Journal of Applied Biological Chemistry

  • 제63권3호
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  • Pages.189-195
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  • 2020
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  • 1976-0442(pISSN)
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  • 2234-7941(eISSN)
한국응용생명화학회 (The Korean Society for Applied Biological Chemistry)
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De novo genome assembly and single nucleotide variations for Soybean yellow common mosaic virus using soybean flower bud transcriptome data

  • Jo, Yeonhwa (Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Choi, Hoseong (Research Institute of Agriculture and Life Sciences, Seoul National University) ;
  • Kim, Sang-Min (Crop Foundation Division, National Institute of Crop Science, RDA) ;
  • Lee, Bong Choon (Crop Foundation Division, National Institute of Crop Science, RDA) ;
  • Cho, Won Kyong (Research Institute of Agriculture and Life Sciences, Seoul National University)
  • 투고 : 2020.04.23
  • 심사 : 2020.07.21
  • 발행 : 2020.09.30
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초록

The soybean (Glycine max L.), also known as the soya bean, is an economically important legume species. Pathogens are always major threats for soybean cultivation. Several pathogens negatively affect soybean production. The soybean is also known as a susceptible host to many viruses. Recently, we carried out systematic analyses to identify viruses infecting soybeans using soybean transcriptome data. Our screening results showed that only few soybean transcriptomes contained virus-associated sequences. In this study, we further carried out bioinformatics analyses using a soybean flower bud transcriptome for virus identification, genome assembly, and single nucleotide variations (SNVs). We assembled the genome of Soybean yellow common mosaic virus (SYCMV) isolate China and revealed two SNVs. Phylogenetic analyses using three viral proteins suggested that SYCMV isolate China is closely related to SYCMV isolates from South Korea. Furthermore, we found that replication and mutation of SYCMV is relatively low, which might be associated with flower bud tissue. The most interesting finding was that SYCMV was not detected in the cytoplasmic male sterility (CMS) line derived from the non-CMS line that was severely infected by SYCMV. In summary, in silico analyses identified SYCMV from the soybean flower bud transcriptome, and a nearly complete genome of SYCMV was successfully assembled. Our results suggest that the low level of virus replication and mutation for SYCMV might be associated with plant tissues. Moreover, we provide the first evidence that male sterility might be used to eliminate viruses in crop plants.

