A ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome

Landicho D, Balendres MA. Possible incursion of cassava virus diseases: risks and potential threats to the Philippine cassava industry. Arch Phytopathol Plant Prot. 2022;55:1725–49. https://doi.org/10.1080/03235408.2022.2110662.

Article  Google Scholar 

Otun S, Escrich A, Achilonu I, Rauwane M, Lerma-Escalera JA, Rubén Morones-Ramírez J, et al. The future of cassava in the era of biotechnology in Southern Africa. Crit Rev Biotechnol. 2023;43:594–612. https://doi.org/10.1080/07388551.2022.2048791.

Article  PubMed  Google Scholar 

Robson F, Hird DL, Boa E. Cassava brown streak: a deadly virus on the move. Plant Pathol. 2023;73:221–41. https://doi.org/10.1111/ppa.13807.

Article  Google Scholar 

Bisimwa E, Walangululu J, Bragard C. Cassava mosaic disease yield loss assessment under various altitude agroecosystems in the sudKivu region. Democr Repub Congo Trop. 2015;33:101–10.

Google Scholar 

Kwibuka Y, Nyirakanani C, Bizimana JP, Bisimwa E, Brostaux Y, Lassois L, et al. Risk factors associated with cassava brown streak disease dissemination through seed pathways in Eastern D.R. Congo Front Plant Sci. 2022;13:1–18. https://doi.org/10.3389/fpls.2022.803980.

Article  Google Scholar 

Crespo-Bellido A, Hoyer JS, Dubey D, Jeannot RB, Duffy S. Interspecies recombination has driven the macroevolution of Cassava Mosaic Begomoviruses. J Virol. 2021;95(17):10–1128. https://doi.org/10.1128/jvi.00541-21.

Article  CAS  Google Scholar 

Mbewe W, Mukasa S, Ochwo-Ssemakula M, Sseruwagi P, Tairo F, Ndunguru J, et al. Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae. Virus Res. 2024;346: 199397. https://doi.org/10.1016/j.virusres.2024.199397.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rey C, Vanderschuren H. Cassava mosaic and brown streak diseases: current perspectives and beyond. Annu Rev Virol. 2017;4:429–52. https://doi.org/10.1146/annurev-virology-101416-041913.

Article  CAS  PubMed  Google Scholar 

Kwibuka Y, Bisimwa E, Blouin AG, Bragard C, Candresse T, Faure C, et al. Novel ampeloviruses infecting cassava in central africa and the south-west indian ocean islands. Viruses. 2021;13:1–17. https://doi.org/10.3390/v13061030.

Article  CAS  Google Scholar 

Scott SW, MacFarlane SA, McGavin WJ, Fargette D. Cassava ivorian bacilliform virus is a member of the genus anulavirus. Arch Virol. 2014;159:2791–3. https://doi.org/10.1007/s00705-014-2086-3.

Article  CAS  PubMed  Google Scholar 

Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, et al. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS ONE. 2015;10:1–22. https://doi.org/10.1371/journal.pone.0117617.

Article  CAS  Google Scholar 

Bejerman N, Roumagnac P, Nemchinov LG. High-throughput sequencing for deciphering the virome of alfalfa (Medicago sativa L.). Front Microbiol. 2020;11: 553109. https://doi.org/10.3389/fmicb.2020.553109.

Article  PubMed  PubMed Central  Google Scholar 

Mutuku JM, Wamonje FO, Mukeshimana G, Njuguna J, Wamalwa M, Choi S-K, et al. Metagenomic analysis of plant virus occurrence in common bean (Phaseolus vulgaris) in central Kenya. Front Microbiol. 2018;9:2939. https://doi.org/10.3389/fmicb.2018.02939.

