Gero, Patrick
Golden, Heidi
King, Ursula

Lawrence, Cera
Lewis, Lily

Meister, Russ

Mitchell, Nora

Razifard, Hamid

Velotta, Jonathan

Zacharczenko, Brigette

Has it come to this already?

The “Tricorder” (stardate 1672.1)

Next-generation sequencing (overviews):

           Glenn, T. C. 2011. Field guide to next-generation DNAsequencers. Molecular Ecology Resources 11: 759–769.

           Hui, P. 2012. Next generation sequencing: chemistry, technology and applications. Topics in Current Chemistry DOI: 10.1007/128_2012_329

           Liu, L., Y. Li, S. Li, N. Hu, Y. He, R. Pong, D. Lin, L. Lu & M. Law. 2012. Comparison of next-generation sequencing systems.
          Journal of Biomedicine and Biotechnology doi:10.1155/2012/251364 [LARGE FILE - LONG LOAD TIME]

           Mardis, E. R. 2008. Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 9: 387–402.

           Niedringhaus, T. P., D. Milanova, M, B. Kerby, M. P. Snyder & A. E. Barron. 2011. Landscape of next-generation sequencing technologies. Analytical Chemistry 83: 4327–4341.

           Schadt, E. E., S. Turner & A. Kasarskis. 2010. A window into third-generation sequencing. Human Molecular Genetics 19: R227–R240.

           Weaver, J. 2012. Promise and pitfalls of third-generation sequencing. BioTechniques 7/25/2012

            LECTURES I-II: download Powerpoint file

NGS PAPERS by category

Microarrays:

     Shiu, S.-H. and J. O. Borevitz. 2008. The next generation of microarray research: applications in evolutionary and ecological genomics. Heredity 100: 141–149.

Adaptation genomics:

     Davidson, W. S. 2012. Adaptation genomics: next generation sequencing reveals a shared haplotype for rapid early development in geographically and genetically distant populations of rainbow trout. Molecular Ecology 21: 219–222.

     Elmer, K. R. & A. Meyer. 2011. Adaptation in the age of ecological genomics: insights from parallelism and convergence. TREE 26: 298–306.

     Fan, S., K. R. Elmer & A. Meyer. 2012. Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages. Philosophical Transactions of the Royal Society B 367: 385–394.

     Hohenlohe, P. A., S. Bassham, M. Currey & W. A. Cresko. 2012. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philosophical Transactions of the Royal Society B 367: 395–408.

     Rice, A. M., A. Rudh, H. Ellegren & A. Qvarnström. 2011. A guide to the genomics of ecological speciation in natural animal populations. Ecology Letters 14: 9–18.

     Stapley, J., J. Reger, P. G. D. Feulner, C. Smadja, J. Galindo, R. Ekblom, C. Bennison, A. D. Ball, A. P. Beckerman & J. Slate. 2010. Adaptation genomics: the next generation. TREE 25: 705–712.

Ancient DNA:

     Paijmans, J. L.A., M. T. P. Gilbert & M. Hofreiter. 2012. Mitogenomic analyses from ancient DNA. Molecular Phylogenetics and Evolution (in press).

Animal diet analysis:

     Bon, C., V.  Berthonaud, F. Maksud, K.  Labadie, J.  Poulain, F.  Artiguenave, P.  Wincker, J.-M. Aury & J.-M. Elalouf. 2012. Coprolites as a source of information on the genome and diet of the cave hyena. Philosophical Transactions of the Royal Society B 279: 2825–2830.

     Pompanon, F., B. E. Deagle, W. O. C. Symondson, D. S. Brown, S. N. Jarman & P. Teberlet. 2012. Who is eating what: diet assessment using next generation sequencing. Molecular Ecology 21: 1931–1950.

     Shehzad, W., T. Riaz, M. A. Nawaz, C. Miquel, C. Poillot, S. A. Shah, F. Pompanon, E. Coissac & P. Taberlet. 2012. Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular Ecology 21: 1951–1965.

Bioinformatics, etc.:

     Baker, M. 2010.  Next-generation sequencing: adjusting to data overload. Nature Methods 7: 495-499.

