Complete Genome of Rice Grassy Stunt Tenuivirus in Thailand and Genetic Relationship Analysis

Authors

  • Kanuengnij Srivilai Sakon Nakhon Rice Research Center
  • Passorn Wonnapinij Department of genetics, Faculty of Science, Kasetsart University
  • Scott Adkins United States Department of Agriculture
  • Sujin Patarapuwadol Departmentof Plant Pathology,Facultyof Agriculture, Kasetsart University

DOI:

https://doi.org/10.14456/thaidoa-agres.2022.10

Keywords:

rice grassy stunt virus, virus genome, rice grassy stunt disease, RGSV2 strain, RNA-Seq technology

Abstract

Rice grassy stunt virus (RGSV) belongs to the genus Tenuivirus. The virus caused stunted and prolific tillering of rice plants, which significantly reduce the yield of the rice crop in many countries. Rice grassy stunt disease was first described in Thailand in 1966 however,a complete genome sequence of RGSV has not been available.This study examined an isolate of RGSV from an infected rice plant collected from Prachin Buri province (isolate PRI). Total RNA was extracted from diseased rice leaves and then used for cDNA library construction. Its genome sequence was read using RNA-Seq technology, and de novo assembly was applied to reconstruct the genome. The qualified 9,680,170 short reads were de novo assembled to reconstruct the complete genome sequence. Results showed that the genome of RGSV isolate PRI consisted of 25,118 nucleotides (nt) of six RNA segments. The lengthof RNAs were 9,760 nt (RNA1), 4,059 nt (RNA2), 3,125 nt (RNA3), 2,892 nt (RNA4), 2,692 nt (RNA5), and 2,590 nt (RNA6). The genome of isolate PRI was compared with that of RGSV isolate IRRI from the Philippines by multiple alignments. Result showed that the RGSV isolate PRI shared 96.6% identity with RGSV isolate IRRI. The Maximum likelihood phylogenetic analysis from the concatenated genome indicated that isolate PRI closely related to isolate FZ0403 from China. The phylogenetic tree reconstructed by using RNA1, RNA4, and RNA5 sequences revealed that isolate PRI closely related to isolate FZ0403.

References

สุชาดา ปัฐยาวัต. 2547. ความหลากหลายของรหัสพันธุกรรมในจีโนมเส้นที่ 5 และเส้นที่ 8 ของไวรัสโรคใบหงิกข้าวใน ประเทศไทย. วิทยานิพนธ์ ปริญญาวิทยาศาสตรมหาบัณฑิต มหาวิทยาลัยเกษตรศาสตร์. 66 หน้า.

Bankevich A., S. Nurk, D. Antipov, A.A Gurevich, M. Dvorkin, A.S Kulikov, V.M Lesin, S.I Nikolenko, S Pham, A.D. Prjibelski, A.V. Pyshkin, A.V. Sirotkin, N. Vyahhi, G. Tesler, M.A. Alekseyev and P.A. Pevzner. 2012. SPAdes: a new genome assembly algorithm and its applications to single–cell sequencing. Comput Biol. 19(5): 455-477.

Bolger, A.M., M. Lohse and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15): 2114-2120.

Cabauatan, P.Q., H. Hibino, D.B. Lapis, T. Omura and T. Tsuchizaki. 1985. Rice Grassy Stunt Virus 2: A New Strain of Rice Grassy Stunt in the Philippines. IRRI Research Paper Series No. 106. 8 p.

Chao, S.; H. Wang, Q. Yan, L Chen, G. Chen, Y. Wu, B. Meng, L. Jin, X. Zhu and G. Feng. 2021. Metatranscriptomic sequencing suggests the presence of novel RNA viruses in rice transmitted by brown planthopper. Viruses. 13(12): 2464.

Chen, C.C. and R.J. Chiu. 1982. Three symptomatologic types of rice virus diseases related to grassy stunt in Taiwan. Plant Dis. 66: 15-18.

Chettanachit D., M. Putta, W. Balaveang, J. Hongkajorn and S. Disthaporn. 1985. New rice grassy stunt virus (GSV) strain in Thailand. Int. Rice Res. Notes. 10(2): 10-11.

Falk, B.W. and J.H. Tsai. 1998. Biology and molecular biology of viruses in the genus Tenuivirus. Annu. Rev. Phytopathol. 36(1): 139-163.

Hereward, J.P., X. Cai, A.M.A. Matias, G.H. Walter, C. Xu and Y. Wang. 2020. Migration dynamics of an important rice pest: The brown planthopper (Nilaparvata lugens) across Asia-Insights from population genomics. Evol. Appl. 13(9): 2449-2459.

Hibino, H., P.Q. Cabauatan, T. Omura and T. Tsuchizaki. 1985a. Rice grassy stunt virus strain causing tungrolike symptoms in the Philippines. Plant Dis. 69(6): 538-541.

Hibino, H., T. Usugi, T. Omura, T. Tsuchizaki, K., Shohara and M. Iwasaki. 1985b. Rice grassy stunt virus: a planthopper–borne circular filament. Phytopathology. 75: 894-899.

Hiraguri, A., O. Netsu, T. Shimizu, T. Uehara–Ichiki, T. Omura, N. Sasaki, H. Nyunoya and T. Sasaya. 2011. The nonstructural protein pC6 of rice grassy stunt virus trans complements the cell–to–cell spread of a movement–defective tomato mosaic virus. Arch. Virol. 156(5): 911-916.

