메뉴 건너뛰기




Volumn 7, Issue , 2016, Pages

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

(34)  Hoshino, Atsushi a,b   Jayakumar, Vasanthan c   Nitasaka, Eiji d   Toyoda, Atsushi e   Noguchi, Hideki e   Itoh, Takehiko f   Shin, Tadasu e   Minakuchi, Yohei e,s   Koda, Yuki c   Nagano, Atsushi J g,h   Yasugi, Masaki a,g,r   Honjo, Mie N g   Kudoh, Hiroshi g   Seki, Motoaki i,j   Kamiya, Asako i   Shiraki, Toshiyuki k   Carninci, Piero l   Asamizu, Erika m,r   Nishide, Hiroyo a   Tanaka, Sachiko a   more..


Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; DIVERGENCE; GENE EXPRESSION; GENOME; GENOMICS; MUTATION; VINE;

EID: 84994403385     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms13295     Document Type: Article
Times cited : (120)

References (70)
  • 1
    • 0029661564 scopus 로고    scopus 로고
    • A synopsis of Ipomoea (Convolvulaceae) in the Americas
    • Austin, D. D. F. & Huáman, Z. A synopsis of Ipomoea (Convolvulaceae) in the Americas. Taxon 45, 3-38 (1996).
    • (1996) Taxon , vol.45 , pp. 3-38
    • Austin, D.D.F.1    Huáman, Z.2
  • 2
    • 0036743053 scopus 로고    scopus 로고
    • Monophyly of the Convolvulaceae and circumscription of their major lineages based on DNA sequences of multiple chloroplast loci
    • Stefanovic, S., Krueger, L. & Olmstead, R. G. Monophyly of the Convolvulaceae and circumscription of their major lineages based on DNA sequences of multiple chloroplast loci. Am. J. Bot. 89, 1510-1522 (2002).
    • (2002) Am. J. Bot. , vol.89 , pp. 1510-1522
    • Stefanovic, S.1    Krueger, L.2    Olmstead, R.G.3
  • 3
    • 0037373635 scopus 로고    scopus 로고
    • Tracing floral adaptations from ecology to molecules
    • Clegg, M. T. & Durbin, M. L. Tracing floral adaptations from ecology to molecules. Nat. Rev. Genet. 4, 206-215 (2003).
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 206-215
    • Clegg, M.T.1    Durbin, M.L.2
  • 5
    • 29444447361 scopus 로고    scopus 로고
    • Shoot circumnutation and winding movements require gravisensing cells
    • Kitazawa, D. et al. Shoot circumnutation and winding movements require gravisensing cells. Proc. Natl Acad. Sci. USA 102, 18742-18747 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 18742-18747
    • Kitazawa, D.1
  • 6
    • 0028388784 scopus 로고
    • Isolation of a Suppressor-mutator/Enhancer-like transposable element, Tpn1, from Japanese morning glory bearing variegated flowers
    • Inagaki, Y., Hisatomi, Y., Suzuki, T., Kasahara, K. & Iida, S. Isolation of a Suppressor-mutator/Enhancer-like transposable element, Tpn1, from Japanese morning glory bearing variegated flowers. Plant Cell 6, 375-383 (1994).
    • (1994) Plant Cell , vol.6 , pp. 375-383
    • Inagaki, Y.1    Hisatomi, Y.2    Suzuki, T.3    Kasahara, K.4    Iida, S.5
  • 7
    • 60849094371 scopus 로고    scopus 로고
    • Identification of r mutations conferring white flowers in the Japanese morning glory (Ipomoea nil)
    • Hoshino, A., Park, K. I. & Iida, S. Identification of r mutations conferring white flowers in the Japanese morning glory (Ipomoea nil). J. Plant Res. 122, 215-222 (2009).
    • (2009) J. Plant Res. , vol.122 , pp. 215-222
    • Hoshino, A.1    Park, K.I.2    Iida, S.3
  • 8
    • 84898463114 scopus 로고    scopus 로고
    • A chalcone isomerase-like protein enhances flavonoid production and flower pigmentation
    • Morita, Y. et al. A chalcone isomerase-like protein enhances flavonoid production and flower pigmentation. Plant J. 78, 294-304 (2014).
