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Volumn 541, Issue 7638, 2017, Pages 536-540

Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus

(44)  Mock, Thomas a   Otillar, Robert P b   Strauss, Jan a   McMullan, Mark c   Paajanen, Pirita c   Schmutz, Jeremy b,d,y   Salamov, Asaf b   Sanges, Remo e   Toseland, Andrew a   Ward, Ben J a,c   Allen, Andrew E f,g   Dupont, Christopher L f   Frickenhaus, Stephan h,i   Maumus, Florian j   Veluchamy, Alaguraj k,z   Wu, Taoyang a   Barry, Kerrie W b   Falciatore, Angela l   Ferrante, Maria I e   Fortunato, Antonio E l   more..


Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; COLD TOLERANCE; CONCENTRATION (COMPOSITION); DIATOM; DISSOLVED MATTER; DIVERGENCE; ENVIRONMENTAL CONDITIONS; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOMICS; PRIMARY PRODUCTION; SEASONAL VARIATION;

EID: 85016137064     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature20803     Document Type: Article
Times cited : (283)

References (81)
  • 1
    • 39149112536 scopus 로고    scopus 로고
    • Evolution and biodiversity of Antarctic organisms: A molecular perspective
    • Rogers, A. D. Evolution and biodiversity of Antarctic organisms: a molecular perspective. Phil. Trans. R. Soc. B 362, 2191-2214 (2007).
    • (2007) Phil. Trans. R. Soc. B , vol.362 , pp. 2191-2214
    • Rogers, A.D.1
  • 2
    • 84911865089 scopus 로고    scopus 로고
    • Gross and net production during the spring bloom along the Western Antarctic Peninsula
    • Goldman, J. A., et al. Gross and net production during the spring bloom along the Western Antarctic Peninsula. New Phytol. 205, 182-191 (2015).
    • (2015) New Phytol. , vol.205 , pp. 182-191
    • Goldman, J.A.1
  • 3
    • 84877966714 scopus 로고    scopus 로고
    • Iron-light interactions differ in Southern Ocean phytoplankton
    • Strzepek, R. F., et al. Iron-light interactions differ in Southern Ocean phytoplankton. Limnol. Oceanogr. 57, 1182-1200 (2012).
    • (2012) Limnol. Oceanogr. , vol.57 , pp. 1182-1200
    • Strzepek, R.F.1
  • 4
    • 84875522321 scopus 로고    scopus 로고
    • Iron limitation of a springtime bacterial and phytoplankton community in the ross sea: Implications for vitamin B12 nutrition
    • Bertrand, E. M., et al. Iron limitation of a springtime bacterial and phytoplankton community in the ross sea: implications for vitamin B12 nutrition. Front. Microbiol. 2, 160 (2011).
    • (2011) Front. Microbiol. , vol.2 , pp. 160
    • Bertrand, E.M.1
  • 5
    • 84897147367 scopus 로고    scopus 로고
    • Surface-water iron supplies in the Southern Ocean sustained by deep winter mixing
    • Tagliabue, A., et al. Surface-water iron supplies in the Southern Ocean sustained by deep winter mixing. Nat. Geosci. 7, 314-320 (2014).
    • (2014) Nat. Geosci. , vol.7 , pp. 314-320
    • Tagliabue, A.1
  • 6
    • 84887086311 scopus 로고    scopus 로고
    • The impact of temperature on marine phytoplankton resource allocation and metabolism
    • Toseland, A., et al. The impact of temperature on marine phytoplankton resource allocation and metabolism. Nat. Clim. Chang. 3, 979-984 (2013).
    • (2013) Nat. Clim. Chang. , vol.3 , pp. 979-984
    • Toseland, A.1
  • 7
    • 84865224501 scopus 로고    scopus 로고
    • Antarctic sea ice variability and trends 1979-2010
    • Parkinson, C. L., Cavalieri, D. J. Antarctic sea ice variability and trends, 1979-2010. Cryosphere 6, 871-880 (2012).
    • (2012) Cryosphere , vol.6 , pp. 871-880
    • Parkinson, C.L.1    Cavalieri, D.J.2
  • 8
    • 0001010458 scopus 로고
    • Light-temperature interactions on the growth of Antarctic diatoms
    • Fiala, M., Oriol, L. Light-temperature interactions on the growth of Antarctic diatoms. Polar Biol. 10, 629-636 (1990).
