Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Jul 11:15:1405042.
doi: 10.3389/fpls.2024.1405042. eCollection 2024.

Seeing in the dark: a metagenomic approach can illuminate the drivers of plant disease

Veronica Roman-Reyna #  1   2 , Sharifa G Crandall #  1   2
Affiliations

Seeing in the dark: a metagenomic approach can illuminate the drivers of plant disease

Veronica Roman-Reyna et al. Front Plant Sci. .
No abstract available

Keywords: functional metagenomics; metagenomics; microbiome; multi-omics; novel genes; plant diagnostics; plant pathogen; workflow.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
A standard metagenomic workflow can be divided into three main stages: Experimental Design, Sequencing Rationale, and Taxonomy & Functional Classification. Experimental Design covers the biological question of the experiment, as well as the controls and limitations of the system being studied. The specific biological question will help determine whether metagenomics is the best approach, or if other methods such as the study of volatiles, genomes, chemical spectra, metabolites, proteins, expressed genes, or evolutionary history reconstruction might be more appropriate for answering the question. The Sequencing Rationale contains aspects such as nucleic acid extractions and considerations for the sequencing platform. Lastly, the Taxonomy & Functional Classification stage allows to select databases for analyzing the reads. Having a clear understanding of these three stages ensures a clear output to address the research question. Created with BioRender.com.
Figure 2
Figure 2
Results in PubMed, Google Scholar, and Web of Science to the query “Metagenomics AND Plants”. The databases were consulted in May 2024 therefore data is included only for complete years.
See this image and copyright information in PMC

References

    1. Agrios G. (2005). Plant pathology., 5th edn (Amsterdam: Elsevier Academic Press; ).
    1. Aravind R., Kumar A., Eapen S. J., Ramana K. V. (2009). Endophytic bacterial flora in root and stem tissues of black pepper (Piper nigrum L.) genotype: isolation, identification and evaluation against Phytophthora capsici. Lett. Appl. Microbiol. 48, 58–64. doi: 10.1111/lam.2009.48.issue-1 - DOI - PubMed
    1. Arenz B. E., Schlatter D. C., Bradeen J. M., Kinkel L. (2015). Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities. L. J. Microbiological Methods 117, 1–3. doi: 10.1016/j.mimet.2015.07.003 - DOI - PubMed
    1. Bolyen E., Rideout J. R., Dillon M. R., Bokulich N. A., Abnet C., Al-Ghalith G. A., et al. . (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857.doi: 10.1038/s41587-019-0209-9 - DOI - PMC - PubMed
    1. Breitwieser F. P., Lu J., Salzberg S. L. (2019). A review of methods and databases for metagenomic classification and assembly. Briefings Bioinf. 20, 1125–1136. doi: 10.1093/bib/bbx120 - DOI - PMC - PubMed

LinkOut - more resources