Metzker ML: Sequencing technologies—the next generation. Nat Rev Gen. 2009, 11 (1): 31-46.
Article
Google Scholar
Koepke T, Schaeffer S, Krishnan V, Jiwan D, Harper A, Whiting M, Oraguzie N, Dhingra A: Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing. BMC Genomics. 2012, 13: 18-10.1186/1471-2164-13-18.
Article
PubMed Central
CAS
PubMed
Google Scholar
Elmer KR, Fan S, Gunter HM, Jones JC, Boekhoff S, Kuraku S, Meyer A: Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Mole Ecol. 2010, 19 (Suppl 1): 197-211.
Article
CAS
Google Scholar
Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JF, Jung HJ, Vance CP, Gronwald JW: Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics. 2011, 12: 199-10.1186/1471-2164-12-199.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, Jiang CJ, Sun J, Li YY, Chen Q, Xia T: Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics. 2011, 12: 131-10.1186/1471-2164-12-131.
Article
PubMed Central
CAS
PubMed
Google Scholar
Garg R, Patel RK, Tyagi AK, Jain M: De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 2011, 18 (1): 53-63. 10.1093/dnares/dsq028.
Article
PubMed Central
CAS
PubMed
Google Scholar
Miller HC, Biggs PJ, Voelckel C, Nelson NJ: De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics. 2012, 13: 439-10.1186/1471-2164-13-439.
Article
PubMed Central
CAS
PubMed
Google Scholar
Crawford JE, Guelbeogo WM, Sanou A, Traore A, Vernick KD, Sagnon N, Lazzaro BP: De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PloS One. 2010, 5 (12): e14202-10.1371/journal.pone.0014202.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pandolfi JM, Bradbury RH, Sala E, Hughes TP, Bjorndal KA, Cooke RG, McArdle D, McClenachan L, Newman MJ, Paredes G: Global trajectories of the long-term decline of coral reef ecosystems. Science. 2003, 301 (5635): 955-958. 10.1126/science.1085706.
Article
CAS
PubMed
Google Scholar
Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV: Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics. 2009, 10: 219-10.1186/1471-2164-10-219.
Article
PubMed Central
PubMed
Google Scholar
Meyer E, Aglyamova GV, Matz MV: Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol Ecol. 2011, 20 (17): 3599-3616.
CAS
PubMed
Google Scholar
Traylor-Knowles N, Granger BR, Lubinski TJ, Parikh JR, Garamszegi S, Xia Y, Marto JA, Kaufman L, Finnerty JR: Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral. Pocillopora damicornis. BMC Genomics. 2011, 12: 585-10.1186/1471-2164-12-585.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vidal-Dupiol J, Zoccola D, Tambutte E, Grunau C, Cosseau C, Smith KM, Freitag M, Dheilly NM, Allemand D, Tambutte S: Genes related to ion-transport and energy production are upregulated in response to CO2-driven pH decrease in corals: new insights from transcriptome analysis. PloS One. 2013, 8 (3): e58652-10.1371/journal.pone.0058652.
Article
PubMed Central
CAS
PubMed
Google Scholar
Moya A, Huisman L, Ball EE, Hayward DC, Grasso LC, Chua CM, Woo HN, Gattuso JP, Foret S, Miller DJ: Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO(2)-driven acidification during the initiation of calcification. Mol Ecol. 2012, 21 (10): 2440-2454. 10.1111/j.1365-294X.2012.05554.x.
Article
CAS
PubMed
Google Scholar
Kitahara MV, Cairns SD, Stolarski J, Blair D, Miller DJ: A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PloS One. 2010, 5 (7): e11490-10.1371/journal.pone.0011490.
Article
PubMed Central
PubMed
Google Scholar
Huang D, Licuanan WY, Baird AH, Fukami H: Cleaning up the 'Bigmessidae': molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evol Biol. 2011, 11: 37-10.1186/1471-2148-11-37.
Article
PubMed Central
PubMed
Google Scholar
Veron J: Corals World. 2000, 3: 100-131.