    • (2014) Plant J. , vol.78 , pp. 294-304
    • Morita, Y.1
  • 9
    • 33750916729 scopus 로고    scopus 로고
    • The FEATHERED gene is required for polarity establishment in lateral organs especially flowers of the Japanese morning glory (Ipomoea nil)
    • Iwasaki, M. & Nitasaka, E. The FEATHERED gene is required for polarity establishment in lateral organs especially flowers of the Japanese morning glory (Ipomoea nil). Plant Mol. Biol. 62, 913-925 (2006).
    • (2006) Plant Mol. Biol. , vol.62 , pp. 913-925
    • Iwasaki, M.1    Nitasaka, E.2
  • 10
    • 0345393090 scopus 로고    scopus 로고
    • Insertion of an En/Spm-related transposable element into a floral homeotic gene DUPLICATED causes a double flower phenotype in the Japanese morning glory
    • Nitasaka, E. Insertion of an En/Spm-related transposable element into a floral homeotic gene DUPLICATED causes a double flower phenotype in the Japanese morning glory. Plant J. 36, 522-531 (2003).
    • (2003) Plant J. , vol.36 , pp. 522-531
    • Nitasaka, E.1
  • 11
    • 85157961642 scopus 로고    scopus 로고
    • The hAT and CACTA superfamilies of plant transposons
    • (eds Craig, N. L., Craigie, R., Gellert, M. & Lambowitz, A. M.) (ASM Press)
    • Kunze, R. & Weil, C. F. The hAT and CACTA superfamilies of plant transposons. in Mobile DNA II (eds Craig, N. L., Craigie, R., Gellert, M. & Lambowitz, A. M.) 565-610 (ASM Press, 2002).
    • (2002) Mobile DNA II , pp. 565-610
    • Kunze, R.1    Weil, C.F.2
  • 12
    • 4344561525 scopus 로고    scopus 로고
    • Characterization of Tpn1 family in the Japanese morning glory: En/Spm-related transposable elements capturing host genes
    • Kawasaki, S. & Nitasaka, E. Characterization of Tpn1 family in the Japanese morning glory: En/Spm-related transposable elements capturing host genes. Plant Cell Physiol. 45, 933-944 (2004).
    • (2004) Plant Cell Physiol. , vol.45 , pp. 933-944
    • Kawasaki, S.1    Nitasaka, E.2
  • 13
    • 84939472671 scopus 로고    scopus 로고
    • Spontaneous mutations of the UDP-glucose:flavonoid 3-O-glucosyltransferase gene confers pale- and dull-colored flowers in the Japanese and common morning glories
    • Morita, Y., Ishiguro, K., Tanaka, Y., Iida, S. & Hoshino, A. Spontaneous mutations of the UDP-glucose:flavonoid 3-O-glucosyltransferase gene confers pale- and dull-colored flowers in the Japanese and common morning glories. Planta 242, 575-587 (2015).
    • (2015) Planta , vol.242 , pp. 575-587
    • Morita, Y.1    Ishiguro, K.2    Tanaka, Y.3    Iida, S.4    Hoshino, A.5
  • 14
    • 0032965956 scopus 로고    scopus 로고
    • Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpn1 in the Japanese morning glory
    • Takahashi, S., Inagaki, Y., Satoh, H., Hoshino, A. & Iida, S. Capture of a genomic HMG domain sequence by the En/Spm-related transposable element Tpn1 in the Japanese morning glory. Mol. Gen. Genet. 261, 447-451 (1999).
    • (1999) Mol. Gen. Genet. , vol.261 , pp. 447-451
    • Takahashi, S.1    Inagaki, Y.2    Satoh, H.3    Hoshino, A.4    Iida, S.5
  • 15
    • 0345044623 scopus 로고
    • Studies on Pharbitis nil Chois. II Chromosome number
    • Yasui, K. Studies on Pharbitis nil Chois. II Chromosome number. Bot. Mag. Tokyo 42, 480-485 (1928).
    • (1928) Bot. Mag. Tokyo , vol.42 , pp. 480-485
    • Yasui, K.1
  • 16
  • 17
    • 84858693964 scopus 로고    scopus 로고
    • Development of EST-SSR markers of Ipomoea nil
    • Ly, T. et al. Development of EST-SSR markers of Ipomoea nil. Breed. Sci. 62, 99-104 (2012).
