Adams, M. J., Antoniw, J. F., & Beaudoin, F. (2005a). Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Molecular Plant Pathology, 6, 471–487.

Article  CAS  PubMed  Google Scholar 

Adams, M. J., Antoniw, J. F., & Fauquet, C. M. (2005b). Molecular criteria for genus and species discrimination within the family Potyviridae. Archives of Virology, 150, 459–479.

Article  CAS  PubMed  Google Scholar 

Bejerman, N., Debat, H., & Dietzgen, R. G. (2020). The plant negative-sense RNA virosphere: Virus discovery through new eyes. Frontiers in Microbiology, 11, 588427.

Article  PubMed  PubMed Central  Google Scholar 

Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009). trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972–1973.

Article  PubMed  PubMed Central  Google Scholar 

Chai, M., Wu, X., Liu, J., Fang, Y., Luan, Y., Cui, X., Zhou, X., Wang, A., & Cheng, X. (2020). P3N-PIPO interacts with P3 via the shared N-terminal domain to recruit viral replication vesicles for cell-to-cell movement. Journal of Virology, 94, e01898-e1919.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi, D., Rai, M., Rai, A., Shin, C., Yamazaki, M., & Hahn, Y. (2023). High-throughput RNA sequencing analysis of Mallotus japonicus revealed novel polerovirus and amalgavirus. Acta Virologica, 67, 13–23.

Article  CAS  PubMed  Google Scholar 

Choi, D., Shin, C., Shirasu, K., & Hahn, Y. (2021). Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica). Acta Virologica, 65, 365–372.

Article  CAS  PubMed  Google Scholar 

Choi, D., Shin, C., Shirasu, K., Ichihashi, Y., & Hahn, Y. (2022). Artemisia capillaris nucleorhabdovirus 1, a novel member of the genus Alphanucleorhabdovirus, identified in the Artemisia capillaris transcriptome. Acta Virologica, 66, 149–156.

Article  CAS  PubMed  Google Scholar 

Chung, B. Y. W., Miller, W. A., Atkins, J. F., & Firth, A. E. (2008). An overlapping essential gene in the Potyviridae. Proceedings of the National Academy of Sciences, 105, 5897–5902.

Article  CAS  Google Scholar 

Cui, H., & Wang, A. (2019). The biological impact of the hypervariable N-terminal region of potyviral genomes. Annual Review of Virology, 6, 255–274.

Article  CAS  PubMed  Google Scholar 

Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.

Article  CAS  PubMed  Google Scholar 

Geng, C., Cong, Q. Q., Li, X. D., Mou, A. L., Gao, R., Liu, J. L., & Tian, Y. P. (2015). Developmentally regulated plasma membrane protein of Nicotiana benthamiana contributes to potyvirus movement and transports to plasmodesmata via the early secretory pathway and the actomyosin system. Plant Physiology, 167, 394–410.

Article  CAS  PubMed  Google Scholar 

Goh, C. J., & Hahn, Y. (2021). Analysis of proteolytic processing sites in potyvirus polyproteins revealed differential amino acid preferences of NIa-Pro protease in each of seven cleavage sites. PLoS ONE, 16, e0245853.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hagiwara-Komoda, Y., Choi, S. H., Sato, M., Atsumi, G., Abe, J., Fukuda, J., Honjo, M. N., Nagano, A. J., Komoda, K., Nakahara, K. S., et al. (2016). Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses. Scientific Reports, 6, 21411.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018). UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35, 518–522.

Article  CAS  PubMed  Google Scholar 

Inoue-Nagata, A. K., Jordan, R., Kreuze, J., Li, F., López-Moya, J. J., Mäkinen, K., Ohshima, K., & Wylie, S. J. (2022). ICTV virus taxonomy profile: Potyviridae 2022. Journal of General Virology, 103, 001738.

Article  CAS  Google Scholar 

Li, F., Xu, D., Abad, J., & Li, R. (2012). Phylogenetic relationships of closely related potyviruses infecting sweet potato determined by genomic characterization of Sweet potato virus G and Sweet potato virus 2. Virus Genes, 45, 118–125.