Google Scholar
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I: ABySS: a parallel assembler for short read sequence data. Genome Res. 2009, 19 (6): 1117-1123. 10.1101/gr.089532.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, Chiari Y, Belkhir K, Ranwez V, Galtier N: Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol Ecol Resour. 2012, 12 (5): 834-845. 10.1111/j.1755-0998.2012.03148.x.
Article
CAS
PubMed
Google Scholar
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ: De novo assembly and analysis of RNA-seq data. Nat Methods. 2010, 7 (11): 909-912. 10.1038/nmeth.1517.
Article
CAS
PubMed
Google Scholar
Mortazavi A, Schwarz EM, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW: Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res. 2010, 20 (12): 1740-1747. 10.1101/gr.111021.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res. 1999, 9 (9): 868-877. 10.1101/gr.9.9.868.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sadamoto H, Takahashi H, Okada T, Kenmoku H, Toyota M, Asakawa Y: De novo sequencing and transcriptome analysis of the central nervous system of mollusc Lymnaea stagnalis by deep RNA sequencing. PloS one. 2012, 7 (8): e42546-10.1371/journal.pone.0042546.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rice P, Longden I, Bleasby A: EMBOSS: the European molecular biology open software suite. Trends Genet. 2000, 16 (6): 276-277. 10.1016/S0168-9525(00)02024-2.
Article
CAS
PubMed
Google Scholar
Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV: Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007, 317 (5834): 86-94. 10.1126/science.1139158.
Article
CAS
PubMed
Google Scholar
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL: NCBI BLAST: a better web interface. Nucleic Acids Res. 2008, 36: W5-W9. 10.1093/nar/gkn201. Web Server issue)
Article
PubMed Central
CAS
PubMed
Google Scholar
Enright A, Van Dongen S, Ouzounis C: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002, 30 (7): 1575-1584. 10.1093/nar/30.7.1575.
Article
PubMed Central
CAS
PubMed
Google Scholar
Martin JA, Wang Z: Next-generation transcriptome assembly. Nat Rev Gen. 2011, 12 (10): 671-682. 10.1038/nrg3068.
Article
CAS
Google Scholar
Wang X-W, Luan J-B, Li J-M, Bao Y-Y, Zhang C-X, Liu S-S: De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics. 2010, 11 (1): 400-10.1186/1471-2164-11-400.
Article
PubMed Central
PubMed
Google Scholar
Finney JC, Pettay DT, Sampayo EM, Warner ME, Oxenford HA, LaJeunesse TC: The relative significance of host-habitat, depth, and geography on the ecology, endemism, and speciation of coral endosymbionts in the genus Symbiodinium. Microbial Ecol. 2010, 60 (1): 250-263. 10.1007/s00248-010-9681-y.
Article
Google Scholar
Hagedorn M, Carter VL, Leong JC, Kleinhans FW: Physiology and cryosensitivity of coral endosymbiotic algae (Symbiodinium). Cryobiology. 2010, 60 (2): 147-158. 10.1016/j.cryobiol.2009.10.005.
Article
CAS
PubMed
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R: Clustal W and clustal X version 2.0. Bioinformatics. 2007, 23 (21): 2947-2948. 10.1093/bioinformatics/btm404.
Article
CAS
PubMed
Google Scholar
Patrick Kück KM: FASconCAT: convenient handling of data matrices. Mole Phylogen Evol. 2010, 56 (2010): 1115-1118.
Article
Google Scholar
Stamatakis A, Ludwig T, Meier H: RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005, 21 (4): 456-463. 10.1093/bioinformatics/bti191.
Article
CAS
PubMed
Google Scholar
Budd AF, Romano SL, Smith ND, Barbeitos MS: Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data. Integ Comp Biol. 2010, 50 (3): 411-427. 10.1093/icb/icq062.
Article
Google Scholar
Fukami H, Budd AF, Paulay G, Solé-Cava A, Allen Chen C, Iwao K, Knowlton N: Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nat Geosci. 2004, 427 (6977): 832-835.