    • (1990) Polar Biol. , vol.10 , pp. 629-636
    • Fiala, M.1    Oriol, L.2
  • 9
    • 0027088510 scopus 로고
    • Fragilariopsis cylindrus (Grunow) Krieger: The most abundant diatom in water column assemblages of the Antarctic marginal ice-edge zones
    • Kang, S.-H., Fryxell, G. A. Fragilariopsis cylindrus (Grunow) Krieger: The most abundant diatom in water column assemblages of the Antarctic marginal ice-edge zones. Polar Biol. 12, 609-627 (1992).
    • (1992) Polar Biol. , vol.12 , pp. 609-627
    • Kang, S.-H.1    Fryxell, G.A.2
  • 10
    • 7044269704 scopus 로고    scopus 로고
    • The diatom Fragilariopsis cylindrus and its potential as an indicator species for cold water rather than for sea ice
    • von Quillfeld, C. H. The diatom Fragilariopsis cylindrus and its potential as an indicator species for cold water rather than for sea ice. Vie Milieu 54, 137-143 (2004).
    • (2004) Vie Milieu , vol.54 , pp. 137-143
    • Von Quillfeld, C.H.1
  • 11
    • 0037169083 scopus 로고    scopus 로고
    • Antarctic Sea ice-A habitat for extremophiles
    • Thomas, D. N., Dieckmann, G. S. Antarctic Sea ice-A habitat for extremophiles. Science 295, 641-644 (2002).
    • (2002) Science , vol.295 , pp. 641-644
    • Thomas, D.N.1    Dieckmann, G.S.2
  • 12
    • 84863971035 scopus 로고    scopus 로고
    • Deep carbon export from a Southern Ocean iron-fertilized diatom bloom
    • Smetacek, V., et al. Deep carbon export from a Southern Ocean iron-fertilized diatom bloom. Nature 487, 313-319 (2012).
    • (2012) Nature , vol.487 , pp. 313-319
    • Smetacek, V.1
  • 13
    • 84907010792 scopus 로고    scopus 로고
    • Impact of sea ice on the marine iron cycle and phytoplankton productivity
    • Wang, S., et al. Impact of sea ice on the marine iron cycle and phytoplankton productivity. Biogeosciences 11, 4713-4731 (2014).
    • (2014) Biogeosciences , vol.11 , pp. 4713-4731
    • Wang, S.1
  • 14
    • 84885952221 scopus 로고    scopus 로고
    • Role of sea ice in global biogeochemical cycles: Emerging views and challenges
    • Vancoppenolle, M., et al. Role of sea ice in global biogeochemical cycles: emerging views and challenges. Quat. Sci. Rev. 79, 207-230 (2013).
    • (2013) Quat. Sci. Rev. , vol.79 , pp. 207-230
    • Vancoppenolle, M.1
  • 15
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes
    • Parra, G., Bradnam, K., Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061-1067 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 16
    • 6044252163 scopus 로고    scopus 로고
    • The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, metabolism
    • Armbrust, E. V., et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, metabolism. Science 306, 79-86 (2004).
    • (2004) Science , vol.306 , pp. 79-86
    • Armbrust, E.V.1
  • 17
    • 56249098614 scopus 로고    scopus 로고
    • The Phaeodactylum genome reveals the evolutionary history of diatom genomes
    • Bowler, C., et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456, 239-244 (2008).
    • (2008) Nature , vol.456 , pp. 239-244
    • Bowler, C.1
  • 18
    • 79955839978 scopus 로고    scopus 로고
    • The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella
    • Alverson, A. J., Beszteri, B., Julius, M. L., Theriot, E. C. The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella. BMC Evol. Biol. 11, 125 (2011).
    • (2011) BMC Evol. Biol. , vol.11 , pp. 125
    • Alverson, A.J.1    Beszteri, B.2    Julius, M.L.3    Theriot, E.C.4
  • 19
    • 34848860166 scopus 로고    scopus 로고
    • Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions
    • De Martino, A., Meichenin, A., Shi, J., Pan, K., Bowler, C. Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions. J. Phycol. 43, 992-1009 (2007).
    • (2007) J. Phycol. , vol.43 , pp. 992-1009
    • De Martino, A.1    Meichenin, A.2    Shi, J.3    Pan, K.4    Bowler, C.5
  • 20
    • 33744966833 scopus 로고    scopus 로고
    • Copper-containing plastocyanin used for electron transport by an oceanic diatom
    • Peers, G., Price, N. M. Copper-containing plastocyanin used for electron transport by an oceanic diatom. Nature 441, 341-344 (2006).
