Complete genome analysis of a novel iflavirus from the spotted lanternfly Lycorma delicatula.

Publisher: Springer-Verlag Country of Publication: Austria NLM ID: 7506870 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-8798 (Electronic) Linking ISSN: 03048608 NLM ISO Abbreviation: Arch Virol Subsets: MEDLINE

Original Publication: Wien, New York, Springer-Verlag.

Hemiptera* ; RNA Viruses*; Animals ; Phylogeny ; RNA-Dependent RNA Polymerase ; Sequence Analysis, DNA

The spotted lanternfly (Lycorma delicatula) is an invasive pest that causes serious economic losses in fruit and wood production. Here, we identified a novel iflavirus named "Lycorma delicatula iflavirus 1" (LDIV1), in a spotted lanternfly. The full genome sequence of LDIV1 is 10,222 nt in length and encodes a polyprotein containing a picornavirus capsid-protein-domain-like domain, a cricket paralysis virus capsid superfamily domain, an RNA helicase domain, a peptidase C3 superfamily domain, and an RNA-dependent RNA polymerase (RdRp) domain. LDIV1 replicates in the host insect and activates small interfering RNA (siRNA)-based host antiviral immunity. Phylogenetic analysis demonstrated that LDIV1 is most closely related to an unspecified member of the order Picornavirales, with 61.7% sequence identity in the RdRp region and 57.6% sequence identity in the coat protein region, and thus meets the demarcation criteria for new species in the genus Iflavirus. To the best of our knowledge, LDIV1 is the first virus discovered in L. delicatula.
(© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Avanesyan A, Lamp WO (2020) Use of molecular gut content analysis to decipher the range of food plants of the invasive spotted lanternfly, Lycorma delicatula. Insects 11(4):215. (PMID: 10.3390/insects11040215)
Dara SK, Barringer L, Arthurs SP (2015) Lycorma delicatula (Hemiptera: Fulgoridae): a new invasive pest in the United States. J Integrated Pest Manag 6(1):20. (PMID: 10.1093/jipm/pmv021)
Han JM, Kim H, Lim EJ, Lee S, Kwon YJ, Cho S (2008) Lycorma delicatula (Hemiptera: Auchenorrhyncha: Fulgoridae: Aphaeninae) finally, but suddenly arrived in Korea. Entomol Res 38(4):281–286. (PMID: 10.1111/j.1748-5967.2008.00188.x)
Kingan SB, Urban J, Lambert CC, Baybayan P, Childers AK, Coates B, Scheffler B, Hackett K, Korlach J, Geib SM (2019) A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system. GigaScience 8(10):122. (PMID: 10.1093/gigascience/giz122)
van Oers MM (2010) Genomics and biology of Iflaviruses. Insect Vrol 231–250.
Wu N, Zhang P, Liu W, Cao M, Wang X (2018) Sequence analysis and genomic organization of a new insect iflavirus, Sogatella furcifera honeydew virus 1. Adv Virol 163(7):2001–2003.
Wang H, Liu Y, Liu W, Cao M, Wang X (2019) Full genome sequence of a novel iflavirus from the leafhopper Psammotettix alienus. Adv Virol 164(1):309–311.
Ye ZX, Li YH, Chen JP, Zhang CX, Li JM (2021) Complete genome analysis of a novel iflavirus from a leaf beetle, Aulacophora lewisii. Arch Virol 166(1):309–312. (PMID: 10.1007/s00705-020-04859-1)
Ryabov EV, Wood GR, Fannon JM, Moore JD, Bull JC, Chandler D, Mead A, Burroughs N, Evans DJ (2014) A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission. PLoS Pathog 10(6):e1004230. (PMID: 10.1371/journal.ppat.1004230)
Bailey L, Gibbs A, Woods R (1964) Sacbrood virus of the larval honey bee (Apis mellifera Linnaeus). Virology 23(3):425–429. (PMID: 10.1016/0042-6822(64)90266-1)
Huang HJ, Ye ZX, Lu G, Zhang CX, Chen JP, Li JM (2021) Identification of salivary proteins in the whitefly Bemisia tabaci by transcriptomic and LC-MS/MS analyses. Insect Sci 28(5):1369–1381. (PMID: 10.1111/1744-7917.12856)
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652. (PMID: 10.1038/nbt.1883)
Sujeevan R, Hebert P, Diego F (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE 8(7):e66213. (PMID: 10.1371/journal.pone.0066213)
Blum M, Chang H-Y, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD (2020) The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 49(D1):D344–D354. (PMID: 10.1093/nar/gkaa977)
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. (PMID: 10.1038/nmeth.1923)
Valles SM, Chen Y, Firth AE, Guerin DMA, Hashimoto Y, Herrero S, de Miranda JR, Ryabov E, Ictv Report C (2017) ICTV virus taxonomy profile: Iflaviridae. J Gen Virol 98(4):527–528. (PMID: 10.1099/jgv.0.000757)
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780. (PMID: 10.1093/molbev/mst010)
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A (2019) RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35(21):4453–4455. (PMID: 10.1093/bioinformatics/btz305)
Lu G, Ye ZX, He YJ, Zhang Y, Wang X, Huang HJ, Zhuo JC, Sun ZT, Yan F, Chen JP, Zhang CX, Li JM (2020) Discovery of two novel negeviruses in a dungfly collected from the Arctic. Viruses 12(7):692. (PMID: 10.3390/v12070692)
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. (PMID: 10.1093/bioinformatics/btu170)
Nigg JC, Kuo YW, Falka BW (2020) Endogenous viral element-derived piwi-interacting RNAs (piRNAs) are not required for production of ping-pong-dependent piRNAs from Diaphorina citri densovirus. MBio 11(5):e02209-e2220. (PMID: 10.1128/mBio.02209-20)
Zhang XD, Lu G, Ye ZX, Chen JP, Zhang CX, Li JM (2022) Complete genome analysis of a nege-like virus in aphids (Astegopteryx formosana). Adv Virol 167(1):267–270.
Huang HJ, Ye ZX, Wang X, Yan XT, Zhang Y, He YJ, Qi YH, Zhang XD, Zhuo JC, Lu G, Lu JB, Mao QZ, Sun ZT, Yan F, Chen JP, Zhang CX, Li JM (2021) Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci. npj Biofilms Microbiomes 7(1):43. (PMID: 10.1038/s41522-021-00216-5)

U20A2036 National Natural Science Foundation of China; 2019B10004 Ningbo Science and Technology Innovation 2025 Major Project

EC 2.7.7.48 (RNA-Dependent RNA Polymerase)

Date Created: 20220625 Date Completed: 20220826 Latest Revision: 20220826

20231215

10.1007/s00705-022-05503-w

35751691