. doi: 10.1371/journal.pone.0192633. PMID: 29561870; PMCID: PMC5862402.