Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses

Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Rondebosch 7701, South Africa.
Journal of Virology (Impact Factor: 4.44). 01/2007; 80(23):11827-32. DOI: 10.1128/JVI.01100-06
Source: PubMed


Foot-and-mouth disease virus (FMDV) is thought to evolve largely through genetic drift driven by the inherently error-prone nature of its RNA polymerase.
There is, however, increasing evidence that recombination is an important mechanism in the evolution of these and other related
picornoviruses. Here, we use an extensive set of recombination detection methods to identify 86 unique potential recombination
events among 125 publicly available FMDV complete genome sequences. The large number of events detected between members of
different serotypes suggests that horizontal flow of sequences among the serotypes is relatively common and does not incur
severe fitness costs. Interestingly, the distribution of recombination breakpoints was found to be largely nonrandom. Whereas
there are clear breakpoint cold spots within the structural genes, two statistically significant hot spots precisely separate
these from the nonstructural genes. Very similar breakpoint distributions were found for other picornovirus species in the
genera Enterovirus and Teschovirus. Our results suggest that genome regions encoding the structural proteins of both FMDV and other picornaviruses are functionally
interchangeable modules, supporting recent proposals that the structural and nonstructural coding regions of the picornaviruses
are evolving largely independently of one another.

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Available from: Arvind Varsani
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    • "Because of the high mutation rate and saturation detected in cyt-b, we only used the 1st and 2nd codon positions when we used the full matrix. In all nuclear genes, recombination was tested using RDP: Recombination Detection Program v3.44 (Martin & Rybicki 2000; Heath et al. 2006). "
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    • "Gene tree and species-tree analyses The best-fit evolutionary model for each gene (cyt-b [794 bp]: TRN+I+G; 12S [951 bp]: GTR+G; MXRA5 [961 bp]: TPM1lf+G, NKTR [1074 bp]: TRN+G, SIN- CAIP [449 bp]: TPM2 lf+G, RBMX [600 bp]: HKY+G, DMXL [959 bp]: HKY+G, ACA4 [1218 bp]: HKY+G, PLRL [543 bp]: TRN+G, Homo_30b [664 bp]: TIM1 + G, Homo_19b [642 bp]: HKY+G,) was selected using the corrected Akaike information criterion in JMODELTEST v0.1.1 (Posada 2008). For all nuclear genes, recombination was tested and excluded using RDP: Recombination Detection Program v3.44 (Martin & Rybicki 2000; Heath et al. 2006). Separate Bayesian analyses (BI) were conducted for each gene using MRBAYES v3.1.2 "
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    ABSTRACT: The genus Homonota was described by Gray (1845) and currently includes 10 species: Homonota andicola, H. borellii, H. darwinii, H. fasciata, H. rupicola, H. taragui, H. underwoodi, H. uruguayensis, H. williamsii & H. whitii and one subspecies of H. darwinii (H. darwinii macrocephala). It is distributed from 15° latitude south in southern Brazil, through much of Bolivia, Paraguay, Uruguay and Argentina to 54° south in Patagonia and across multiple different habitats. Several morphological taxonomic studies on a subset of these species have been published, but no molecular phylogenetic hypotheses are available for the genus. The objective of this study is to present a molecular phylogenetic hypothesis for all the described species in the genus. We sequenced two mitochondrial genes (cyt-b & 12S: 1745 bp), seven nuclear protein coding (RBMX, DMLX, NKTR, PLRL, SINCAIP, MXRA5, ACA4: 5804 bp) and two anonymous nuclear loci (30Hb, 19Hb: 1306 bp) and implemented traditional concatenated analyses (MP, ML, BI) as well as species-tree (*beast) approaches. All methods recovered almost the same topology. We recovered the genus Homonota as monophyletic with strong statistical support. Within Homonota, there are three strongly supported clades (whitii, borellii and fasciata), which differ from those previously proposed based on scale shape, osteology, myology and quantitative characters. Detailed morphological analyses based on this highly resolved and well-supported phylogeny will provide a framework for understanding morphological evolution and historical biogeography of this phenotypically conservative genus. We hypothesize that extensive marine transgressions during Middle and Late Miocene most probably isolated the ancestors of the three main clades in eastern Uruguay (borellii group), north-western Argentina-southern Bolivia (fasciata group), and central-western Argentina (whitii group). Phylogeographic and morphological/morphometric analyses coupled with paleo-niche modelling are needed to better understand its biogeographical history.
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    • "Haplotypes were inferred using PHASE (Stephens et al. 2001, Stephens and Donelly 2003), with an output threshold of 0.7, as implemented in DnaSP (Librado and Rozas 2009). Using RDP3, and seven inclusive tests in the program (Smith 1992, Padidam et al. 1999, Gibbs et al. 2000, Martin and Rybicki 2000, Posada and Crandall 2001, Martin et al. 2005, Heath et al. 2006, Boni et al. 2007), we checked for recombination. Using these tests, recombination was not detected in any of the Z-linked loci. "
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