    • (2012) Breed. Sci. , vol.62 , pp. 99-104
    • Ly, T.1
  • 18
    • 84941996767 scopus 로고    scopus 로고
    • De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification
    • Wei, C. et al. De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification. Mol. Genet. Genomics 290, 1873-1884 (2015).
    • (2015) Mol. Genet. Genomics , vol.290 , pp. 1873-1884
    • Wei, C.1
  • 19
    • 84928410357 scopus 로고    scopus 로고
    • Survey of genome sequences in a wild sweet potato, ipomoea trifida (H. B. K.) G. Don
    • Hirakawa, H. et al. Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Res. 22, 171-179 (2015).
    • (2015) DNA Res. , vol.22 , pp. 171-179
    • Hirakawa, H.1
  • 20
    • 84948661005 scopus 로고    scopus 로고
    • The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome
    • Sakai, H. et al. The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome. Sci. Rep. 5, 16780 (2015).
    • (2015) Sci. Rep. , vol.5 , pp. 16780
    • Sakai, H.1
  • 21
    • 84948440327 scopus 로고    scopus 로고
    • Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
    • Van Buren, R. et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527, 508-511 (2015).
    • (2015) Nature , vol.527 , pp. 508-511
    • Van Buren, R.1
  • 22
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012).
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1
  • 23
    • 54449098752 scopus 로고    scopus 로고
    • Rapid SNP discovery and genetic mapping using sequenced RAD markers
    • Baird, N. A. et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376 (2008).
    • (2008) PLoS ONE , vol.3 , pp. e3376
    • Baird, N.A.1
  • 24
    • 84884299558 scopus 로고    scopus 로고
    • Stacks: Building and genotyping loci de novo from short-read sequences
    • Catchen, J. M. et al. Stacks: building and genotyping loci de novo from short-read sequences. G3 1, 171-182 (2011).
    • (2011) G3 , vol.1 , pp. 171-182
    • Catchen, J.M.1
  • 25
    • 84883757684 scopus 로고    scopus 로고
    • The first 50 plant genomes
    • Michael, T. P. & Jackson, S. The first 50 plant genomes. Plant Genome 6, 1-7 (2013).
    • (2013) Plant Genome , vol.6 , pp. 1-7
    • Michael, T.P.1    Jackson, S.2
  • 26
    • 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
  • 27
    • 84940907209 scopus 로고    scopus 로고
    • BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs
    • Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212 (2015).
    • (2015) Bioinformatics , vol.31 , pp. 3210-3212
    • Simão, F.A.1    Waterhouse, R.M.2    Ioannidis, P.3    Kriventseva, E.V.4    Zdobnov, E.M.5
  • 28
    • 0025783786 scopus 로고
    • The transposable element Tam1 from Antirrhinum majus shows structural homology to the maize transposon En/Spm and has no sequence specificity of insertion
    • Nacken, W. F., Piotrowiak, R., Saedler, H. & Sommer, H. The transposable element Tam1 from Antirrhinum majus shows structural homology to the maize transposon En/Spm and has no sequence specificity of insertion. Mol. Gen. Genet. 228, 201-208 (1991).
    • (1991) Mol. Gen. Genet. , vol.228 , pp. 201-208
    • Nacken, W.F.1    Piotrowiak, R.2    Saedler, H.3    Sommer, H.4
  • 29
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, ii215-ii225 (2003).
    • (2003) Bioinformatics , vol.19 , pp. ii215-ii225
    • Stanke, M.1    Waack, S.2
  • 30
    • 0343833154 scopus 로고
    • Linkage groups of the Japanese morning glory
    • Imai, Y. Linkage groups of the Japanese morning glory. Genetics 14, 223-255 (1929).
    • (1929) Genetics , vol.14 , pp. 223-255
    • Imai, Y.1
  • 31
    • 0001629916 scopus 로고
    • On the mutable genes of Pharbitis, with special reference to their bearing on the mechanism of bud-variation
    • Imai, Y. On the mutable genes of Pharbitis, with special reference to their bearing on the mechanism of bud-variation. J. Coll. Agr. Tokyo Imp. Univ 12, 479-523 (1934).
