Abstract
Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that might explain their coordinated evolution during speciation events and their parental function. Here, we will address the following issues: (1) is there any conserved hypothetical structure along ortholog gene sequences? (2) If any, are such conserved structures maintained and conserved during speciation events? The data presented show evidences supporting this hypothesis. We have found that, (1) most orthologs studied share highly conserved compositional structures not observed previously. (2) While the percent identity of nucleotide sequences of orthologs correlates with the percent identity of composon sequences, the number of emergent compositional structures conserved during speciation does not correlate with the percent identity. (3) A broad range of species conserves the emergent compositional stretches. We will also discuss the concept of critical gene structure.
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Funding
This work was funded by a program of the Instituto de Salud Carlos III-Redes Temáticas de Investigación Cooperativa en Salud (ISCIII-RETIC RD06/0021/0008 program) and Laboratorios LETI. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. An institutional grant from Fundación Ramón Areces is also acknowledged.
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Online Resource 1
. Sample of mouse genes contained into specific tCP-clusters different from those of their human orthologs (DOCX 65 KB)
Online Resource 2
. Dataset of human-mouse orthologs that change during speciation from a compositional cluster in mouse to another different in human (sample 1) showing both NT and tCP alignment data and the number of tCPs conserved per ortholog (DOCX 38 KB)
Online Resource 3
. Dataset of human-mouse orthologs that do not change during speciation from a compositional cluster in mouse to another different in human showing both NT and tCP alignment data (sample 2) and the number of tCPs conserved per ortholog (DOCX 36 KB)
Online Resource 4
. Multiple alignment of 12 orthologs of the human sterile alpha motif domain-containing protein 12 (SAMD12). NTs associated with the conserved tCPs are shaded in blue. The * symbol indicates NTs conserved in all species. The interspersed structure is composed of 42 stretches distributed along the gene length. (DOCX 31 KB)
Online Resource 5
. Panel comparing the 14 tCP-profiles of the human-mouse ortholog SAMD12. Red and blue lines correspond to tCP-distributions along the trend line of the cumulative tCP-usage profile of the mouse and the human, respectively. The inset in upper right corner display the name of the ortholog and the mouse and human tCP-clusters containing the ortholog. The inset in the bottom right corner represent a table with the correlations (r) found between human-mouse tCP-profiles for numerical comparison. In bold, the r values higher than the cut-off. (DOCX 344 KB)
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Fuertes, M.A., Rodrigo, J.R. & Alonso, C. Conserved Critical Evolutionary Gene Structures in Orthologs. J Mol Evol 87, 93–105 (2019). https://doi.org/10.1007/s00239-019-09889-1
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DOI: https://doi.org/10.1007/s00239-019-09889-1