Marine genomics: methods and protocols
Bourlat, S.J. (Ed.) (2016). Marine genomics: methods and protocols. Methods in Molecular Biology, 1452. Humana Press/Springer Science+Business Media, Inc: New York. ISBN 978-1-4939-3772-1. 253 pp. https://dx.doi.org/10.1007/978-1-4939-3774-5
Part of: Methods in Molecular Biology. Humana Press. ISSN 1064-3745, more
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| Available in | Author |
VLIZ: Biology and ecology (General) COB [101274]
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| Keywords |
Disciplines > Biology > Molecular biology > Genetics > Genomics
Marine/Coastal |
| Author keywords |
bacterial communities; DNA extraction in marine organisms; high-throughput sequencing; phylogenomics; mitochondrial genomes; SNP discovery; invasive species; surveillance; metabarcoding; eukaryotic |
| Content |
- Lehmann, K. (2016). Sampling of riverine or marine bacterial communities in remote locations: from field to publication, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 1-11. https://dx.doi.org/10.1007/978-1-4939-3774-5_1, more
- Panova, M.; Aronsson, H.; Cameron, R.A.; Dahl, P.; Godhe, A.; Lind, U.; Ortega-Martinez, O.; Pereyra, R.; Tesson, S.V.M.; Wrange, A-L.; Blomberg, A.; Johannesson, K. (2016). DNA Extraction protocols for whole-genome sequencing in marine organisms, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 13-44. https://dx.doi.org/10.1007/978-1-4939-3774-5_2, more
- Briscoe, A.G.; Hopkins, K.P.; Waeschenbach, A. (2016). High-throughput sequencing of complete mitochondrial genomes, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 45-64. https://dx.doi.org/10.1007/978-1-4939-3774-5_3, more
- Cannon, J.T.; Kocot, K.M. (2016). Phylogenomics using transcriptome data, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 65-80. https://dx.doi.org/10.1007/978-1-4939-3774-5_4, more
- De Wit, P. (2016). SNP Discovery using next generation transcriptomic sequencing, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 81-95. https://dx.doi.org/10.1007/978-1-4939-3774-5_5, more
- Wenne, R.; Drywa, A.; Kent, M.; Sundsaasen, K.K.; Lien, S. (2016). SNP Arrays for species identification in salmonids, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 97-111. https://dx.doi.org/10.1007/978-1-4939-3774-5_6, more
- Cao, Y.; Griffith, J.F.; Weisberg, S.B. (2016). The next-generation PCR-based quantification method for ambient waters: digital PCR, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 113-130. https://dx.doi.org/10.1007/978-1-4939-3774-5_7, more
- Mahon, A.R.; Jerde, C.L. (2016). Using environmental DNA for invasive species surveillance and monitoring, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 131-142. https://dx.doi.org/10.1007/978-1-4939-3774-5_8, more
- Vale, F. (2016). Microarrays/DNA chips for the detection of waterborne pathogens, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 143-153. https://dx.doi.org/10.1007/978-1-4939-3774-5_9, more
- Steinke, D.; Prosser, S.W.J.; Hebert, P.D.N. (2016). DNA Barcoding of marine metazoans, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 155-168. https://dx.doi.org/10.1007/978-1-4939-3774-5_10, more
- Nikinmaa, M.; Götting, M. (2016). DNA Barcoding marine biodiversity: steps from mere cataloguing to giving reasons for biological differences, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 169-182. https://dx.doi.org/10.1007/978-1-4939-3774-5_11, more
- Fonseca, V.G.; Lallias, D. (2016). Metabarcoding marine sediments: preparation of amplicon libraries, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 183-196. https://dx.doi.org/10.1007/978-1-4939-3774-5_12, more
- Bourlat, S.J.; Haenel, Q.; Finnman, J.; Leray, M. (2016). Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq: the dual-PCR Method, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 197-207. https://dx.doi.org/10.1007/978-1-4939-3774-5_13, more
- Leray, M.; Haenel, Q.; Bourlat, S.J. (2016). Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq: the adapter ligation method, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 209-218. https://dx.doi.org/10.1007/978-1-4939-3774-5_14, more
- Leray, M.; Knowlton, N. (2016). Visualizing patterns of marine eukaryotic diversity from metabarcoding data using QIIME, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 219-235. https://dx.doi.org/10.1007/978-1-4939-3774-5_15, more
- Aylagas, E.; Rodríguez-Ezpeleta, N. (2016). Analysis of Illumina MiSeq metabarcoding data: application to benthic indices for environmental monitoring, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 237-249. https://dx.doi.org/10.1007/978-1-4939-3774-5_16, more
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| Abstract |
This volume presents the latest protocols for both laboratory and bioinformatics based analyses in the field of marine genomics. The chapters presented in the book cover a wide range of topics, including the sampling and genomics of bacterial communities, DNA extraction in marine organisms, high-throughput sequencing of whole mitochondrial genomes, phylogenomics, SNP discovery, SNP-arrays for species identification, digital PCR-based quantification methods, environment DNA for invasive species surveillance and monitoring, microarrays for the detection of waterborne pathogens, DNA barcoding of marine biodiversity, metabarcoding protocols for marine eukaryotes, analytical protocols for the visualization of eukaryotic diversity, and applications for genomic data to benthic indices for environmental monitoring. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. |
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