CAS
Google Scholar
Ilagan RP, Rhoades E, Gruber DF, Kao HT, Pieribone VA, Regan L: A new bright green-emitting fluorescent protein–engineered monomeric and dimeric forms. FEBS J. 2010, 277 (8): 1967-1978. 10.1111/j.1742-4658.2010.07618.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Labas YA, Gurskaya NG, Yanushevich YG, Fradkov AF, Lukyanov KA, Lukyanov SA, Matz MV: Diversity and evolution of the green fluorescent protein family. Proc Natl Acad Sci USA. 2002, 99 (7): 4256-4261. 10.1073/pnas.062552299.
Article
PubMed Central
CAS
PubMed
Google Scholar
Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA: Fluorescent proteins from nonbioluminescent Anthozoa species. Nat Biotech. 1999, 17 (10): 969-973. 10.1038/13657.
Article
CAS
Google Scholar
Bogdanov AM, Mishin AS, Yampolsky IV, Belousov VV, Chudakov DM, Subach FV, Verkhusha VV, Lukyanov S, Lukyanov KA: Green fluorescent proteins are light-induced electron donors. Nature chemical biology. 2009, 5 (7): 459-461. 10.1038/nchembio.174.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sullivan JC, Ryan JF, Watson JA, Webb J, Mullikin JC, Rokhsar D, Finnerty JR: StellaBase: the Nematostella vectensis genomics database. Nucleic acids research. 2006, 34 (Database issue): D495-D499.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bomati EK, Manning G, Deheyn DD: Amphioxus encodes the largest known family of green fluorescent proteins, which have diversified into distinct functional classes. BMC evolutionary biology. 2009, 9: 77-10.1186/1471-2148-9-77.
Article
PubMed Central
PubMed
Google Scholar
Haddock SHD, Mastroianni N, Christianson LM: A photoactivatable green-fluorescent protein from the phylum Ctenophora. Proc Royal Soc B Biol Sci. 2010, 277 (1685): 1155-1160. 10.1098/rspb.2009.1774.
Article
CAS
Google Scholar
Darriba D, Taboada GL, Doallo R, Posada D: ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011, 27 (8): 1164-1165. 10.1093/bioinformatics/btr088.
Article
CAS
PubMed
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology. 2011, 29 (7): 644-652. 10.1038/nbt.1883.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang F, Moss LG, Phillips GN: The molecular structure of green fluorescent protein. 1997, Dept of biochemistry and cell biology: Rice University
Google Scholar
Ormö M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ: Crystal structure of the Aequorea victoria green fluorescent protein. Science. 1996, 273 (5280): 1392-1395. 10.1126/science.273.5280.1392.
Article
PubMed
Google Scholar
Kozak M: An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 1987, 15 (20): 8125-8148. 10.1093/nar/15.20.8125.
Article
PubMed Central
CAS
PubMed
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech. 2010, 28 (5): 511-515. 10.1038/nbt.1621.
Article
CAS
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Gruber D, Kao H, Janoschka S, Tsai J, Pieribone V: Patterns of fluorescent protein expression in scleractinian corals. Biol Bull. 2008, 215 (2): 143-10.2307/25470695.
Article
PubMed
Google Scholar
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S: Database resources of the national center for biotechnology information. Nucleic Acids Res. 2010, 38 (Database issue): D5-D16.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T: Using the Acropora digitifera genome to understand coral responses to environmental change. Nat Geosci. 2011, 476 (7360): 320-323.
CAS
Google Scholar
Katoh K, Asimenos G, Toh H: Multiple alignment of DNA sequences with MAFFT. Methods Mole Biol (Clifton, NJ). 2009, 537: 39-64. 10.1007/978-1-59745-251-9_3.
Article
CAS
Google Scholar
Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R: Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinforma. 2007, 8 (1): 460-10.1186/1471-2105-8-460.
Article
Google Scholar
Sambrook J, Fritsch EF, Maniatis T: Molecular cloning, vol. 2. 1989, New York: Cold spring harbor laboratory press
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotech. 2011, 29 (1): 24-26. 10.1038/nbt.1754.
Article
CAS
Google Scholar