Poster: Diseases of Plants: New & Emerging Diseases
Identification and proposed species demarcation for Cacao swollen shoot virus and previously unidentified badnaviruses of Theobroma cacao
N. CHINGANDU (1), M. Zia-Ur-Rehman (2), T. Sreenivasan (3), S. Surujdeo-Maharaj (4), P. Umaharan (4), K. Kouakou (5), R. Aka (5), G. Ameyaw (6), O. Gutierrez (7), J. Brown (1) (1) University of Arizona, Tucson, AZ, U.S.A.; (2) IAGS, University of Punjab,
Sustained production of cacao (Theobroma cacao) in West Africa, which supplies over 70% of the world’s bulk cacao, is hindered by virus-like diseases. To date, Cacao swollen shoot virus (CSSV) (Caulimoviridae, Badnavirus), endemic to West Africa, is the only known cacao-infecting badnavirus. In West Africa, CSSV-like symptoms became prevalent during 2000-2003, and continue to persist. Since the 1940s, virus-like symptoms in cacao of suspect badnaviral etiology have been recognized in Trinidad at the International Cocoa Genebank, one of the custodians of cacao germplasm resources. To identify the suspect viruses, total DNA isolated from symptomatic cacao leaves collected in Ghana, Cote d’Ivoire and Trinidad was subjected to rolling circle amplification and sequenced using Illumina HiSeq. DNA sequences were assembled using DNASTAR, and annotated using the NCBI ORF Finder, and the results were validated by sequencing PCR-amplified full-length genomes. Genome characterization revealed seven previously unidentified badnavirus isolates, each with four open reading frames, characteristic of other badnaviruses. Pairwise comparisons using Standard Demarcation Tool (SDT) of the RT-RNaseH sequence (80% nucleotide identity) with analogous badnavirus sequences indicated that the isolates represented three new badnavirus species. However, SDT analysis of the full-length genome sequences suggested at least five previously unidentified badnavirus species are associated with cacao.