     Bao, S., R. Jiang, W. Kwan, B. Wang, X. Ma & Y.-Q. Song. 2011. Evaluation of next-generation sequencing software in mapping and assembly. Journal of Human Genetics 56: 406–414.

     Barrett, T., K. Clark, R. Gevorgyan, V. Gorelenkov, E. Gribov, I. Karsch-Mizrachi, M. Kimelman, K. D. Pruitt, S. Resenchuk, T. Tatusova, E. Yaschenko & J. Ostell. 2012. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Research 40: D57–D63.

     Cahais, V., P. Gayral, G. Tsagkogeorga, J. Melo-Ferreira, M. Ballenghein, L. Weinert, Y. Chiari, K. Belkhir, V. Ranwez & N. Galtier. 2012. Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Molecular Ecology Resources doi: 10.1111/j.1755-0998.2012.03148.x

     Coissac, E., T. Riaz & N. Puillandre. 2012. Bioinformatic challenges for DNA metabarcoding of plants and animals. Molecular Ecology 21: 1834–1847.

     Li, C., J.-J. M. Riethoven & G. J. P. Naylor. 2012. EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies. Molecular Ecology Resources (in press)

     Sahl, J. W., M. N. Matalka & D. A. Rasko. 2012 . Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments. Applied Environmental Microbiology 78: 4884-4892.

     Shanker, A. 2012. Genome research in the cloud. OMICS: A Journal of Integrative Biology 16: 422–428.

     Wall, D. P., P. Kudtarkar, V. A. Fusaro, R. Pivovarov, P. Patil & P. J. Tonellato. 2010. Cloud computing for comparative genomics. BMC Bioinformatics 11: 259 http://www.biomedcentral.com/1471-2105/11/259

     Zhang, L., S. Gu, Y. Liu, B. Wang & F. Azuaje. 2012. Gene set analysis in the cloud. Bioinformatics 28: 294–295.

Cultivated plants:

     Barabaschi, D., D. Guerra, K. Lacrima, P. Laino, V. Michelotti, S. Urso, G. Valè & L. Cattivelli. 2012. Emerging knowledge from genome sequencing of crop species. Molecular Biotechnology 50: 250-266.

Dioecy:

     Macas, J., E. Kejnovský, P. Neumann, P. Novák, A. Koblížková & B. Vyskot. 2011. Next generation sequencing-based analysis of repetitive DNA in the model dioceous plant Silene latifolia. PLoS ONE 6(11): e27335. doi:10.1371/journal.pone.0027335

Ecology:                                                                                         

     In 2010 a special issue of Molecular Ecology was devoted to NGS:

     Tautz, D., H. Ellergren & D. Weigel. 2010. Special Issue: Next Generation Molecular Ecology. Molecular Ecology 19: 1–3.

     See contents: http://onlinelibrary.wiley.com/doi/10.1111/mec.2010.19.issue-s1/issuetoc

     Baird, D. J. & M. Hajibabae. 2012. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology 21: 2039–2044.

     Funk, W. C., J. K. McKay, P. A. Hohenlohe & F. W. Allendorf. 2012. Harnessing genomics for delineating conservation units. TREE (in press).

     Hajibabaei, M., S. Shokralla, X. Zhou , G. A. C. Singer & D. J. Baird. 2011. Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6(4): e17497. doi:10.1371/journal.pone.0017497

     Taberlet, P., E. Coissac, F. Pompanon, C. Brochmann & E. Willerslev. 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology 21: 2045–2050.

     Yoccoz, N. G. 2012. The future of environmental DNA in ecology. Molecular Ecology 21: 2031–2038.

Genetic markers:

     Bertozzi, T., K. L. Sanders, M. J. Sistrom & M. G. Gardner. 2012. Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys. Bioinformatics 28: 1807–1810.

     Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen & M. L. Blaxter. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews (Genetics) 12: 499–510.

Hybridization:

     Goedbloed, D. J., H. J. Megens, P. van Hooft, J. M. Herrero-Medrano, W. Lutz, P. Alexandri, R. P. M. A. Crooijmans, M. Groenen, S. E. van Wieren, R. C. Ydenberg & H. H. T. Prins. Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations. Molecular Ecology (in press).