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참고문헌

  1. Singh R, Hymowitz T (1999) Soybean genetic resources and crop improvement. Genome 42: 605-616 https://doi.org/10.1139/g99-039
  2. Messina MJ (1999) Legumes and soybeans: overview of their nutritional profiles and health effects. Am J Clin Nutr 70: 439s-450s https://doi.org/10.1093/ajcn/70.3.439s
  3. Pimentel D, Patzek TW (2005) Ethanol production using corn, switchgrass, and wood; biodiesel production using soybean and sunflower. Nat Resour Res 14: 65-76 https://doi.org/10.1007/s11053-005-4679-8
  4. Herridge DF, Peoples MB, Boddey RM (2008) Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil 311: 1-18 https://doi.org/10.1007/s11104-008-9668-3
  5. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell- Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183 https://doi.org/10.1038/nature08670
  6. Wrather J, Stienstra W, Koenning S (2001) Soybean disease loss estimates for the United States from 1996 to 1998. Can J Plant Pathol 23: 122-131 https://doi.org/10.1080/07060660109506919
  7. Hill JH, Whitham SA (2014) Control of Virus Diseases in Soybeans. Control of Plant Virus Diseases: Seed-Propagated Crops 90: 355 https://doi.org/10.1016/B978-0-12-801246-8.00007-X
  8. Domier LL, Hobbs HA, McCoppin NK, Bowen CR, Steinlage TA, Chang S, Wang Y, Hartman GL (2011) Multiple loci condition seed transmission of Soybean mosaic virus (SMV) and SMV-induced seed coat mottling in soybean. Phytopathology 101: 750-756 https://doi.org/10.1094/PHYTO-09-10-0239
  9. Hobbs HA, Hill CB, Grau CR, Koval NC, Wang Y, Pedersen WL, Domier LL, Hartman GL (2006) Green stem disorder of soybean. Plant Dis 90: 513-518 https://doi.org/10.1094/PD-90-0513
  10. Calvert L, Ghabrial S (1983) Enhancement by soybean mosaic virus of bean pod mottle virus titre in doubly infected soybeans. Phytopathology 73: 992-997 https://doi.org/10.1094/Phyto-73-992
  11. Domier LL, Steinlage TA, Hobbs HA, Wang Y, Herrera-Rodriguez G, Haudenshield JS, McCoppin NK, Hartman GL (2007) Similarities in seed and aphid transmission among Soybean mosaic virus isolates. Plant Dis 91: 546-550 https://doi.org/10.1094/PDIS-91-5-0546
  12. Mabry TR, Hobbs HA, Steinlage TA, Johnson BB, Pedersen WL, Spencer JL, Levine E, Isard SA, Domier LL, Hartman GL (2003) Distribution of leaf-feeding beetles and Bean pod mottle virus (BPMV) in Illinois and transmission of BPMV in soybean. Plant Dis 87: 1221- 1225 https://doi.org/10.1094/PDIS.2003.87.10.1221
  13. Fulton J, Cumberland D, Hodgsen O, Amsoy C, Vickery W (1983) Bean pod mottle virus: occurrence in Nebraska and seed transmission in soybeans. Plant Dis 67: 230-233 https://doi.org/10.1094/PD-67-230
  14. Mowat W, Dawson S (1987) Detection and identification of plant viruses by ELISA using crude sap extracts and unfractionated antisera. J Virol Methods 15: 233-247 https://doi.org/10.1016/0166-0934(87)90101-7
  15. Thomson D, Dietzgen RG (1995) Detection of DNA and RNA plant viruses by PCR and RT-PCR using a rapid virus release protocol without tissue homogenization. J Virol Methods 54: 85-95 https://doi.org/10.1016/0166-0934(95)00022-M
  16. Barba M, Czosnek H, Hadidi A (2014) Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6: 106-136 https://doi.org/10.3390/v6010106
  17. Li R, Gao S, Hernandez AG, Wechter WP, Fei Z, Ling K-S (2012) Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS One 7: e37127 https://doi.org/10.1371/journal.pone.0037127
  18. Jo Y, Choi H, Yoon J-Y, Choi S-K, Cho WK (2016) In silico identification of Bell pepper endornavirus from pepper transcriptomes and their phylogenetic and recombination analyses. Gene 575: 712-717 https://doi.org/10.1016/j.gene.2015.09.051
  19. Jo Y, Choi H, Cho JK, Yoon J-Y, Choi S-K, Cho WK (2015) In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data. Scientific Rep 5: 15841 https://doi.org/10.1038/srep15841
  20. Li J, Han S, Ding X, He T, Dai J, Yang S, Gai J (2015) Comparative transcriptome analysis between the cytoplasmic male sterile line njcms1a and its maintainer njcms1b in soybean (Glycine max (L.) Merr.). PLoS One 10: e0126771 https://doi.org/10.1371/journal.pone.0126771
  21. Leinonen R, Sugawara H, Shumway M (2010) The sequence read archive. Nucleic Acids Res 39: D19-D21 https://doi.org/10.1093/nar/gkq1019
  22. Madden T (2013) The BLAST sequence analysis tool. The NCBI Handbook, National Center for Biotechnology Information (US)
  23. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Prot 8: 1494-1512 https://doi.org/10.1038/nprot.2013.084
  24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30: 2725-2729 https://doi.org/10.1093/molbev/mst197
  25. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760 https://doi.org/10.1093/bioinformatics/btp324
  26. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079 https://doi.org/10.1093/bioinformatics/btp352
  27. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST (2011) The variant call format and VCFtools. Bioinformatics 27: 2156-2158 https://doi.org/10.1093/bioinformatics/btr330
  28. Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D (2010) Tablet-next generation sequence assembly visualization. Bioinformatics 26: 401-402 https://doi.org/10.1093/bioinformatics/btp666
  29. Roossinck MJ (2010) Lifestyles of plant viruses. Phil Trans R Soc B 365: 1899-1905 https://doi.org/10.1098/rstb.2010.0057
  30. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63 https://doi.org/10.1038/nrg2484
  31. Strong MJ, Xu G, Morici L, Bon-Durant SS, Baddoo M, Lin Z, Fewell C, Taylor CM, Flemington EK (2014) Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog 10: e1004437 https://doi.org/10.1371/journal.ppat.1004437
  32. Chase CD (2007) Cytoplasmic male sterility: a window to the world of plant mitochondrial-nuclear interactions. Trends in Genet 23: 81-90 https://doi.org/10.1016/j.tig.2006.12.004
  33. Bohra A, Jha UC, Adhimoolam P, Bisht D, Singh NP (2016) Cytoplasmic male sterility (CMS) in hybrid breeding in field crops. Plant Cell Rep 35: 967-993 https://doi.org/10.1007/s00299-016-1949-3
  34. Evenor D, Joseph MB, Izhar S (1988) Attempts to detect extra genomial factors in cytoplasmic male-sterile petunia lines. Theor Appl Genet 76: 455-458 https://doi.org/10.1007/BF00265349