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Genetic Diversity of Viral Populations Associated with Ananas Germplasm and Improvement of Virus Diagnostic Protocols. Pathogens 2022; 11:pathogens11121470. [PMID: 36558805 PMCID: PMC9787488 DOI: 10.3390/pathogens11121470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Pineapple (Ananas comosus L. [Merr.]) accessions from the U.S. Tropical Plant Genetic Resources and Disease Research (TPGRDR) in Hilo, Hawaii were subjected to RNA-sequencing to study the occurrence of viral populations associated with this vegetatively propagated crop. Analysis of high-throughput sequencing data obtained from 24 germplasm accessions and public domain transcriptome shotgun assembly (TSA) data identified two novel sadwaviruses, putatively named "pineapple secovirus C" (PSV-C) and "pineapple secovirus D" (PSV-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 (7485 bp) corresponding to a previously reported partial sequence of the badnavirus, pineapple bacilliform ER virus (PBERV), was retrieved from one of the datasets. Overall, we discovered a total of 69 viral sequences representing ten 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 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 congruent with the diversity found by phylogenetic analyses. Here, we also report the development and improvement of RT-PCR diagnostic protocols for the specific identification and detection of viruses infecting pineapple based on the diverse viral populations characterized in this study. Given the high occurrence of recombination events, diversity, and discovery of viruses found in Ananas germplasm, the reported and validated RT-PCR assays represent an important advance for surveillance of viral infections of pineapple.
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Larrea-Sarmiento A, Geering AD, Olmedo-Velarde A, Wang X, Borth W, Matsumoto TK, Suzuki JY, Wall MM, Melzer M, Moyle R, Sharman M, Hu J, Thomas JE. Genome sequence of pineapple secovirus B, a second sadwavirus reported infecting Ananas comosus. Arch Virol 2022; 167:2801-2804. [PMID: 36269415 PMCID: PMC9741570 DOI: 10.1007/s00705-022-05590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/28/2022] [Indexed: 12/14/2022]
Abstract
The complete genome sequence of pineapple secovirus B (PSV-B), a new virus infecting pineapple (Ananas comosus) on the island of Oahu, Hawaii, was determined by high-throughput sequencing (HTS). The genome comprises two RNAs that are 5,956 and 3,808 nt long, excluding the 3'-end poly-A tails, both coding for a single large polyprotein. The RNA1 polyprotein contains five conserved domains associated with replication, while the RNA2 polyprotein is cleaved into the movement protein and coat protein. PSV-B is representative of a new species in the subgenus Cholivirus (genus Sadwavirus; family Secoviridae), as the level of amino acid sequence identity to recognized members of this subgenus in the Pro-Pol and coat protein regions is below currently valid species demarcation thresholds.
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Affiliation(s)
- Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI USA
| | - Andrew D.W. Geering
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, Ecosciences Precinct, 4001 Brisbane, QLD GPO Box 267, Australia
| | - Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI USA
| | - Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI USA
| | - Wayne Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI USA
| | - Tracie K Matsumoto
- Department of Agriculture, Agricultural Research Service, United States, Daniel K. Inouye U. S. Pacific Basin Agricultural Research Center, Hilo, HI USA
| | - Jon Y Suzuki
- Department of Agriculture, Agricultural Research Service, United States, Daniel K. Inouye U. S. Pacific Basin Agricultural Research Center, Hilo, HI USA
| | - Marisa M Wall
- Department of Agriculture, Agricultural Research Service, United States, Daniel K. Inouye U. S. Pacific Basin Agricultural Research Center, Hilo, HI USA
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI USA
| | - Richard Moyle
- School of Agriculture and Food Sciences, The University of Queensland, 4072 St Lucia, QLD Australia
| | - Murray Sharman
- Department of Agriculture and Fisheries, Ecosciences Precinct, 4001 Brisbane, QLD GPO Box 267, Australia
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI USA
| | - John E. Thomas
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, Ecosciences Precinct, 4001 Brisbane, QLD GPO Box 267, Australia
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