    • (1934) J. Coll. Agr. Tokyo Imp. Univ , vol.12 , pp. 479-523
    • Imai, Y.1
  • 32
    • 0344099562 scopus 로고    scopus 로고
    • A dwarf mutant strain of Pharbitis nil, Uzukobito (kobito), has defective brassinosteroid biosynthesis
    • Suzuki, Y. et al. A dwarf mutant strain of Pharbitis nil, Uzukobito (kobito), has defective brassinosteroid biosynthesis. Plant J. 36, 401-410 (2003).
    • (2003) Plant J. , vol.36 , pp. 401-410
    • Suzuki, Y.1
  • 33
    • 0032145507 scopus 로고    scopus 로고
    • The ROTUNDIFOLIA3 gene of Arabidopsis thaliana encodes a new member of the cytochrome P-450 family that is required for the regulated polar elongation of leaf cells
    • Kim, G. T., Tsukaya, H. & Uchimiya, H. The ROTUNDIFOLIA3 gene of Arabidopsis thaliana encodes a new member of the cytochrome P-450 family that is required for the regulated polar elongation of leaf cells. Genes Dev. 12, 2381-2391 (1998).
    • (1998) Genes Dev. , vol.12 , pp. 2381-2391
    • Kim, G.T.1    Tsukaya, H.2    Uchimiya, H.3
  • 34
    • 33845751984 scopus 로고    scopus 로고
    • C-23 hydroxylation by Arabidopsis CYP90C1 and CYP90D1 reveals a novel shortcut in brassinosteroid biosynthesis
    • Ohnishi, T. et al. C-23 hydroxylation by Arabidopsis CYP90C1 and CYP90D1 reveals a novel shortcut in brassinosteroid biosynthesis. Plant Cell 18, 3275-3288 (2006).
    • (2006) Plant Cell , vol.18 , pp. 3275-3288
    • Ohnishi, T.1
  • 35
    • 33846101405 scopus 로고    scopus 로고
    • The TIGR rice genome annotation resource: Improvements and new features
    • Ouyang, S. et al. The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 35, D883-D887 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. D883-D887
    • Ouyang, S.1
  • 36
    • 34848886909 scopus 로고    scopus 로고
    • The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    • Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-467 (2007).
    • (2007) Nature , vol.449 , pp. 463-467
    • Jaillon, O.1
  • 37
    • 84886052631 scopus 로고    scopus 로고
    • Draft genome of the kiwifruit Actinidia chinensis
    • Huang, S. et al. Draft genome of the kiwifruit Actinidia chinensis. Nat. Commun. 4, 2640 (2013).
    • (2013) Nat. Commun. , vol.4 , pp. 2640
    • Huang, S.1
  • 38
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • Tomato sequencing consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635-641 (2012).
    • (2012) Nature , vol.485 , pp. 635-641
  • 39
    • 79960422847 scopus 로고    scopus 로고
    • Genome sequence and analysis of the tuber crop potato
    • Sequencing Consortium, T. P. G. Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195 (2011).
    • (2011) Nature , vol.475 , pp. 189-195
    • Sequencing Consortium, T.P.G.1
  • 40
    • 84895880054 scopus 로고    scopus 로고
    • Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species
    • Kim, S. et al. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat. Genet. 46, 270-278 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 270-278
    • Kim, S.1
  • 41
    • 0141519279 scopus 로고    scopus 로고
    • Ortho MCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C. J. & Roos, D. S. Ortho MCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 42
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 43
    • 84901305512 scopus 로고    scopus 로고
    • BEAST 2: A software platform for Bayesian evolutionary analysis
    • Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, 1-6 (2014).
    • (2014) PLoS Comput. Biol. , vol.10 , pp. 1-6
    • Bouckaert, R.1
  • 44
    • 84926663837 scopus 로고    scopus 로고
    • Tree of life reveals clock-like speciation and diversification
    • Hedges, S. B., Marin, J., Suleski, M., Paymer, M. & Kumar, S. Tree of life reveals clock-like speciation and diversification. Mol. Biol. Evol. 32, 832-845 (2015).
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 832-845
    • Hedges, S.B.1    Marin, J.2    Suleski, M.3    Paymer, M.4    Kumar, S.5
  • 45
    • 84963548310 scopus 로고    scopus 로고
    • Long-read sequence assembly of the gorilla genome
    • Gordon, D. et al. Long-read sequence assembly of the gorilla genome. Science 352, aae0344 (2016).
