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Rajabu CA, Dallas MM, Chiunga E, De León L, Ateka EM, Tairo F, Ndunguru J, Ascencio-Ibanez JT, Hanley-Bowdoin L. SEGS-1 a cassava genomic sequence increases the severity of African cassava mosaic virus infection in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1250105. [PMID: 37915512 PMCID: PMC10616593 DOI: 10.3389/fpls.2023.1250105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Cassava is a major crop in Sub-Saharan Africa, where it is grown primarily by smallholder farmers. Cassava production is constrained by Cassava mosaic disease (CMD), which is caused by a complex of cassava mosaic begomoviruses (CMBs). A previous study showed that SEGS-1 (sequences enhancing geminivirus symptoms), which occurs in the cassava genome and as episomes during viral infection, enhances CMD symptoms and breaks resistance in cassava. We report here that SEGS-1 also increases viral disease severity in Arabidopsis thaliana plants that are co-inoculated with African cassava mosaic virus (ACMV) and SEGS-1 sequences. Viral disease was also enhanced in Arabidopsis plants carrying a SEGS-1 transgene when inoculated with ACMV alone. Unlike cassava, no SEGS-1 episomal DNA was detected in the transgenic Arabidopsis plants during ACMV infection. Studies using Nicotiana tabacum suspension cells showed that co-transfection of SEGS-1 sequences with an ACMV replicon increases viral DNA accumulation in the absence of viral movement. Together, these results demonstrated that SEGS-1 can function in a heterologous host to increase disease severity. Moreover, SEGS-1 is active in a host genomic context, indicating that SEGS-1 episomes are not required for disease enhancement.
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Affiliation(s)
- Cyprian A. Rajabu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Evangelista Chiunga
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Elijah M. Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Fred Tairo
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Joseph Ndunguru
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Jose T. Ascencio-Ibanez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Kennedy GG, Sharpee W, Jacobson AL, Wambugu M, Mware B, Hanley-Bowdoin L. Genome segment ratios change during whitefly transmission of two bipartite cassava mosaic begomoviruses. Sci Rep 2023; 13:10059. [PMID: 37344614 DOI: 10.1038/s41598-023-37278-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/19/2023] [Indexed: 06/23/2023] Open
Abstract
Cassava mosaic disease is caused by a complex of whitefly-transmitted begomoviruses, which often occur in co-infections. These viruses have bipartite genomes consisting of DNA-A and DNA-B that are encapsidated into separate virions. Individual viruses exist in plants and whitefly vectors as populations comprising both genome segments, which can occur at different frequencies. Both segments are required for infection, and must be transmitted for virus spread to occur. Cassava plants infected with African cassava mosaic virus (ACMV) and/or East African cassava mosaic Cameroon virus (EACMCV), in which the ratios of DNA-A:DNA-B titers differed between plants, were used to examine how titers of the segments in a plant relate to their respective probabilities of acquisition by whiteflies and to the titers of each segment acquired and subsequently transmitted by whiteflies. The probabilities of acquiring each segment of ACMV did not reflect their relative titers in the source plant but they did for EACMCV. However, for both viruses, DNA-A:DNA-B ratios acquired by whiteflies differed from those in the source plant and the ratios transmitted by the whitefly did not differ from one - the ratio at which the highest probability of transmitting both segments is expected.
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Grants
- OISE-1545553 to L.H-B., G.G.K., and A.L.J. National Science Foundation
- OISE-1545553 to L.H-B., G.G.K., and A.L.J. National Science Foundation
- OISE-1545553 to L.H-B., G.G.K., and A.L.J. National Science Foundation
- OISE-1545553 to L.H-B., G.G.K., and A.L.J. National Science Foundation
- OISE-1545553 to L.H-B., G.G.K., and A.L.J. National Science Foundation
- OISE-1545553 to L.H-B., G.G.K., and A.L.J. National Science Foundation
- Hatch Project NCO2784 U.S. Department of Agriculture
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Affiliation(s)
- George G Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695-7630, USA.
| | - William Sharpee
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695-7630, USA
| | - Alana L Jacobson
- Department of Entomology, Auburn University, Auburn, AL, 36849, USA
| | - Mary Wambugu
- International Livestock Research Institute (BecA), Nairobi, Kenya
| | - Benard Mware
- International Livestock Research Institute (BecA), Nairobi, Kenya
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
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Dye AE, Muga B, Mwangi J, Hoyer JS, Ly V, Rosado Y, Sharpee W, Mware B, Wambugu M, Labadie P, Deppong D, Jackai L, Jacobson A, Kennedy G, Ateka E, Duffy S, Hanley-Bowdoin L, Carbone I, Ascencio-Ibáñez JT. Cassava begomovirus species diversity changes during plant vegetative cycles. Front Microbiol 2023; 14:1163566. [PMID: 37303798 PMCID: PMC10248227 DOI: 10.3389/fmicb.2023.1163566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/17/2023] [Indexed: 06/13/2023] Open
Abstract
Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.
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Affiliation(s)
- Anna E. Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Brenda Muga
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jenniffer Mwangi
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, United States
| | - Vanessa Ly
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Yamilex Rosado
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - William Sharpee
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Benard Mware
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Mary Wambugu
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Paul Labadie
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - David Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Louis Jackai
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - George Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, United States
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
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Aimone CD, Hoyer JS, Dye AE, Deppong DO, Duffy S, Carbone I, Hanley-Bowdoin L. An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing. J Virol Methods 2021; 300:114405. [PMID: 34896458 DOI: 10.1016/j.jviromet.2021.114405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 08/26/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.
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Affiliation(s)
- Catherine D Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - J Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Anna E Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - David O Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
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Aimone CD, De León L, Dallas MM, Ndunguru J, Ascencio-Ibáñez JT, Hanley-Bowdoin L. A New Type of Satellite Associated with Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0043221. [PMID: 34406866 PMCID: PMC8513466 DOI: 10.1128/jvi.00432-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022] Open
Abstract
Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is coinoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus-resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of an SEGS-2-encoded protein that may also be encoded by the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world's cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought, and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | | | - José T. Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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Aimone CD, Lavington E, Hoyer JS, Deppong DO, Mickelson-Young L, Jacobson A, Kennedy GG, Carbone I, Hanley-Bowdoin L, Duffy S. Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation. J Gen Virol 2021; 102:001622. [PMID: 34310272 PMCID: PMC8491896 DOI: 10.1099/jgv.0.001622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/05/2021] [Indexed: 01/06/2023] Open
Abstract
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.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Erik Lavington
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - George G. Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
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