Genes encoding teleost orthologues of human signal transduction proteins remain duplicated or triplicated more frequently than the whole genome - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Heliyon Year : 2023

Genes encoding teleost orthologues of human signal transduction proteins remain duplicated or triplicated more frequently than the whole genome

Abstract

Cell signalling involves a myriad of proteins, many of which belong to families of related proteins, and these proteins display a huge number of interactions. One of the events that has led to the creation of new genes is whole genome duplication (WGD), a phenomenon that has made some major innovations possible. In addition to the two WGDs that happened before gnathostome radiation, teleost genomes underwent one (the 3WGD group) or two (the 4WGD group) extra WGD after separation from the lineage leading to holostei. In the present work, we studied in 63 teleost species whether the orthologues of human genes involved in 47 signalling pathways (HGSP) remain more frequently duplicated, triplicated or in the singleton state compared with the whole genome. We found that these genes have remained duplicated and triplicated more frequently in teleost of the 3WGD and 4WGD groups, respectively. Moreover, by examining pairs of interacting gene products in terms of conserved copy numbers, we found a majority of the 1:1 and 1:2 proportions in the 3WGD group (between 54% and 60%) and of the 2:2 and 2:4 proportions in the 4WGD group (30%). In both groups, we observed the 0:n proportion at a mean of approximately 10%, and we found some pseudogenes in the concerned genomes. Finally, the proportions were very different between the studied pathways. The n:n (i.e. same) proportion concerned 20%-65% of the interactions, depending on the pathways, and the n:m (i.e. different) proportion concerned 34%-70% of the interactions. Among the n:n proportion, the 1:1 ratio is most represented (25.8%) and among the n:m ratios, the 1:2 is most represented (25.0%). We noted the absence of gene loss for the JAK-STAT, FoxO and glucagon pathways. Overall, these results show that the teleost gene orthologues of HGSP remain duplicated (3WGD) and triplicated (4WGD) more frequently than the whole genome, although some genes have been lost, and the proportions have not always been maintained.

Dates and versions

hal-04250936 , version 1 (20-10-2023)

Licence

Attribution - NonCommercial - NoDerivatives

Identifiers

Cite

Floriane Picolo, Benoît Piégu, Philippe Monget. Genes encoding teleost orthologues of human signal transduction proteins remain duplicated or triplicated more frequently than the whole genome. Heliyon, 2023, 9 (9), pp.e20217. ⟨10.1016/j.heliyon.2023.e20217⟩. ⟨hal-04250936⟩
20 View
0 Download

Altmetric

Share

Gmail Facebook X LinkedIn More