Jimenez, J., M. Carvajal–Yepes, A.M. Leiva, M. Cruz, L.E. Romero, C.A. Bolaños, I. Lozano and W.J. Cuellar. 2018. Complete genome sequence of Rice hoja blanca tenuivirus isolated from a susceptible rice cultivar in Colombia. Genome Announc. 6(7): e01490-17.

King, A.M. Q., M.J. Adams, E.B. Carstens and E.J. Lefkowitz. 2012. Virus Taxonomy. Ninth report of the International Committee on Taxonomy of Viruses. 1327 p.

Kumar, S., G. Stecher, M. Li, C. Knyaz and K. Tamura. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6): 1547-1549.

Ling, K.C., V.M. Aguiero and S.H. Lee. 1970. A mass screening method for testing resistance to grassy stunt disease of rice. Plant Dis. Rep. 54(7): 565-569.

Ling, K.C. 1972. Rice Virus Diseases. Los Banos, Philippines: IRRI. 142 p.

Li, H. and R. Durbin. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 25(14): 1754-1760.

Miranda, J.G., O. Azzam and Y. Shirako. 2000. Comparison of nucleotide sequences between northern and southern Philippine isolates of rice grassy stunt virus indicates occurrence of natural genetic reassortment. Virol. 266(1): 26-32.

Nguyen, T.D., S. Lacombe, M. Bangratz, H.A. Ta, D.N. Vinh, P. Gantet and C. Brugidou. 2015. P2 of Rice grassy stunt virus (RGSV) and p6 and p9 of Rice ragged stunt virus (RRSV) isolates from Vietnam exert suppressor activity on the RNA silencing pathway. Virus Genes. 51(2): 267-275.

Schmieder, R. and R. Edwards. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 27(6): 863-864.

Shikata, E., T. Senboku and T. Ishimizu. 1980. The causal agent of rice grassy stunt disease. Proc Jpn Acad, Ser B. 56(2): 89-94.

Ta, H.A., D.P. Nguyen, S. Causse, T.D. Nguyen, V.V. Ngo and E. Hébrard. 2013. Molecular diversity of Rice grassy stunt virus in Vietnam. Virus Genes. 46(2): 383-386.

Takahashi, M., S. Toriyama, Y. Kikuchi, T. Hayakawa and A. Ishihama. 1990. Complementarity between the 5´-and 3´-terminal sequences of rice stripe virus RNAs. J. Gen. Virol. 71(12): 2817-2821.

Thompson, J. D., D.G., Higgins and T.J. Gibson. 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position–specific gap penalties, and weight matrix choice. Nucleic Acids Res. 22(22): 4673-4680.

Toriyama, S. 1987. Ribonucleic acid polymerase activity in filamentous nucleoproteins of rice grassy stunt virus. J. Gen. Virol. 68: 925-929.

Toriyama, S., M. Takahashi, Y. Sano, T. Shimizu and A. Ishihama. 1994. Nucleotide sequence of RNA1, the largest genomic segment of rice stripe virus, the prototype of the tenuiviruses. J. Gen. Virol. 75(12): 3569-3579.

Toriyama, S., T. Kimishima and M. Takahashi 1997. The proteins encoded by rice grassy stunt virus RNA5 and RNA6 are only distantly related to the corresponding proteins of other members of the genus Tenuivirus. J. Gen. Virol. 78: 2355-2363.

Toriyama, S., T. Kimishima, M. Takahashi, T. Shimizu, N. Minaka and K. Akutsu. 1998. The complete nucleotide sequence of the rice grassy stunt virus genome and genomic comparisons with viruses of the genus Tenuivirus. J. Gen. Virol. 79(8): 2051-2058.

Visser, M., R. Bester, J.T. Burger and H.J. Maree. 2016. Next-generation sequencing for virus detection: covering all the bases. Virol. J. 13(1): 1-6.

Wathanakul, L. and P. Weerapat. 1969. Virus diseases of rice in Thailand. pp. 78-85. In: The Virus Diseases of the Rice Plant. Proceedings of a symposium at the International Rice Research Institute, April, 1967. Baltimore, Maryland, USA: John Hopkins Press.

Zhang, C., X.J. Liu, K.C. Wu, L.P. Zheng, Z.M. Ding, F. Li, P. Zou, L. Yang, J. Wu and Z.J. Wu. 2015. Rice grassy stunt virus nonstructural protein p5 serves as a viral suppressor of RNA silencing and interacts with nonstructural protein p3. Arch. Virol. 160 (11): 2769-2779.

Zhao, W., Z. Xu, X. Zhang, M. Yang, L. Kang, R. Liu and F. Cui. 2018. Genomic variations in the 3´–termini of Rice stripe virus in the rotation between vector insect and host plant. New Phytol. 219(3): 1085-1096.

Published

2022-10-01

How to Cite

Srivilai, K., Wonnapinij, P. ., Adkins, S., & Patarapuwadol, S. . (2022). Complete Genome of Rice Grassy Stunt Tenuivirus in Thailand and Genetic Relationship Analysis. Thai Agricultural Research Journal, 40(2). https://doi.org/10.14456/thaidoa-agres.2022.10

Issue

Section

Technical or research paper