The Role of Extensive Recombination in the Evolution of Geminiviruses

Fiallo‐Olivé, Elvira; Navas‐Castillo, Jesús

doi:10.1007/978-3-031-15640-3_4

Cited by 7 publications

(8 citation statements)

References 123 publications

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“…Recombination is a major mechanism of speciation for begomoviruses [4, 108, 109]. Although we see frequent recombination within regions, cross-region recombinants are rare in our analyses (Fig.…”

Section: Discussionmentioning

confidence: 78%

“…While widely accepted, not all begomovirus species follow this coarse geographic grouping. The sweetpotato-infecting begomoviruses (known as “sweepoviruses”) are not split at continent scales, but rather form a distinct clade, with some viruses discovered in samples collected in the Americas and others discovered in samples from the AAEO region [4, 8, 9]. An additional group of legume-infecting begomoviruses known as the “legumoviruses” is also considered a distinct lineage from the two broad regional groups, although all legumoviruses have been sampled in the AAEO region [8, 10, 11].…”

Section: Introductionmentioning

confidence: 99%

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Phylogeographic analysis ofBegomoviruscoat and replication-associated proteins

Crespo-Bellido,

Hoyer,

Burgos-Amengual

et al. 2023

Preprint

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Begomoviruses are globally distributed plant pathogens that significantly limit crop production. These viruses are traditionally described according to phylogeographic distribution and categorized into two groups: begomoviruses from the Africa, Asia, Europe, and Oceania (AAEO) region and begomoviruses from the Americas. Monopartite begomoviruses are more common in the AAEO region while bipartite viruses predominate in the Americas, where the begomoviruses lack the V2/AV2 gene involved in inter-cellular movement and RNA silencing suppression found in AAEO begomoviruses. While these features are generally accepted as lineage-defining, the number of known species has doubled due to sequence-based discovery since 2010. To reevaluate the geographic groupings after the rapid expansion of the genus, we conducted phylogenetic analyses for begomovirus species representatives of the two longest and most conserved begomovirus proteins: the coat and replication-associated proteins. Both proteins still largely support the broad AAEO and Americas begomovirus groupings, except for sweetpotato-infecting begomoviruses that form an independent, well-supported clade for their coat protein regardless of the region they were isolated from. Our analyses do not support more fine-scaled phylogeographic groupings. Monopartite and bipartite genome organizations are broadly interchanged throughout the phylogenies and the absence of the V2/AV2 gene is highly reflective of the split between Americas and AAEO begomoviruses. We observe significant evidence of recombination within the Americas and within the AAEO region, but rarely between the regions. We speculate that increased globalization of agricultural trade, the invasion of polyphagous whitefly vector biotypes and recombination will blur begomovirus phylogeographic delineations in the future.

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Section: Discussionmentioning

confidence: 78%

Section: Introductionmentioning

confidence: 99%

Phylogeographic analysis ofBegomoviruscoat and replication-associated proteins

Crespo-Bellido,

Hoyer,

Burgos-Amengual

et al. 2023

Preprint

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“…2011a , 2011b ; Lefeuvre and Moriones 2015 ; Crespo-Bellido et al. 2021 ; Fiallo-Olivé and Navas-Castillo 2023 ). While numerous studies have investigated the genetic diversity of natural populations ( De Bruyn et al.…”

Section: Geminiviridae — Begomovirusmentioning

confidence: 99%

“…2009 ; De Bruyn et al. 2012 ; Lefeuvre and Moriones 2015 ; Fiallo-Olivé and Navas-Castillo 2023 ) even though mutation is reported to predominantly drive their diversification ( Lima et al. 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations

Torralba,

Blanc,

Michalakis

2024

Virus Evolution

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Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle, and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of inter-specific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.

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“…These evolutionary forces cause the appearance of novel viral genomes upon which natural selection, genetic drift, and gene flow act [31,32]. Although the role of mutation and pseudo-recombination in the evolution of begomoviruses is evident, it is recombination that plays a key role in the generation and emergence of new variants, strains, and species within the genus, and even in the emergence of new genera within the family Geminiviridae (e.g., [33][34][35][36]).…”

Section: Glossarymentioning

confidence: 99%