Skip to main content

Table 1 Predicted conserved protein domains identified in cacao-infecting badnavirus genome sequences

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

Viral isolate or species ORF1 ORF2 ORF3 ORF4 ORFX ORFY *Clade
CI311 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND ND I
CI135 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CI275 DUF1319 ND Zn, Pepsin, RT, RNase H ND I
CIS2 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CIS3 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CI44 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
GH64 DUF1319 ND Zn, Pepsin, RT, RNase H ND I
GH67 DUF1319 ND Zn, Pepsin, RT, RNase H ND I
GH75 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND ND I
CI134 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CI215 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CI286 DUF1319 ND Zn, Pepsin, RT, RNase H ND I
CIT5 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CI301 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND ND I
TG_AJ781003 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CI_JN606110 DUF1319 ND Pepsin, RT, RNase H ND DUF3187 I
TG_L14546 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
TG_AJ534983 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
GH_AJ609020 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
GH_AJ609019 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND ND I
GH_AJ608931 DUF1319 ND Zn, Pepsin, RT, RNase H ND ND I
CaMMV DUF1319 ND Zn, DUF4200, Pepsin, RT, RNase H ND I
CYVBV DUF1319 ND Zn, PHD, Trim, Pepsin, RT, RNase H ND II
  1. Legend: The West African field isolates are designated by sample code. The Genbank Accession number for each cacao-infecting badnavirus reference sequence is indicated. Predicted open reading frames (ORFs) were located using the ORF Finder tool (NCBI). The country abbreviations used are: CI-Cote d’Ivoire, GH-Ghana, and TG-Togo, for West African field isolates studied here, and available in GenBank. The conserved protein domains are indicated as: DUF domain of unknown function, Zn zinc knuckle finger, Pepsin pepsin-like aspartate protease, RT reverse transcriptase, RNase H ribonuclease H, PHD plant homeodomain finger, Trim trimeric-dUTPase, H, ND no domain predicted. The asterisk *Clade = phylogenetic clade designation based on full-length genome sequence (Fig. 3b)