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Genome-Wide Variation in Potyviruses.
Deepti Nigam1, Katherine LaTourrette1, Pedro F N Souza1
1Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States.
Frontiers in Plant Science
|December 5, 2019
Summary
Potyviruses exhibit stable genomes but possess specific hypervariable regions. These adaptable areas are crucial for host adaptation and are linked to their broad host range and aphid transmission.
Area of Science:
- Virology
- Molecular Evolution
- Plant Pathology
Background:
- Potyviruses, a large genus within the Potyviridae family, infect numerous plant species and are transmitted by aphids.
- Despite their wide host range and global distribution, the genetic factors enabling potyvirus adaptability remain poorly understood.
- Viral RNA-dependent RNA polymerases contribute to genetic diversity through nucleotide substitutions.
Purpose of the Study:
- To investigate genomic and polyprotein variation across the genus Potyvirus.
- To identify genomic regions and evolutionary pressures associated with host adaptation in potyviruses.
- To understand the molecular basis of potyvirus adaptability and host-vector interactions.
Main Methods:
- Profiling of genomic and polyprotein variation across all species in the genus Potyvirus.
- Analysis of nucleotide and amino acid substitutions to identify patterns of selection.
- Structural alignment of hypervariable regions, particularly in the coat protein (CP).
Main Results:
- The potyviral genome is under strong negative selection, indicating overall sequence stability.
- Substitutions are not random but concentrate in specific hypervariable areas across the genome.
- These hypervariable areas show higher frequencies of non-synonymous substitutions and positive selection, correlating with host range.
- Key adaptable regions identified in proteins P1, HC-Pro, P3, VPg, NIb, and CP, with CP hypervariable region linked to aphid transmission.
Conclusions:
- Potyviruses possess fixed hypervariable genomic regions that confer mutational robustness.
- These adaptable regions are likely critical for potyvirus host adaptation and evolution.
- Understanding these hypervariable areas provides insights into the mechanisms driving potyvirus diversity and spread.