Article  PubMed  PubMed Central  Google Scholar 

Schönegger D, Moubset O, Margaria P, Menzel W, Winter S, Roumagnac P, et al. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. J Virol. 2023;97(11):e01300-e1323. https://doi.org/10.1128/jvi.01300-23.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wainaina JM, Ateka E, Makori T, Kehoe MA, Boykin LM. A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya. PeerJ. 2019;7: e6465. https://doi.org/10.7717/peerj.6465.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gaafar YZA, Ziebell H. Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing. PLoS ONE. 2020;15: e0237951. https://doi.org/10.1371/journal.pone.0237951.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Roossinck MJ, Martin DP, Roumagnac P. Plant virus metagenomics: Advances in virus discovery. Phytopathology. 2015;105:716–27. https://doi.org/10.1094/PHYTO-12-14-0356-RVW.

Article  CAS  PubMed  Google Scholar 

Cobbin JC, Charon J, Harvey E, Holmes EC, Mahar JE. Current challenges to virus discovery by meta-transcriptomics. Curr Opin Virol. 2021;51:48–55. https://doi.org/10.1016/j.coviro.2021.09.007.

Article  CAS  PubMed  Google Scholar 

Haegeman A, Foucart Y, De Jonghe K, Goedefroit T, Al Rwahnih M, Boonham N, et al. Looking beyond virus detection in RNA sequencing data: lessons learned from a community-based effort to detect cellular plant pathogens and pests. Plants. 2023;12(11):2139. https://doi.org/10.3390/plants12112139.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Adiconis X, Borges-Rivera D, Satija R, Deluca DS, Busby MA, Berlin AM, et al. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat Methods. 2013;10:623–9. https://doi.org/10.1038/nmeth.2483.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baldwin A, Morris AR, Mukherjee N. An easy, cost-effective, and scalable method to deplete human ribosomal RNA for RNA-seq. Curr Protoc. 2021;1:1–13. https://doi.org/10.1002/cpz1.176.

Article  CAS  Google Scholar 

Fowkes AR, McGreig S, Pufal H, Duffy S, Howard B, Adams IP, et al. Integrating high throughput sequencing into survey design reveals turnip yellows virus and soybean dwarf virus in pea (Pisum sativum) in the united kingdom. Viruses. 2021;13:2530. https://doi.org/10.3390/v13122530.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Harimalala M, Chiroleu F, Giraud-carrier C, Hoareau M, Zinga I, Randriamampianina J, et al. Molecular epidemiology of cassava mosaic disease in Madagascar. Plant Pathol. 2015;64(3):501–7. https://doi.org/10.1111/ppa.12277.

Article  Google Scholar 

Azali HA, Maillot V, Cassam N, Chesneau T, Soulezelle J, Scussel S, et al. Occurrence of cassava brown streak disease and associated Cassava brown streak virus and Ugandan cassava brown streak virus in the Comoros Islands. New Dis Reports. 2017;36(1):19–19. https://doi.org/10.5197/j.2044-0588.2017.036.019.

Article  Google Scholar 

Phelps WA, Carlson AE, Lee MT. Optimized design of antisense oligomers for targeted rRNA depletion. Nucleic Acids Res. 2021;49(1):1–12. https://doi.org/10.1093/nar/gkaa1072.

Article  CAS  Google Scholar 

François S, Filloux D, Fernandez E, Ogliastro M, Roumagnac P. 2018 Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities. In: Pantaleo V, Chiumenti M, (Eds.) Viral Metagenomics Methods Protoc. Springer. Newyork. https://doi.org/10.1007/978-1-4939-7683-6_7

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2. https://doi.org/10.14806/ej.17.1.200.

Article  Google Scholar 

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35:1026–8. https://doi.org/10.1038/nbt.3988.

Article  CAS  PubMed  Google Scholar 

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinforma. 2020;70: e102. https://doi.org/10.1002/cpbi.102.

Article  CAS  Google Scholar 

Vasimuddin M, Misra S, Li H, Aluru S. 2019 Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rio de Janeiro, Brazil, 314–324. https://doi.org/10.1109/IPDPS.2019.00041

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience.

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