title: Molecular characterization of previously elusive badnaviruses associated with symptomatic cacao in the New World.
abstract: Suspected virus-like symptoms were observed in cacao plants in Trinidad during 1943, and the viruses associated with these symptoms were designated as strains A and B of cacao Trinidad virus (CTV). However, viral etiology has not been demonstrated for either phenotype. Total DNA was isolated from symptomatic cacao leaves exhibiting the CTV A and B phenotypes and subjected to Illumina HiSeq and Sanger DNA sequencing. Based on de novo assembly, two apparently full-length badnavirus genomes of 7,533 and 7,454 nucleotides (nt) were associated with CTV strain A and B, respectively. The Trinidad badnaviral genomes contained four open reading frames, three of which are characteristic of other known badnaviruses, and a fourth that is present in only some badnaviruses. Both badnaviral genomes harbored hallmark caulimovirus-like features, including a tRNAMetpriming site, a TATA box, and a polyadenylation-like signal. Pairwise comparisons of the RT-RNase H region indicated that the Trinidad isolates share 57-71% nt sequence identity with other known badnaviruses. Based on the system for badnavirus species demarcation in which viruses with less than 80% nt sequence identity in the RT-RNase gene are considered members of separate species, these isolates represent two previously unidentified badnaviruses, herein named cacao mild mosaic virus and cacao yellow vein banding virus, making them the first cacao-infecting badnaviruses identified thus far in the Western Hemisphere.
authors.affiliation: School of Plant Sciences, University of Arizona, 1140 E, South Campus Drive, Tucson, AZ, 85721, USA.
authors.forename: Nomatter
authors.identifier: http://orcid.org/0000-0003-3401-4403
authors.initials: N
authors.lastname: Chingandu
authors.affiliation: IAGS, University of Punjab, Lahore, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Zia-Ur-Rehman
authors.affiliation: Cocoa Research Centre, The University of the West Indies, St. Augustine, Trinidad and Tobago.
authors.forename: Thyail N
authors.initials: TN
authors.lastname: Sreenivasan
authors.affiliation: Cocoa Research Centre, The University of the West Indies, St. Augustine, Trinidad and Tobago.
authors.forename: Surendra
authors.initials: S
authors.lastname: Surujdeo-Maharaj
authors.affiliation: Cocoa Research Centre, The University of the West Indies, St. Augustine, Trinidad and Tobago.
authors.forename: Pathmanathan
authors.initials: P
authors.lastname: Umaharan
authors.affiliation: USDA-ARS Subtropical Horticultural Research Station, Miami, FL, 33158, USA.
authors.forename: Osman A
authors.initials: OA
authors.lastname: Gutierrez
authors.affiliation: School of Plant Sciences, University of Arizona, 1140 E, South Campus Drive, Tucson, AZ, 85721, USA. jkbrown@email.arizona.edu.
authors.forename: Judith K
authors.initials: JK
authors.lastname: Brown
mesh_terms: D019195:Badnavirus / Q000235:genetics* / Q000302:isolation & purification; D001483:Base Sequence; D002099:Cacao / Q000821:virology*; D004279:DNA, Viral / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D010935:Plant Diseases / Q000821:virology*; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral