This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Open AccessArticle
A Genetic Study of Spillovers in the Bean Common Mosaic Subgroup of Potyviruses
by
Mohammad Hajizadeh
Mohammad Hajizadeh 1,*,
Karima Ben Mansour
Karima Ben Mansour 2,3
and
Adrian J. Gibbs
Adrian J. Gibbs 4,*
1
Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj 66177-15175, Iran
2
Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic
3
Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
4
Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
*
Authors to whom correspondence should be addressed.
Viruses 2024, 16(9), 1351; https://doi.org/10.3390/v16091351 (registering DOI)
Submission received: 28 July 2024
/
Revised: 16 August 2024
/
Accepted: 20 August 2024
/
Published: 23 August 2024
Abstract
Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their “centre of emergence”. We have compared over 700 of the complete genomic ORFs of the crop pandemic and the non-crop viruses in various ways. Only one-third of crop virus genomes are non-recombinant, but more than half the non-crop virus genomes are. Four of the viruses were from crops domesticated in the Old World (Africa to SE Asia), and the other five were from New World crops. There was a temporal signal in only three of the crop virus datasets, but it confirmed that the most recent common ancestors of all the crop viruses were before inter-continental marine trade started after 1492 CE, whereas all the crown clusters of the phylogenies are from after that date. The non-crop virus datasets are genetically more diverse than those of the crop viruses, and Tajima’s D analyses showed that their populations were contracting, and only one of the crop viruses had a significantly expanding population. dN/dS analyses showed that most of the genes and codons in all the viruses were under significant negative selection, and the few that were under significant positive selection were mostly in the PIPO-encoding region of the P3 protein, or the PIPO protein itself. Interestingly, more positively selected codons were found in non-crop than in crop viruses, and, as the hosts of the former were taxonomically more diverse than the latter, this may indicate that the positively selected codons are involved in host range determination; AlphaFold3 modelling was used to investigate this possibility.
Share and Cite
MDPI and ACS Style
Hajizadeh, M.; Ben Mansour, K.; Gibbs, A.J.
A Genetic Study of Spillovers in the Bean Common Mosaic Subgroup of Potyviruses. Viruses 2024, 16, 1351.
https://doi.org/10.3390/v16091351
AMA Style
Hajizadeh M, Ben Mansour K, Gibbs AJ.
A Genetic Study of Spillovers in the Bean Common Mosaic Subgroup of Potyviruses. Viruses. 2024; 16(9):1351.
https://doi.org/10.3390/v16091351
Chicago/Turabian Style
Hajizadeh, Mohammad, Karima Ben Mansour, and Adrian J. Gibbs.
2024. "A Genetic Study of Spillovers in the Bean Common Mosaic Subgroup of Potyviruses" Viruses 16, no. 9: 1351.
https://doi.org/10.3390/v16091351
Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details
here.
Article Metrics
Article metric data becomes available approximately 24 hours after publication online.