     Hohenlohe, P. A., S. J. Amish, J. M. Catchen, F. W. Allendorf & G. Luikart. 2011. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources (Suppl. 1) 11: 117–122.

     Twyford, A. D. & R. A. Ennos. 2012. Next-generation hybridization and introgression. Heredity 108: 179–189.

Invasive plants:

     He, R., M.-J. Kim, W. Nelson, T. S. Balbuena, R. Kim, R. Kramer, J. A. Crow, G. D. May, J. J. Thelen, C. A. Soderlund & D. R. Gang. 2012. Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity.  American Journal of Botany 99: 232–247.

     Stewart, C. N. 2009. Weedy and invasive plant genomics. John Wiley & Sons, Inc., Hoboken.

Metagenomics:

     Desai, N., D. Antonopoulos, J. A. Gilbert, E. M. Glass & F. Meyer. 2012. From genomics to metagenomics. Current Opinion in Biotechnology 23: 72–76.

     Foster, J. A., J. Bunge, J. A. Gilbert & J. H. Moore. 2012. Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life. Briefings in Bioinformatics doi:10.1093/bib/bbr080

     Yoccoz, N. G., K. A. Bråthen,L. Gielly, J . Haile, M. E. Edwards, T. Goslar, H. Von Sstedingk, A. K. Brysting, E. Coissac, F. Pompanon, J . H. Sønstebø, C. Miquel, A. Valentini, F. De Bello, J. Chave, W. Thuiller, P. Wincker, C. Cruaud, F. Gavory, M. Rasmussen, M. T. P. Gilbert, L. Orlando, C. Brichmann, E. Willerslev & P. Taberlet. 2012. DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology 21: 3647–3655.

Microsatellites:

     Castoe, T, A. , A. W. Poole, A. P. J. de Koning, K. L. Jones, D. F. Tomback, S. J. Oyler-McCance, J. A. Fike, S. L. Lance, J. W. Streicher, E. N. Smith & D. D. Pollock. 2012. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE 7(2): e30953. doi:10.1371/journal.pone.0030953

     Gardner, M. G., A. J. Fitch, T. Bertozzi & A. J. Lowe. 2011. Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources 11: 1093–1101.

     Karan, M., D. S. Evans, D. Reilly, K. Schulte, C. Wright, D. Innes, T. A. Holton, D. G. Nikles & G. R. Dickinson. 2012. Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity. Molecular Ecology Resources 12: 344–353.

     Perry, J. C. & L. Rowe. 2011. Rapid microsatellite development for water striders by next-generation sequencing. Journal of Heredity 102: 125–129.

     Peterman, W. E., G. M. Connette, B. Spatola, L. S. Eggert & R. D. Semlitsch. 2012. Identification of polymorphic loci in Ambystoma annulatum and review of cross-species microsatellite use in the genus Ambystoma. Copeia 2012: 570–577.

     Shinmura, Y., A. K. S. Wee, K. Takayama, T. Asakawa, O. B. Yllano,  S. G. Salmo III,  E. R. Ardl, N. X. Tung, N. B. Malekal, Onrizal, S. H. Meenakshisundaram, S. Sungkaew, M. N. Saleh, B. Adjie, K. K. Soe, E. Oguri, N. Murakami, Y. Watano, S. Baba, E. L. Webb & T. Kajita. 2012. Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing. Conservation Genetics Resources 4: 811–814.

Museum specimens (animal mtDNA):

     Mason, V. C., G. Li, K. M. Helgen & W. J. Murphy. 2011. Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. Genome Research 21: 1695–1704.

Non-model organisms:

     Ekblom, R. & J. Galindo. 2011. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107: 1–15.

     Gayral, P., L. Weinert, Y. Chiari, G. Tsagkogeorga, M. Ballenghien & N. Galtier. 2011. Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals. Molecular Ecology Resources 11: 650–661.

Parasites:

     Cantacessi, C., B. E. Campbell & R. B. Gasser. 2012. Key strongylid nematodes of animals — Impact of next-generation transcriptomics on systems biology and biotechnology. Biotechnology Advances 30: 469–488.

