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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)