Genetic diversity of viral populations associated with Ananas germplasm and improvement of virus diagnostic protocols

Authors: LARREA-SARMIENTO, ADRIANA - University Of Hawaii; OLMEDO-VELARDE, ALEJANDRO - University Of Hawaii; WANG, XUPENG - University Of Hawaii; BORTH, WAYNE - University Of Hawaii; Domingo, Ryan; Matsumoto Brower, Tracie; Suzuki, Jon; Wall, Marisa; MELZER, MICHAEL - University Of Hawaii; HU, JOHN - University Of Hawaii

Submitted to: Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2022
Publication Date: 12/5/2022
Citation: Larrea-Sarmiento, A., Olmedo-Velarde, A., Wang, X., Borth, W., Domingo, R., Matsumoto Brower, T.K., Suzuki, J.Y., Wall, M.M., Melzer, M., Hu, J. 2022. Genetic diversity of viral populations associated with Ananas germplasm and improvement of virus diagnostic protocols. Pathogens. 11(12). Article 1470. https://doi.org/10.3390/pathogens11121470.
DOI: https://doi.org/10.3390/pathogens11121470

Interpretive Summary: Pineapple is a major agricultural product with worldwide production at 28 million metric tons. Plants such as pineapple that are propagated through crowns, slips, or suckers over time tend to accumulate plant viruses that are transmitted to the new plants. There is evidence suggesting that pineapple viruses are behind certain diseases causing damage to pineapple plants and subsequently pineapple production. Advances in sequencing technologies have increased our ability to identify not only a organism's genes, but potential pathogens infecting the organisms. To assess the prevalence of viruses in pineapple, tissues from a subset of the diverse pineapple plant collection conserved by the U.S. Department of Agriculture, Agricultural Research Service, Tropical Plant Genetic Resources and Disease Research Unit in Hilo were analysed using this modern comprehensive sequencing approach. Results indicate the presence of two new viruses among sequences representing 10 members of major plant virus groups known as Ampelovirus, Sadwavirus, and Badnavirus. This information will be useful for detecting occurance of pineapple viruses to support development of management strategies to curb diseases associated with these viruses in production fields and germplasm collections.

Technical Abstract: Pineapple (Ananas comosus L. [Merr.]) accessions from the National Clonal Germplasm Repository (NCGR) were subjected to RNA-sequencing to study the occurrence of viral populations associated with this vegetably propagated crop. Analysis of high-throughput sequencing data obtained from 24 germplasm accessions and from transcriptome shotgun assembly (TSA) data identified two novel sadwaviruses, putatively named “pineapple secovirus C” and “pineapple secovirus D”. They shared low amino acid sequence identity (from 34.8 to 41.3%) compared with their homologs in the Pro-pol region of the previously reported PSV-A and PSV-B. The complete genome (7,485 bp) of the partially reported badnavirus, pineapple bacilliform ER virus (PBERV), was retrieved from one of the datasets. Overall, we discovered a total of 69 viral sequences representing 10 members within the Ampelovirus, Sadwavirus, and Badnavirus genera. Genetic diversity and recombination events were found in members of the pineapple mealybug wilt-associated virus (PMWaV) complex as well as PSVs. PMWaV-1, -3, and -6 presented recombination events located across the quintuple gene block while no recombination events were found for PMWaV-2. High recombination frequency of the RNA1 and RNA2 molecules from PSV-A and PSV-B were compatible with the diversity found by phylogenetic analyses. Here, we report the development and improvement of RT-PCR diagnostic protocols based on the diversity in viral populations for the specific identification and detection of viruses infecting pineapple. Given the high occurrence of recombination events, diversity and discovery of viruses found in Ananas germplasm, the reported and validated RT-PCR assays are significant for viral surveillance in pineapple.