TY - JOUR
T1 - Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation
AU - Aimone, Catherine D.
AU - Lavington, Erik
AU - Hoyer, J. Steen
AU - Deppong, David O.
AU - Mickelson-Young, Leigh
AU - Jacobson, Alana
AU - Kennedy, George G.
AU - Carbone, Ignazio
AU - Hanley-Bowdoin, Linda
AU - Duffy, Siobain
N1 - Funding Information: This work was supported by the National Science Foundation grant OISE-1545553 to L.H.-B, G.G.K. and S.D. C.D.A. was supported with NSF Graduate Research Fellowship and an NCSU Provost Fellowship. Funding Information: This work was supported by the National Science Foundation grant OISE-1545553 to L.H.-B, G.G.K. and S.D. C.D.A. was supported with NSF Graduate Research Fellowship and an NCSU Provost Fellowship. We thank Mary Beth Dallas for her help growing cassava plants. Infectious clones were generously provided by Vincent Fondong (Addgene plasmids 159 134 to 159137; https://www.addgene.org/browse/article/28211870/). We thank the NC State University Genome Science Laboratory for their support. The Cassava Virus Evolution Galaxy server (https://cassavavirusevolution.vcl.ncsu.edu/) is hosted in the NC State University Virtual Computing Lab, and we thank Matthew Gronke, Saahil Chawande, and Jim White for server setup and maintenance. This work also used the Amarel cluster maintained by the Office of Advanced Research Computing (OARC) at Rutgers, The State University of New Jersey. Publisher Copyright: 001622 © 2021 The Authors
PY - 2021
Y1 - 2021
N2 - Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5′ intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.
AB - Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5′ intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.
KW - Cassava mosaic begomoviruses
KW - Vegetative propagation
KW - Viral diversity
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U2 - https://doi.org/10.1099/JGV.0.001622
DO - https://doi.org/10.1099/JGV.0.001622
M3 - Article
C2 - 34310272
SN - 0022-1317
VL - 102
JO - Journal of General Virology
JF - Journal of General Virology
IS - 7
M1 - 001622
ER -