1
|
Iqbal Z, Shafiq M, Sattar MN, Ali I, Khurshid M, Farooq U, Munir M. Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus. Viruses 2023; 15:2358. [PMID: 38140599 PMCID: PMC10747432 DOI: 10.3390/v15122358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Pedilanthus leaf curl virus (PeLCV) is a monopartite begomovirus (family Geminiviridae) discovered just a few decades ago. Since then, it has become a widely encountered virus, with reports from ca. 25 plant species across Pakistan and India, indicative of its notable evolutionary success. Viruses mutate at such a swift rate that their ecological and evolutionary behaviors are inextricably linked, and all of these behaviors are imprinted on their genomes as genetic diversity. So, all these imprints can be mapped by computational methods. This study was designed to map the sequence variation dynamics, genetic heterogeneity, regional diversity, phylogeny, and recombination events imprinted on the PeLCV genome. Phylogenetic and network analysis grouped the full-length genome sequences of 52 PeLCV isolates into 7 major clades, displaying some regional delineation but lacking host-specific demarcation. The progenitor of PeLCV was found to have originated in Multan, Pakistan, in 1977, from where it spread concurrently to India and various regions of Pakistan. A high proportion of recombination events, distributed unevenly throughout the genome and involving both inter- and intraspecies recombinants, were inferred. The findings of this study highlight that the PeLCV population is expanding under a high degree of genetic diversity (π = 0.073%), a high rate of mean nucleotide substitution (1.54 × 10-3), demographic selection, and a high rate of recombination. This sets PeLCV apart as a distinctive begomovirus among other begomoviruses. These factors could further exacerbate the PeLCV divergence and adaptation to new hosts. The insights of this study that pinpoint the emergence of PeLCV are outlined.
Collapse
Affiliation(s)
- Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa P.O. Box 55110, Saudi Arabia;
| | - Muhammad Shafiq
- Department of Biotechnology, University of Management and Technology, Sialkot Campus, Sialkot P.O. Box 51340, Pakistan;
| | | | - Irfan Ali
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad P.O. Box 38000, Pakistan;
| | - Muhammad Khurshid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore P.O. Box 54590, Pakistan;
| | - Umer Farooq
- Department of Biotechnology, University of Sialkot, Sialkot P.O. Box 51340, Pakistan;
| | - Muhammad Munir
- Date Palm Research Center of Excellence, King Faisal University, Al-Ahsa P.O. Box 31982, Saudi Arabia;
| |
Collapse
|
2
|
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.
Collapse
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
| | | |
Collapse
|