    • (2006) Nature , vol.441 , pp. 341-344
    • Peers, G.1    Price, N.M.2
  • 22
    • 80054718835 scopus 로고    scopus 로고
    • The distribution of dissolved zinc in the Atlantic sector of the Southern Ocean
    • Croot, P. L., Baars, O., Streu, P. The distribution of dissolved zinc in the Atlantic sector of the Southern Ocean. Deep Sea Res. Part II Top. Stud. Oceanogr. 58, 2707-2719 (2011).
    • (2011) Deep Sea Res. Part II Top. Stud. Oceanogr. , vol.58 , pp. 2707-2719
    • Croot, P.L.1    Baars, O.2    Streu, P.3
  • 23
    • 84860436217 scopus 로고    scopus 로고
    • Possible role of horizontal gene transfer in the colonization of sea ice by algae
    • Raymond, J. A., Kim, H. J. Possible role of horizontal gene transfer in the colonization of sea ice by algae. PLoS One 7, e35968 (2012).
    • (2012) PLoS One , vol.7 , pp. e35968
    • Raymond, J.A.1    Kim, H.J.2
  • 24
    • 84857134530 scopus 로고    scopus 로고
    • Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability
    • Marchetti, A., et al. Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc. Natl Acad. Sci. USA 109, E317-E325 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. E317-E325
    • Marchetti, A.1
  • 25
    • 1242271304 scopus 로고    scopus 로고
    • Allele-specific gene expression uncovered
    • Knight, J. C. Allele-specific gene expression uncovered. Trends Genet. 20, 113-116 (2004).
    • (2004) Trends Genet. , vol.20 , pp. 113-116
    • Knight, J.C.1
  • 26
    • 3142750575 scopus 로고    scopus 로고
    • Allelic variation of gene expression in maize hybrids
    • Guo, M., et al. Allelic variation of gene expression in maize hybrids. Plant Cell 16, 1707-1716 (2004).
    • (2004) Plant Cell , vol.16 , pp. 1707-1716
    • Guo, M.1
  • 27
    • 0035808565 scopus 로고    scopus 로고
    • Timing of millennial-scale climate change in Antarctica and Greenland during the last glacial period
    • Blunier, T., Brook, E. J. Timing of millennial-scale climate change in Antarctica and Greenland during the last glacial period. Science 291, 109-112 (2001).
    • (2001) Science , vol.291 , pp. 109-112
    • Blunier, T.1    Brook, E.J.2
  • 28
    • 0000479431 scopus 로고
    • Isolation of plant DNA from fresh tissue
    • Doyle, J. J., Doyle, J. L. Isolation of plant DNA from fresh tissue. Focus 12, 13-15 (1990).
    • (1990) Focus , vol.12 , pp. 13-15
    • Doyle, J.J.1    Doyle, J.L.2
  • 29
    • 16444367523 scopus 로고    scopus 로고
    • Real-time PCR-based method for the estimation of genome sizes
    • Wilhelm, J., Pingoud, A., Hahn, M. Real-time PCR-based method for the estimation of genome sizes. Nucleic Acids Res. 31, e56 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. e56
    • Wilhelm, J.1    Pingoud, A.2    Hahn, M.3
  • 30
    • 0037267048 scopus 로고    scopus 로고
    • Whole-genome sequence assembly for mammalian genomes: Arachne 2
    • Jaffe, D. B., et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 13, 91-96 (2003).
    • (2003) Genome Res. , vol.13 , pp. 91-96
    • Jaffe, D.B.1
  • 31
    • 33846062023 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Wheeler, D. L., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35, D5-D12 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. D5-D12
    • Wheeler, D.L.1
  • 32
    • 84938423867 scopus 로고    scopus 로고
    • Assembly and diploid architecture of an individual human genome via single-molecule technologies
    • Pendleton, M., et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780-786 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 780-786
    • Pendleton, M.1
  • 33
    • 84991694364 scopus 로고    scopus 로고
    • Phased diploid genome assembly with single-molecule real-time sequencing
    • Chin, C.-S., et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050-1054 (2016).
    • (2016) Nat. Methods , vol.13 , pp. 1050-1054
    • Chin, C.-S.1
  • 34
    • 67649884743 scopus 로고    scopus 로고
    • And accurate short read alignment with Burrows-Wheeler transform
    • Li, H., Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Fast, D.R.2
  • 36
    • 23844525077 scopus 로고    scopus 로고
    • Repbase Update a database of eukaryotic repetitive elements
    • Jurka, J., et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467 (2005).
    • (2005) Cytogenet. Genome Res. , vol.110 , pp. 462-467
    • Jurka, J.1
  • 37
    • 29144455282 scopus 로고    scopus 로고
    • De novo identification of repeat families in large genomes
    • Price, A. L., Jones, N. C., Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21 (Suppl. 1), i351-i358 (2005).
