Acknowledgement
This work was funded by the National Natural Science Foundation of China (U20A2036) and Ningbo Yongjiang Grant (2022A-220-G).
References
- Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
- Asensio-S.-Manzanera, M. C., Asensio, C. and Singh, S. P. 2006. Gamete selection for resistance to common and halo bacterial blights in dry bean intergene pool populations. Crop Sci. 46:131-135.
- Atreya, P. L., Atreya, C. D. and Pirone, T. P. 1991. Amino acid substitutions in the coat protein result in loss of insect transmissibility of a plant virus. Proc. Natl. Acad. Sci. U. S. A. 88:7887-7891.
- Cao, Y., Zhi, J., Zhang, R., Li, C., Liu, Y., Lv, Z. and Gao, Y. 2018. Different population performances of Frankliniella occidentalis and Thrips hawaiiensis on flowers of two horticultural plants. J. Pest Sci. 91:79-91.
- Chen, S., Zhou, Y., Chen, Y. and Gu, J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884-i890.
- Cho, Y. S. 2022. Genipin, an inhibitor of UCP2 as a promising new anticancer agent: a review of the literature. Int. J. Mol. Sci. 23:5637.
- Diaz-Pendon, J. A., Li, F., Li, W.-X. and Ding, S.-W. 2007. Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell 19:2053-2063.
- Ding, S.-W. 2023. Transgene silencing, RNA interference, and the antiviral defense mechanism directed by small interfering RNAs. Phytopathology 113:616-625.
- Fang, L., Xie, Y., Wu, J., Wang, L. and Wang, H. 2023. First report of Diaporthe gardeniae causing branch blight of Gardenia jasminoides Ellis in Zhejiang Province, China. Plant Dis. 107:1218.
- Feng, X., Orellana, G. E., Green, J. C., Melzer, M. J., Hu, J. S. and Karasev, A. V. 2019. A new strain of bean common mosaic virus from lima bean (Phaseolus lunatus): biological and molecular characterization. Plant Dis. 103:1220-1227.
- Fresnillo, P., Jover-Gil, S., Samach, A. and Candela, H. 2022. Complete genome sequence of an isolate of Passiflora chlorosis virus from passion fruit (Passiflora edulis Sims). Plants 11:1838.
- Hajimorad, M. R., Domier, L. L., Tolin, S. A., Whitham, S. A. and Saghai Maroof, M. A. 2018. Soybean mosaic virus: a successful potyvirus with a wide distribution but restricted natural host range. Mol. Plant Pathol. 19:1563-1579.
- Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., MacManes, M. D., Ott, M., Orvis. J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., Henschel, R., LeDuc, R. D., Friedman, N. and Regev, A. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8:1494-1512.
- Jin, C., Zongo, A. W.-S., Du, H., Lu, Y., Yu, N., Nie, X., Ma, A., Ye, Q., Xiao, H. and Meng, X. 2023. Gardenia (Gardenia jasminoides Ellis) fruit: a critical review of its functional nutrients, processing methods, health-promoting effects, comprehensive application and future tendencies. Crit. Rev. Food Sci. Nutr. Advanced online publication. https://doi.org/10.1080/10408398.2023.2270530.
- Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. and Jermiin, L. S. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14:587-589.
- Katoh, K. and Standley, D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30:772-780.
- Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. L. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
- Larrea-Sarmiento, A., Wang, X., Borth, W. B., Barone, R. P., Olmedo-Velarde, A., Melzer, M. J., Sugano, J. S. K., Galanti, R., Suzuki, J. Y., Wall, M. M. and Hu, J. S. 2020. First report of bean common mosaic virus infecting flowering ginger (Alpinia purpurata) in Hawaii. Plant Dis. 104:603.
- Lu, X. H., Solangi, G. S., Huang, J. L., Liu, Z. M. and Qin, L.- P. 2023. First report of root-knot nematode Meloidogyne enterolobii on Antirrhinum majus in China. Plant Dis. 107:2555.
- Maia, I. G., Haenni, A. and Bernardi, F. 1996. Potyviral HC-Pro: a multifunctional protein. J. Gen. Virol. 77:1335-1341.
- Marie-Jeanne, V., Ioos, R., Peyre, J., Alliot, B. and Signoret, P. 2000. Differentiation of Poaceae potyviruses by reverse transcription-polymerase chain reaction and restriction analysis. J. Phytopathol. 148:141-151.
- Martin, M. 2011. Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet J. 17:10-12.
- Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G. J. and Qi, Y. 2008. Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5' terminal nucleotide. Cell 133:116-127.
- Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. and Minh, B. Q. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32:268-274.
- Saiz, M., Dopazo, J., Castro, S. and Romero, J. 1994. Evolutionary relationships among bean common mosaic virus strains and closely related potyviruses. Virus Res. 31:39-48.
- Seo, J.-K., Kang, M., Shin, O. J., Kwak, H.-R., Kim, M.-K., Choi, H.-S. and Ko, S.-J. 2015. First report of bean common mosaic virus in Cudrania tricuspidata in Korea. Plant Dis. 99:292.
- Su, X., Zhou, X., Li, Y., Ma, L., Cheng, X. and Guo, K. 2022. First report of bean common mosaic virus infecting heavenly bamboo (Nandina domestica) in China. Plant Dis. 106:1079.
- Tang, M. and Feng, X. 2022. Bean common mosaic disease: etiology, resistance resource, and future prospects. Agronomy 13:58.
- Wang, L., Zhang, W., Shen, W., Li, M., Fu, Y., Li, Z., Li, J., Liu, H., Su, X., Zhang, B. and Zhao, J. 2023. Integrated transcriptome and microRNA sequencing analyses reveal gene responses in poplar leaves infected by the novel pathogen bean common mosaic virus (BCMV). Front. Plant Sci. 14:1163232.
- Xu, X., Chen, B., Zhang, J., Lan, S. and Wu, S. 2023. Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides. PeerJ 11:e16056.
- Xu, Z., Pu, X., Gao, R., Demurtas, O. C., Fleck, S. J., Richter, M., He, C., Ji, A., Sun, W., Kong, J., Hu, K., Ren, F., Song, J. J. Wang, Z., Gao, T., Xiong, C., Yu, H., Xin, T., Albert, V. A., Giuliano, G., Chen, S. and Song, J. 2020. Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants. BMC Biol. 18:63.