Phylogeography:

     Emerson, K. J., C. R. Merz, J. M. Catchen, P. A. Hohenlohe, W. A. Cresko, W. E. Bradshaw & C. M. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. PNAS 107: 16196-16200.

     Puritz, J. B., J. A. Addison & R. J. Toonen. 2012. Next-generation phylogeography: A targeted approach for multilocus sequencing of non-model organisms. PLoS ONE 7(3): e34241. doi:10.1371/journal.pone.0034241

     McCormack, J. E., J. M. Maley, S. M. Hird, E. P. Derryberry, G. R. Graves & R. T. Brumfield. 2012. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Molecular Phylogenetics and Evolution 62: 397–406.

Plants:

     Cronn, R., B. J. Knaus, A. Liston, P. J. Maughan, M. Parks, J. V. Syring & J. Udall. 2012. Targeted enrichment strategies for next-generation plant biology. American Journal of Botany 99: 291–311.

     Egan, A. N., J. Schlueter & D. M. Spooner. 2012. Applications of next-generation sequencing in plant biology. American Journal of Botany 99: 175–185.

     Kelly, L. J. & I. J. Leitch. 2011. Exploring giant plant genomes with next-generation sequencing technology. Chromosome Research 19: 939–953.

     Marroni, F., S. Pinosio & M. Morgante. The quest for rare variants: pooled multiplexed next generation sequencing in plants. Frontiers in Plant Science 3: doi: 10.3389/fpls.2012.00133

     Piednoël, M., A. J. Aberer, G. M. Schneeweiss, J. Macas, P. Novak, H. Gundlach, E. M. Temsch & S. S. Renner. 2012. Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae. Molecular Biology and Evolution (in press).

Polyploidy:

     Buggs, R. J. A., S. Renny-Byfield,M. Chester, I. E. Jordon-Thaden, L. Facio Viccini, S. Chamala, A. R. Leitch, P. S. Schnable, W. B. Barbazuk, P. S. Soltis & D. E. Soltis. 2012. Next-generation sequencing and genome evolution in allopolyploids. American Journal of Botany 99: 372–382.

     Griffin, P. C., C. Robin & A. A Hoffmann. 2011. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biology 9:19  http://www.biomedcentral.com/1741-7007/9/19

     Jiao, Y., J. Leebens-Mack, S. Ayyampalayam, J. E. Bowers, M. R. McKain, J. McNeal, M. Rolf, D. R. Ruzicka, E. Wafula, N. J. Wickett, X. Wu, Y. Zhang, J. Wang, Y. Zhang, E. J. Carpenter, M. K. Deyholos, T. M. Kutchan, A. S. Chanderbali, P. S. Soltis, D. W. Stevenson, R. McCombie, J. C. Pires, G. K.S. Wong, D. E. Soltis and C. W. dePamphilis. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13:R3 doi:10.1186/gb-2012-13-1-r3

     Renny-Byfield, S., M. Chester, A. Kovařík, S. C. Le Comber, M.-A. Grandbastien, M, Deloger, R. A. Nichols, J. Macas, P. Novák, M. W. Chase & A. R. Leitch. 2011. Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Molecular Biology and Evolution 28: 2843–2854.

Protists:                                                   

     Messenger, L. A., M. S. Llewellyn, T. Bhattacharyya, O. Franzén, M. D. Lewis, J. D. Ramírez, H. J. Carrasco, B. Andersson, M. A. Miles. 2012. Multiple mitochondrial introgression events and heteroplasmy in Trypanosoma cruzi revealed by maxicircle MLST and next generation sequencing. PLoS Neglected Tropical Diseases 6(4): e1584. doi:10.1371/journal.pntd.0001584.

RAD sequencing:

     Amish, S. J., P. A. Hohenlohe, S. Painter, R. F. Leary, C. Muhlfeld, F. W. Allendorf & G. Luikart. 2012. RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays. Molecular Ecology Resources 12: 653–660.

     Davey, J. W. & M. L. Blaxter. 2010. RADSeq: next-generation population genetics. Briefings in Functional Genomics 9: 416-423.

     Etter, P. D., S. Bassham, P. A. Hohenlohe, E. A. Johnson & W. A. Cresko. 2011. SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Methods in Molecular Biology 772: 157-78.