    • (2005) Bioinformatics , vol.21 , pp. i351-i358
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 38
    • 0034065724 scopus 로고    scopus 로고
    • Ab initio gene finding in Drosophila genomic DNA
    • Salamov, A. A., Solovyev, V. V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522 (2000).
    • (2000) Genome Res. , vol.10 , pp. 516-522
    • Salamov, A.A.1    Solovyev, V.V.2
  • 39
    • 0034098730 scopus 로고    scopus 로고
    • Using GeneWise in the Drosophila annotation experiment
    • Birney, E., Durbin, R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 10, 547-548 (2000).
    • (2000) Genome Res. , vol.10 , pp. 547-548
    • Birney, E.1    Durbin, R.2
  • 40
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T. M., Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 41
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen, H., Engelbrecht, J., Brunak, S., von Heijne, G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1-6 (1997).
    • (1997) Protein Eng. , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Von Heijne, G.4
  • 42
    • 0344406716 scopus 로고    scopus 로고
    • Reliability measures for membrane protein topology prediction algorithms
    • Melén, K., Krogh, A., von Heijne, G. Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol. 327, 735-744 (2003).
    • (2003) J. Mol. Biol. , vol.327 , pp. 735-744
    • Melén, K.1    Krogh, A.2    Von Heijne, G.3
  • 43
    • 23144458473 scopus 로고    scopus 로고
    • InterProScan: Protein domains identifier
    • Quevillon, E., et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116-W120 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. W116-W120
    • Quevillon, E.1
  • 44
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the Universal Protein Resource (UniProt)
    • UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 42, D191-D198 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D191-D198
    • UniProt Consortium1
  • 45
    • 38549126643 scopus 로고    scopus 로고
    • KEGG for linking genomes to life and the environment
    • Kanehisa, M., et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2007).
    • (2007) Nucleic Acids Res. , vol.36 , pp. D480-D484
    • Kanehisa, M.1
  • 46
    • 16444381885 scopus 로고    scopus 로고
    • A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    • Koonin, E. V., et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5, R7 (2004).
    • (2004) Genome Biol. , vol.5 , pp. R7
    • Koonin, E.V.1
  • 47
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29 (2000).
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
  • 48
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G., Brenner, S. E., Hubbard, T., Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540 (1995).
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 49
    • 78651345652 scopus 로고    scopus 로고
    • The RCSB Protein Data Bank: Redesigned web site and web services
    • Rose, P. W., et al. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 39, D392-D401 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. D392-D401
    • Rose, P.W.1
  • 50
    • 77953778296 scopus 로고    scopus 로고
    • History of biological metal utilization inferred through phylogenomic analysis of protein structures
    • Dupont, C. L., Butcher, A., Valas, R. E., Bourne, P. E., Caetano-Anollés, G. History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc. Natl Acad. Sci. USA 107, 10567-10572 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 10567-10572
    • Dupont, C.L.1    Butcher, A.2    Valas, R.E.3    Bourne, P.E.4    Caetano-Anollés, G.5
  • 51
    • 33845230241 scopus 로고    scopus 로고
    • Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry
    • Dupont, C. L., Yang, S., Palenik, B., Bourne, P. E. Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc. Natl Acad. Sci. USA 103, 17822-17827 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 17822-17827
    • Dupont, C.L.1    Yang, S.2    Palenik, B.3    Bourne, P.E.4
  • 52
    • 38549161051 scopus 로고    scopus 로고
    • PROCOGNATE: A cognate ligand domain mapping for enzymes
    • Bashton, M., Nobeli, I., Thornton, J. M. PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Res. 36, D618-D622 (2007).
    • (2007) Nucleic Acids Res. , vol.36 , pp. D618-D622
    • Bashton, M.1    Nobeli, I.2    Thornton, J.M.3
  • 53
    • 33746808240 scopus 로고    scopus 로고
    • Genomic scale sub-family assignment of protein domains
    • Gough, J. Genomic scale sub-family assignment of protein domains. Nucleic Acids Res. 34, 3625-3633 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3625-3633
    • Gough, J.1
  • 54
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough, J., Karplus, K., Hughey, R., Chothia, C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313, 903-919 (2001).
    • (2001) J. Mol. Biol. , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 55
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, maximum parsimony methods
    • Tamura, K., et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 56
    • 65649117685 scopus 로고    scopus 로고
    • DnaSP v5: A software for comprehensive analysis of DNA polymorphism data
    • Librado, P., Rozas, J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1451-1452
    • Librado, P.1    Rozas, J.2
  • 57
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond, A. J., Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 58
    • 0022376704 scopus 로고
    • Dating of the human-Ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., Kishino, H., Yano, T. Dating of the human-Ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174 (1985).
