Selection upon genome architecture: conservation of functional neighborhoods with changing genes

Fátima Al-Shahrour1,2, Pablo Minguez1,3, Tomás Marqués-Bonet 4,5, Elodie Gazave4, Arcadi Navarro4,6,7 and Joaquín Dopazo1,8,9

1 Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, E-46013, Spain
2 Present address: Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
3 Present address: Structural and Computational Biology Unit. EMBL Heidelberg. Meyerhofstraße 1, 69117 Heidelberg, Germany
4 Institut de Biologia Evolutiva. Universitat Pompeu Fabra (UPF) and Consejo Superior de Investgaciones Científicas (CSIC), Dr. Aiguader 88. 08003. Barcelona, Spain.
5 Department of Genome Sciences, Howard Hughes Medical Institute, University of
Washington, Seattle, WA, 98195, USA.
6 Population Genomics Node (National Institute for Bioinformatics, INB), Barcelona Biomedical Research Park, Dr. Aiguader 88. 08003. Barcelona, Spain.
7 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
8 CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
9 Functional Genomics Node (National Institute for Bioinformatics, INB), CIPF, Valencia, Spain

We describe here the most extensive multispecies functional cartography carried out to date. Our study shows, for the first time, how neighborhoods of functionally related genes arise and how they are maintained through evolution following a pattern that is fully consistent with the phylogenies of the analyzed species. Surprisingly, and contrarily to what it would be expected, such neighborhoods, that are present in different species, are not composed by orthologous genes but rather by genes phylogenetically unrelated, annotated however with the same function. A synteny analysis reveals that such neighborhoods are dynamically rebuilt in a way that, while the particular genes often change, it is the functional neighbourhood, as the ultimate target of selection, what is preserved.


Supplementary Material

Functional analysis Statistical analysis to detect Functional enriched regions in the chromosomes.
Duplication Are the functional clusters a consequence of gene duplications?
Coexpression Are the genes sharing GO term within the functional clusters more coexpressed than the rest of genes with that GO annotated?
Gene density Do the functional clusters have a higher index of gene density?
GC content Do the functional clusters have a higher GC content?
Repeats Do The functional clusters have more repeated regions (SINEs,LINEs,etc)?


Figure 1 Distribution of functions present in functional clusters along the phylogeny. The point at which a function makes up a functional neighbourhood has been deduced from the species sharing functional clusters with this particular GO term. Boxes in yellow contain GO terms unique to taxas, boxes in blue contain GO terms common to clades and boxes in pink contain GO terms lost in these lineages.
 Distribution of functions present in functional clusters along the phylogeny