     Etter, P. D., J. L. Preston , S. Bassham, W. A. Cresko & E.A. Johnson. 2011. Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS ONE 6(4): e18561. doi:10.1371/journal.pone.0018561

     Rowe, H. C., S. Renaut & A. Guggisberg. 2011. RAD in the realm of next-generation sequencing technologies. Molecular Ecology 20: 3499–3502.

     Scaglione, D., A. Acquadro, E. Portis, M. Tirone, S. J Knapp & S. Lanteri. 2012. RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics 2012, 13:3 doi:10.1186/1471-2164-13-3

SNPs:

     Seeb, J. E., G. Carvalho, L. Hauser, K. Naish, S. Roberts & L. W. Seeb. 2011. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources 11 (Suppl. 1): 1–8.

     Helyar, S. J., J. Hemmer-Hansen, D. Bekkevold, M. I. Taylor, R. Ogden, M. T. Limborg, A. Cariani, G. E. Maes, E. Diopere, G. R. Carvalho & E. E. Nielsen. 2011. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources 11 (Suppl. 1): 123–136.

Speciation:

     Garrigan, D.,  S. B. Kingan, A. J. Geneva, P. Andolfatto, A. G. Clark, K. R. Thornton & D. C. Presgraves. 2012. Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Research (in press) doi: 10.1101/gr.130922.111

     Lessios, H. A. 2011. Speciation genes in free-spawning marine invertebrates. Integrative and Comparative Biology 51: 456–465.

     Nosil, P., Z. Gompert, T. E. Farkas, A. A. Comeault, J. L. Feder, C. A. Buerkle & T. L. Parchman. 2012. Genomic consequences of multiple speciation processes in a stick insect. Philosophical Transactions of the Royal Society B (in press)

     Nosil, P. & J. L. Feder. 2012. Genomic divergence during speciation: causes and consequences. Philosophical Transactions of the Royal Society B 367: 332–342.

     Renaut, S., N. Maillet, E. Normandeau, C. Sauvage, N. Derome,  S. M. Rogers and L. Bernatchez. 2012. Genome-wide patterns of divergence during speciation: the lake whitefish case study. Philosophical Transactions of the Royal Society B 367: 354–363.

     Via, S. 2012. Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Philosophical Transactions of the Royal Society B 367: 451–460.

Systematics:

     Baum, B. R., T. Edwards, M. Mamuti & D. A. Johnson. 2012. Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from the nuclear 5S rDNA sequences (Poaceae: Triticeae). Genome 55: 177–193.

     Bybee, S. M., H. D. Bracken-Grissom, R. A. Hermansen, M. J. Clement, K. A. Crandall & D. L. Felder. 2011. Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea). Zoologischer Anzeiger 250: 497–506.

     Czesny, S., J. Epifanio & P. Michalak. 2012. Genetic divergence between freshwater and marine morphs of alewife (Alosa pseudoharengus): A ‘next-generation’ sequencing analysis. PLoS ONE 7(3): e31803. doi:10.1371/journal.pone.0031803

     Grover, C. E., A. Salmon & J. F. Wendel. 2012. Targeted sequence capture as a powerful tool for evolutionary analysis. American Journal of Botany 99: 312–319.

     Harrison, N. & C. A. Kidner. 2011. Next-generation sequencing and systematics: What can a billion base pairs of DNA sequence data do for you? Taxon 60: 1552–1566.

     McCormack, J. E., S. M. Hird, A. J. Zellmer, B. C. Carstens & R. T. Brumfield. 2012. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution (in press).

     Osigus, H.-J., M. Eitel & B. Schierwater. 2012. Chasing the urmetazoon: Striking a blow for quality data? Molecular Phylogenetics and Evolution (in press)

     Rosenfeld, J. A. & R. DeSalle. 2012. E value cutoff and eukaryotic genome content phylogenetics. Molecular Phylogenetics and Evolution 63: 342–350.

     Straub, S. C. K., M. Parks, K. Weitemier, M. Fishbein, R. C. Cronn & A. Liston. 2012. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany 99: 349–364. [plants]

     The Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635–641.