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Table 3 Pairwise nucleotide identity for the complete genome sequence of cacao-infecting badnavirus isolates determined in this study

From: The proposed new species, cacao red vein virus, and three previously recognized badnavirus species are associated with cacao swollen shoot disease

CRVV CI286 100                     
  GH64 78 100                    
CRVV CI275 78 82 100                   
  GH67 77 80 81 100                  
CSSCDV CI_JN606110 71 71 71 71 100                 
  TG_AJ781003 72 70 72 72 76 100                
  TG_L14546 71 71 72 72 75 80 100               
  TG_AJ534983 71 71 71 72 75 80 98 100              
  CI44 71 71 71 71 75 76 83 83 100             
  GH_AJ609020 72 72 71 71 75 77 85 85 89 100            
  GH75 72 71 72 71 75 77 85 85 89 97 100           
  GH_AJ608931 72 71 72 71 75 77 85 85 89 97 99 100          
CSSV GH_AJ609019 72 71 71 71 75 77 86 85 89 97 98 98 100         
  CIS3 72 71 71 71 75 77 85 85 89 97 97 97 97 100        
  CI311 72 72 71 71 75 77 86 85 89 97 98 98 98 98 100       
  CI301 72 72 71 72 75 77 86 85 89 97 97 98 98 98 99 100      
  CI135 72 72 71 71 75 77 86 85 89 98 98 98 98 98 98 98 100     
  CIT5 72 72 71 71 75 77 86 85 90 97 98 98 98 98 98 98 98 100    
  CIS2 72 71 71 71 75 77 85 85 89 97 98 98 98 98 98 98 98 100 100   
  CI215 72 72 72 71 75 77 86 85 89 97 97 97 98 98 98 98 98 98 98 100  
  CI134 72 72 71 71 75 77 86 85 89 97 97 97 97 98 98 98 98 98 98 98 100
  1. Legend: The GenBank reference sequences are indicated by Accession number, with country code. The 14 badnaviral genome sequences determined here are indicated by country code of collection and sample number. The sequence alignment was carried out using MUSCLE, implemented in the Species Demarcation Tool v1.2 software, using ≥80% as the species cutoff. The abbreviations indicating the country origin of each isolate are as follows: CI = Cote d’Ivoire, GH = Ghana, and TG = Togo. Virus species abbreviations are indicated as: CSSV = Cacao swollen shoot virus; CSSTAV = Cacao swollen shoot Togo A virus; CSSCDV = Cacao swollen shoot CD virus; and CRVV = Cacao red vein virus