The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Next‐generation sequencing technologies for environmental DNA research
Open accessAbstract
Since 2005, advances in next‐generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species‐specific DNA barcodes has been a key application of next‐generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next‐generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next‐generation sequencing technologies in regard to their application for environmental DNA analysis.
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Citations
Cites
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058 · cited 1×
“Also, several studies have been conducted on the effect of diet on the gut microbiome of mice using 16S rDNA amplicons (Turnbaugh et al. 2008, 2009; Murphy et al. 2010; Ravussin et al. 2011; Serino et al. 2011).”
BackgroundArchaea predominate among ammonia-oxidizing prokaryotes in soils
Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G. W., Prosser, J. I., Schuster, S. C., & Schleper, C. (2006) · Nature · doi:10.1038/nature04983 · Cited by 2,497
Direct detection of DNA methylation during single-molecule, real-time sequencing
Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G. A. C., & Baird, D. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017497 · Cited by 584
Self-citationThe impact of next-generation sequencing on genomics
Zhang, J., Chiodini, R., Badr, A., & Zhang, G. (2011) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2011.02.003 · Cited by 577 · cited 2×
“Although available NGS technologies utilize quite diverse chemistry and base incorporation ⁄ detection tools, they share two main steps: library fragmentation ⁄ amplicon library preparation and detection of the incorporated nucleotides (Glenn 2011; Zhang et al. 2011).”
BackgroundFlanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P., et al. (2007) · Journal of Clinical Microbiology · doi:10.1128/jcm.02187-06 · Cited by 180
Cited by
Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity
Thomsen, P. F., & Willerslev, E. (2015) · Biological Conservation · doi:10.1016/j.biocon.2014.11.019 · Cited by 2,082
Ancient and modern environmental DNA
Pedersen, M. W., Overballe-Petersen, S., Ermini, L., Sarkissian, C. D., Haile, J., Hellstrom, M., Spens, J., Thomsen, P. F., Bohmann, K., Cappellini, E., et al. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0383 · Cited by 329
Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies
Zimmermann, J., Glöckner, G., Jahn, R., Enke, N., & Gemeinholzer, B. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12336 · Cited by 317
Fouhy, F., Clooney, A. G., Stanton, C., Claesson, M. J., & Cotter, P. D. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0738-z · Cited by 310
Allali, I., Arnold, J. W., Roach, J., Cadenas, M. B., Butz, N., Hassan, H. M., Koci, M., Ballou, A., Mendoza, M., Ali, R., et al. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1101-8 · Cited by 298
Carew, M. E., Pettigrove, V. J., Metzeling, L., & Hoffmann, A. A. (2013) · Frontiers in Zoology · doi:10.1186/1742-9994-10-45 · Cited by 243
Cropping With Slag to Address Soil, Environment, and Food Security
Das, S., Kim, G. W., Hwang, H. Y., Verma, P. P., & Kim, P. J. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01320 · Cited by 107
Rocha-Martin, J., Harrington, C., Dobson, A., & O'Gara, F. (2014) · Marine Drugs · doi:10.3390/md12063516 · Cited by 84
Kang, D.-W., DiBaise, J. K., Ilhan, Z. E., Crowell, M. D., Rideout, J. R., Caporaso, J. G., Rittmann, B. E., & Krajmalnik-Brown, R. (2015) · Anaerobe · doi:10.1016/j.anaerobe.2015.01.005 · Cited by 55
Marine Actinobacteria: New Horizons in Bioremediation
Rathore, D. S., Sheikh, M., & Singh, S. P. (2021) · Environmental and Microbial Biotechnology · doi:10.1007/978-981-15-4439-2_20 · Cited by 20
Metadata
- Authors
- SHOKRALLA, S., SPALL, J. L., GIBSON, J. F., & HAJIBABAEI, M.
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2012-04
- Volume
- 21
- Issue
- 8
- Pages
- 1794-1805
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W2132543522
- Cited by
- 925
- References
- 8
- FWCI
- 61.77
- Type
- journal article
- Language
- en
- Open access
- bronze
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