Article  CAS  PubMed  Google Scholar 

Li, H. (2014). Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics, 30, 2843–2851.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37, 1530–1534.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mostafavi, F. S., Sabbagh, S. K., Yamchi, A., Nasrollanejad, S., & Panjehkeh, N. (2019). Differential molecular response of maize and Johnson grass against maize dwarf mosaic virus and bermuda grass southern mosaic virus. Acta Virologica, 63, 70–79.

Article  CAS  PubMed  Google Scholar 

Nakamura, T., Yamada, K. D., Tomii, K., & Katoh, K. (2018). Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics, 34, 2490–2492.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Olspert, A., Carr, J. P., & Firth, A. E. (2016). Mutational analysis of the Potyviridae transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins. Nucleic Acids Research, 44, 7618–7629.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Olspert, A., Chung, B. Y. W., Atkins, J. F., Carr, J. P., & Firth, A. E. (2015). Transcriptional slippage in the positive-sense RNA virus family Potyviridae. EMBO Reports, 16, 995–1004.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Palani, S. N., Sankaranarayanan, R., & Tennyson, J. (2021). Comparative study of potyvirid NIa proteases and their cleavage sites. Archives of Virology, 166, 1141–1149.

Article  CAS  PubMed  Google Scholar 

Park, D., Goh, C. J., & Hahn, Y. (2021). Two novel closteroviruses, fig virus A and fig virus B, identified by the analysis of the high-throughput RNA-sequencing data of fig (Ficus carica) latex. Acta Virologica, 65, 42–48.

Article  CAS  PubMed  Google Scholar 

Park, D., & Hahn, Y. (2021). Identification of genome sequences of novel partitiviruses in the quinoa (Chenopodium quinoa) transcriptome datasets. Journal of General Plant Pathology, 87, 236–241.

Article  CAS  Google Scholar 

Park, D., Kim, H., & Hahn, Y. (2017). Genome sequence of a distinct watermelon mosaic virus identified from ginseng (Panax ginseng) transcriptome. Acta Virologica, 61, 479–482.

Article  CAS  PubMed  Google Scholar 

Pasin, F., Daròs, J. A., & Tzanetakis, I. E. (2022). Proteome expansion in the Potyviridae evolutionary radiation. FEMS Microbiology Reviews, 46, 11.

Article  Google Scholar 

Pearson, W. R., & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the USA, 85, 2444–2448.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qing, Z., Ahmad, S., Chen, Y., Liang, Q., Zhang, L., Chen, B., & Wen, R. (2023). P3/P3N-PIPO of PVY interacting with BI-1 inhibits the degradation of NIb by ATG6 to facilitate virus replication in N. benthamiana. Frontiers in Plant Science, 14, 1183144.

Article  PubMed  PubMed Central  Google Scholar 

Rodamilans, B., Valli, A., Mingot, A., San León, D., Baulcombe, D., López-Moya, J. J., & García, J. A. (2015). RNA polymerase slippage as a mechanism for the production of frameshift gene products in plant viruses of the Potyviridae family. Journal of Virology, 89, 6965–6967.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shin, C., Choi, D., Shirasu, K., & Hahn, Y. (2022a). Identification of dicistro-like viruses in the transcriptome data of Striga asiatica and other plants. Acta Virologica, 66, 157–165.

Article  CAS  PubMed  Google Scholar 

Shin, C., Choi, D., Shirasu, K., Ichihashi, Y., & Hahn, Y. (2022b). A novel RNA virus, Thesium chinense closterovirus 1, identified by high-throughput RNA-sequencing of the parasitic plant Thesium chinense. Acta Virologica, 66, 206–215.

Article  CAS  PubMed  Google Scholar 

Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38, 3022–3027.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Untiveros, M., Olspert, A., Artola, K., Firth, A. E., Kreuze, J. F., & Valkonen, J. P. (2016). A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing. Molecular Plant Pathology, 17, 1111–1123.

Article  CAS  PubMed