    • (2016) Science , vol.352 , pp. aae0344
    • Gordon, D.1
  • 46
    • 84964854635 scopus 로고    scopus 로고
    • Chromosomal-level assembly of the asian seabass genome using long sequence reads and multi-layered scaffolding
    • Vij, S. et al. Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genet. 12, e1005954 (2016).
    • (2016) PLoS Genet. , vol.12 , pp. e1005954
    • Vij, S.1
  • 47
    • 0344961281 scopus 로고    scopus 로고
    • A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinosteroid receptor
    • Chono, M. et al. A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinosteroid receptor. Plant Physiol. 133, 1209-1219 (2003).
    • (2003) Plant Physiol. , vol.133 , pp. 1209-1219
    • Chono, M.1
  • 48
    • 84945269965 scopus 로고    scopus 로고
    • High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species
    • Sakaguchi, S. et al. High-throughput linkage mapping of Australian white cypress pine (Callitris glaucophylla) and map transferability to related species. Tree Genet. Genomes 11, 121 (2015).
    • (2015) Tree Genet. Genomes , vol.11 , pp. 121
    • Sakaguchi, S.1
  • 49
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10 (2011).
    • (2011) EMBnet J. , vol.17 , pp. 10
    • Martin, M.1
  • 50
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563-569 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 563-569
    • Chin, C.-S.1
  • 51
    • 67649884743 scopus 로고    scopus 로고
    • Fast 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    Durbin, R.2
  • 52
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 53
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
    • (2004) Genome Biol. , vol.5 , pp. R12
    • Kurtz, S.1
  • 55
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with pacific biosciences RS long-read sequencing technology
    • English, A. C. et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS ONE 7, e47768 (2012).
    • (2012) PLoS ONE , vol.7 , pp. e47768
    • English, A.C.1
  • 56
    • 34547190185 scopus 로고    scopus 로고
    • One map: Software for genetic mapping in outcrossing species
    • Margarido, G. R. A., Souza, A. P. & Garcia, A. A. F. One Map: software for genetic mapping in outcrossing species. Hereditas 144, 78-79 (2007).
    • (2007) Hereditas , vol.144 , pp. 78-79
    • Margarido, G.R.A.1    Souza, A.P.2    Garcia, A.A.F.3
  • 57
    • 34548451177 scopus 로고    scopus 로고
    • Genetic mapping in the presence of genotyping errors
    • Cartwright, D. A., Troggio, M., Velasco, R. & Gutin, A. Genetic mapping in the presence of genotyping errors. Genetics 176, 2521-2527 (2007).
    • (2007) Genetics , vol.176 , pp. 2521-2527
    • Cartwright, D.A.1    Troggio, M.2    Velasco, R.3    Gutin, A.4
  • 58
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 59
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 60
    • 84876996918 scopus 로고    scopus 로고
    • Top hat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. Top Hat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1
  • 61
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 62
    • 84890037468 scopus 로고    scopus 로고
    • Infernal 1.1: 100-fold faster RNA homology searches
    • Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933-2935 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2933-2935
    • Nawrocki, E.P.1    Eddy, S.R.2
  • 63
    • 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, i351-i358 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 351-358
    • Price, A.L.1    Jones, N.C.2    Pevzner, P.A.3
  • 65
    • 84899518211 scopus 로고    scopus 로고
    • Inter pro scan 5: Genome-scale protein function classification
    • Jones, P. et al. Inter Pro Scan 5: genome-scale protein function classification. Bioinformatics 30, 1236-1240 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 1236-1240
    • Jones, P.1
  • 66
    • 77954299992 scopus 로고    scopus 로고
    • AgriGO: A GO analysis toolkit for the agricultural community
    • Du, Z., Zhou, X., Ling, Y., Zhang, Z. & Su, Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38, w64-w70 2010:
    • (2010) Nucleic Acids Res. , vol.38 , pp. w64-w70
    • Du, Z.1    Zhou, X.2    Ling, Y.3    Zhang, Z.4    Su, Z.5
  • 67
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-3066 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 68
    • 67650757433 scopus 로고    scopus 로고
    • TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 69
    • 84860137835 scopus 로고    scopus 로고
    • MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity
    • Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. e49
    • Wang, Y.1
  • 70
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.