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 60
    • 0001778604 scopus 로고
    • A mathematical theory of evolution. Based on the conclusions of Dr. J. C. Willis, F. R. S.
    • Yule, G. U. A mathematical theory of evolution. Based on the conclusions of Dr. J. C. Willis, F. R. S. Phil. Trans. R. Soc. B 213, 21-87 (1925).
    • (1925) Phil. Trans. R. Soc. B , vol.213 , pp. 21-87
    • Yule, G.U.1
  • 61
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 62
    • 77956193448 scopus 로고    scopus 로고
    • ProgressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling, A. E., Mau, B., Perna, N. T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5, e11147 (2010).
    • (2010) PLoS One , vol.5 , pp. e11147
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 63
    • 85016136703 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289-300 (1995).
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 64
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0.
    • Larkin, M. A., et al. Clustal W and Clustal X version 2. 0. Bioinformatics 23, 2947-2948 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 65
    • 18644368714 scopus 로고    scopus 로고
    • The Bioperl toolkit: Perl modules for the life sciences
    • Stajich, J. E., et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12, 1611-1618 (2002).
    • (2002) Genome Res. , vol.12 , pp. 1611-1618
    • Stajich, J.E.1
  • 66
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models
    • Brady, A., Salzberg, S. L. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat. Methods 6, 673-676 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 67
    • 79960610118 scopus 로고    scopus 로고
    • REVIGO summarizes and visualizes long lists of gene ontology terms
    • Supek, F., Bošnjak, M., Škunca, N., Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6, e21800 (2011).
    • (2011) PLoS One , vol.6 , pp. e21800
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4
  • 68
    • 0001743979 scopus 로고
    • Preparation and chemistry of the artificial algal culture medium Aquil
    • Price, N. M., et al. Preparation and chemistry of the artificial algal culture medium Aquil. Biol. Oceanogr. 6, 443-461 (1988/89).
    • (1988) Biol. Oceanogr. , vol.6 , pp. 443-461
    • Price, N.M.1
  • 69
    • 34248663955 scopus 로고    scopus 로고
    • The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: Twenty-something years on
    • Chomczynski, P., Sacchi, N. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat. Protocols 1, 581-585 (2006).
    • (2006) Nat. Protocols , vol.1 , pp. 581-585
    • Chomczynski, P.1    Sacchi, N.2
  • 70
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu, T. D., Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 71
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-A Python framework to work with high-throughput sequencing data
    • Anders, S., Pyl, P. T., Huber, W. HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 72
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M. D., McCarthy, D. J., Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 73
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: Accounting for selection bias
    • Young, M. D., Wakefield, M. J., Smyth, G. K., Oshlack, A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 11, R14 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R14
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3    Oshlack, A.4
  • 75
    • 84858041341 scopus 로고    scopus 로고
    • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
    • McCarthy, D. J., Chen, Y., Smyth, G. K. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40, 4288-4297 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. 4288-4297
    • McCarthy, D.J.1    Chen, Y.2    Smyth, G.K.3
  • 76
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 77
    • 84956811928 scopus 로고    scopus 로고
    • HYBRIDCHECK: Software for the rapid detection, visualization and dating of recombinant regions in genome sequence data
    • Ward, B. J., van Oosterhout, C. HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data. Mol. Ecol. Resour. 16, 534-539 (2016).
    • (2016) Mol. Ecol. Resour. , vol.16 , pp. 534-539
    • Ward, B.J.1    Van Oosterhout, C.2
  • 78
    • 33646167864 scopus 로고    scopus 로고
    • A simple and robust statistical test for detecting the presence of recombination
    • Bruen, T. C., Philippe, H., Bryant, D. A simple and robust statistical test for detecting the presence of recombination. Genetics 172, 2665-2681 (2006).
    • (2006) Genetics , vol.172 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3
  • 79
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson, D. H., Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254-267 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 80
    • 24644505748 scopus 로고    scopus 로고
    • SimuPOP: A forward-time population genetics simulation environment
    • Peng, B., Kimmel, M. simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21, 3686-3687 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3686-3687
    • Peng, B.1    Kimmel, M.2
  • 81
    • 33645108873 scopus 로고    scopus 로고
    • LAMARC 2. 0: Maximum likelihood and Bayesian estimation of population parameters
    • Kuhner, M. K. LAMARC 2. 0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22, 768-770 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 768-770
    • Kuhner, M.K.1


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