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1
Plant virus metagenomics: what we know and why we need to know more.
Front Plant Sci. 2014 Apr 16;5:150. doi: 10.3389/fpls.2014.00150. eCollection 2014.
2
Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses.
Trends Microbiol. 2018 Nov;26(11):955-965. doi: 10.1016/j.tim.2018.05.015. Epub 2018 Jun 21.
3
Ecogenomics: using massively parallel pyrosequencing to understand virus ecology.
Mol Ecol. 2010 Mar;19 Suppl 1:81-8. doi: 10.1111/j.1365-294X.2009.04470.x.
4
Plant virus metagenomics: biodiversity and ecology.
Annu Rev Genet. 2012;46:359-69. doi: 10.1146/annurev-genet-110711-155600. Epub 2012 Aug 29.
5
Plant Virus Metagenomics: Advances in Virus Discovery.
Phytopathology. 2015 Jun;105(6):716-27. doi: 10.1094/PHYTO-12-14-0356-RVW. Epub 2015 Jun 9.
6
Unravelling virus community ecology in bats through the integration of metagenomics and community ecology.
Mol Ecol. 2020 Jan;29(1):23-25. doi: 10.1111/mec.15306. Epub 2019 Nov 28.
8
Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics.
Nat Commun. 2017 Oct 11;8(1):858. doi: 10.1038/s41467-017-01086-2.
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Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence.
Phytopathology. 2021 Jan;111(1):32-39. doi: 10.1094/PHYTO-08-20-0355-FI. Epub 2020 Dec 11.

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Conventional and cutting-edge advances in plant virus detection: emerging trends and techniques.
3 Biotech. 2025 Apr;15(4):100. doi: 10.1007/s13205-025-04253-1. Epub 2025 Mar 25.
3
Whitefly-Transmitted Viruses of Cucurbits in the Southern United States.
Viruses. 2023 Nov 20;15(11):2278. doi: 10.3390/v15112278.
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Metagenomics reveals the structure of -host interaction network within an agro-ecosystem.
Virus Evol. 2023 Jul 6;9(2):vead043. doi: 10.1093/ve/vead043. eCollection 2023.
5
Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems.
Plant Environ Interact. 2021 Mar 25;2(2):87-99. doi: 10.1002/pei3.10043. eCollection 2021 Apr.
7
Wild and weedy Hesperis matronalis hosts turnip mosaic virus across heterogeneous landscapes in upstate New York.
Virus Res. 2023 Jan 2;323:199011. doi: 10.1016/j.virusres.2022.199011. Epub 2022 Nov 28.
9
VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data.
Front Bioinform. 2022 May 13;2:867111. doi: 10.3389/fbinf.2022.867111. eCollection 2022.

本文引用的文献

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Biosecurity implications of new technology and discovery in plant virus research.
PLoS Pathog. 2013;9(8):e1003337. doi: 10.1371/journal.ppat.1003337. Epub 2013 Aug 1.
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E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics.
J Microbiol Methods. 2013 Sep;94(3):356-66. doi: 10.1016/j.mimet.2013.07.002. Epub 2013 Jul 16.
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Previously unknown and highly divergent ssDNA viruses populate the oceans.
ISME J. 2013 Nov;7(11):2169-77. doi: 10.1038/ismej.2013.110. Epub 2013 Jul 11.
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Scalable metagenomic taxonomy classification using a reference genome database.
Bioinformatics. 2013 Sep 15;29(18):2253-60. doi: 10.1093/bioinformatics/btt389. Epub 2013 Jul 4.
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Plant virus ecology.
PLoS Pathog. 2013;9(5):e1003304. doi: 10.1371/journal.ppat.1003304. Epub 2013 May 23.
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Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
Nat Biotechnol. 2013 Jun;31(6):533-8. doi: 10.1038/nbt.2579. Epub 2013 May 26.
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Plant virus metagenomics: biodiversity and ecology.
Annu Rev Genet. 2012;46:359-69. doi: 10.1146/annurev-genet-110711-155600. Epub 2012 Aug 29.
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DNA sequencing with nanopores.
Nat Biotechnol. 2012 Apr 10;30(4):326-8. doi: 10.1038/nbt.2181.
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Eukaryotic origin of a metabolic pathway in virus by horizontal gene transfer.
Genomics. 2011 Nov;98(5):367-9. doi: 10.1016/j.ygeno.2011.08.006. Epub 2011 Aug 28.
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Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes.
PLoS Pathog. 2011 Jul;7(7):e1002146. doi: 10.1371/journal.ppat.1002146. Epub 2011 Jul 14.

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