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Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Irene Hoxie, John J. Dennehy
doi: https://doi.org/10.1101/2021.03.20.436270
Irene Hoxie
1The Graduate Center of The City University of New York, New York City, NY, USA
2Biology Department, Queens College of The City University of New York, Queens, NY, USA
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  • For correspondence: ihoxie@yahoo.com
John J. Dennehy
1The Graduate Center of The City University of New York, New York City, NY, USA
2Biology Department, Queens College of The City University of New York, Queens, NY, USA
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Abstract

Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortant-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different treespaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable treespaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the least conservation by host species. Bayesian skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to common host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 21, 2021.
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Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns
Irene Hoxie, John J. Dennehy
bioRxiv 2021.03.20.436270; doi: https://doi.org/10.1101/2021.03.20.436270
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Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns
Irene Hoxie, John J. Dennehy
bioRxiv 2021.03.20.436270; doi: https://doi.org/10.1101/2021.03.20.436270

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