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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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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