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Table 2 Putative recombination events in the genomes and individual open reading frames of viruses of RMV cluster of subgroup 3 tobamoviruses

From: Molecular characterisation of a novel recombinant Ribgrass mosaic virus strain FSHS

    Parental isolate Break points  
  Method Recombinant Major Minor Beginning Ending Average P-value
Genome RDP RMV FSHS RMV NZ-439 RMV Actinidia-AC 1906 2564 5×10-26
  GeneConv 2148 2479 5×10-10
  Bootscan 1905 2564 8×10-23 − 5×10-22
  MaxChi 1906 2564 3×10-17 − 8×10-14
  Chimaera 1926 2558 1×10-06 − 3×10-05
  SciScan 2148 2414 1×10-10 − 6×10-10
  3Seq 1926 2558 2×10-21 − 5×10-06
ORF 1-2 RDP RMV FSHS RMV NZ-439 RMV Actinidia-AC 1839−1858 2498 5×10-23 − 9×10-20
  GeneConv 1839 2498 8×10-11 − 3×10-08
  Bootscan 1839 2498 3×10-22 − 2×10-18
  MaxChi 1839 2498 6×10-18 − 3×10-12
  Chimaera 1839 2498 2×10-16 − 1×10-02
  SciScan 1807−1862 2461−2522 3×10-11 − 4×10-10
  3Seq 1839 2498 2×10-22 − 8×10-04
ORF 3   No recombination
ORF 4   No recombination
  1. RDP, Bootscan and SiScan are phylogeny-based methods, while GeneCov, MaxChi, and Chimaera are substitution-based methods. 3SEQ recombination detection algorithm tests for mosaicism between three nucleotide sequences. No recombinations were detected using Lard. ‘Major’ and ‘Minor’ parents refer to parental isolates contributing the larger and smaller fractions of recombinant sequence respectively. P-values < 0.05 were considered significant. [Genomes of RMV strains: Kons. 1105-V2 isolate R14 (HQ667980) and Actinidia-AD (GQ401366.1) were not included in the analysis as they were 99 % and 100 % similar to RMV Kons. 1105 isolate R14 (HQ667979) and Actinidia-AC (GQ401365.1) respectively]