Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus

Authors: ADEGBOLA, RAPHAEL - University Of Arizona; KEITH, CORY - University Of Arizona; Gutierrez, Osman; Goenaga, Ricardo; BROWN, JUDITH - University Of Arizona

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2024
Publication Date: 3/23/2024
Citation: Adegbola, R.O., Keith, C.V., Gutierrez, O.A., Goenaga, R.J., Brown, J.K. 2024. Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus. Archives of Virology. 169:83. https://doi.org/10.1007/s00705-024-06013-7.
DOI: https://doi.org/10.1007/s00705-024-06013-7

Interpretive Summary: Cacao is a tropical perennial whose production worldwide is substantially reduced by diseases and pests. Since the 1930s, Badnaviruses have been causing serious damage in cacao farms in West Africa. In contrast, Poleroviruses have been reported affecting cereal grains, fruits, and vegetable crops production. However, recently, Poleroviruses have been found infecting cacao under quarantine and field conditions. Germplasm exchange is crucial for breeding programs and germplasm banks since genetic diversity is of paramount importance for the development of new cultivars with disease resistance. In addition, the identification of pathogens during the quarantine process is also critical to avoid the introduction of new diseases to production areas. In order to develop new assays that identify emergent pathogens, sequencing data must be available. This research reports sequenced RNA obtained from plants presenting cacao leafroll virus (CaLRV) symptoms under quarantine conditions. Results of genome sequence analysis obtained using high-throughput sequencing confirmed the presence of four CaLRV genomes. Comparison with other well-characterized poleroviruses, indicated that CaLRV has a high similarity with potato leafroll virus (PLRV). Further analyses indicated that cotton leafroll dwarf virus (CLRDV) is a close relative. Also, CLRDV has been recently reported affecting cacao production in Brazil. The sequence information obtained herein will be utilized for the development of diagnostic tools for the detection of these poleroviruses in cacao.

Technical Abstract: The complete genome sequence of cacao leafroll virus (CaLRV; family Solemoviridae, genus Polerovirus) was deter- mined by high-throughput sequencing of total RNA isolated from symptomatic cacao Theobroma cacao L. plants (n = 4). The CaLRV genome sequences ranged from 5,976 to 5,997 nucleotides (nt) in length and contained seven open reading frames (ORFs). Nucleotide and amino acid (aa) sequence comparisons showed that, among selected well-characterized poleroviruses, the CaLRV genome shared the highest nt sequence identity of 62% with that of potato leafroll virus (PLRV, NC_076505). A comparison of the predicted aa sequence of the CaLRV coat protein indicated that cotton leafroll dwarf virus (CLRDV, NC_014545) and melon aphid-borne yellows virus (MABYV, NC_010809) were the closest relatives, sharing 57% aa sequence identity. Bayesian phylogenetic analysis based on complete genome sequences showed that CaLRV grouped with well-characterized poleroviruses that cause diseases of cereal and vegetable crops. During the course of publishing this work, the nearly complete genome sequence of a member of the same polerovirus species, referred to as “cacao polerovirus” (OR605721), with which CaLRV shares 99% nt sequence identity, was reported.