메뉴 건너뛰기




Volumn 28, Issue 11, 2016, Pages 2700-2714

Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

(20)  Hirsch, Candice N a   Hirsch, Cory D a   Brohammer, Alex B a   Bowman, Megan J b   Soifer, Ilya c   Barad, Omer d   Shem Tov, Doron d   Baruch, Kobi d   Lu, Fei e   Hernandez, Alvaro G f   Fields, Christopher J f   Wright, Chris L f   Koehler, Klaus g   Springer, Nathan M a   Buckler, Edward e,h   Buell, C Robin b,i   de Leon, Natalia i,j   Kaeppler, Shawn M i,j   Childs, Kevin L b   Mikel, Mark A f  


Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 85006263051     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.16.00353     Document Type: Article
Times cited : (143)

References (90)
  • 4
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq-a Python framework to work with high-throughput sequencing data
    • Anders, S., Pyl, P.T., and Huber, W. (2015). HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166-169.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 6
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 7
    • 75849136053 scopus 로고    scopus 로고
    • Allelic genome structural variations in maize detected by array comparative genome hybridization
    • Beló, A., Beatty, M.K., Hondred, D., Fengler, K.A., Li, B., and Rafalski, A. (2010). Allelic genome structural variations in maize detected by array comparative genome hybridization. Theor. Appl. Genet. 120: 355-367.
    • (2010) Theor. Appl. Genet. , vol.120 , pp. 355-367
    • Beló, A.1    Beatty, M.K.2    Hondred, D.3    Fengler, K.A.4    Li, B.5    Rafalski, A.6
  • 8
    • 0142060823 scopus 로고    scopus 로고
    • In search of the molecular basis of heterosis
    • Birchler, J.A., Auger, D.L., and Riddle, N.C. (2003). In search of the molecular basis of heterosis. Plant Cell 15: 2236-2239.
    • (2003) Plant Cell , vol.15 , pp. 2236-2239
    • Birchler, J.A.1    Auger, D.L.2    Riddle, N.C.3
  • 11
    • 20344407697 scopus 로고    scopus 로고
    • Evolution of DNA sequence nonhomologies among maize inbreds
    • Brunner, S., Fengler, K., Morgante, M., Tingey, S., and Rafalski, A. (2005). Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17: 343-360.
    • (2005) Plant Cell , vol.17 , pp. 343-360
    • Brunner, S.1    Fengler, K.2    Morgante, M.3    Tingey, S.4    Rafalski, A.5
  • 13
    • 84893466287 scopus 로고    scopus 로고
    • MAKER-P: A tool kit for the rapid creation, management, and quality control of plant genome annotations
    • Campbell, M.S., et al. (2014b). MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 164: 513-524.
    • (2014) Plant Physiol. , vol.164 , pp. 513-524
    • Campbell, M.S.1
  • 14
    • 80053384429 scopus 로고    scopus 로고
    • Whole-genome sequencing of multiple Arabidopsis thaliana populations
    • Cao, J., et al. (2011). Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43: 956-963.
    • (2011) Nat. Genet. , vol.43 , pp. 956-963
    • Cao, J.1
  • 15
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • Chen, F., Mackey, A.J., Vermunt, J.K., and Roos, D.S. (2007). Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2: e383.
    • (2007) PLoS One , vol.2
    • Chen, F.1    Mackey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 16
    • 84863007735 scopus 로고    scopus 로고
    • Maize HapMap2 identifies extant variation from a genome in flux
    • Chia, J.M., et al. (2012). Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44: 803-807.
    • (2012) Nat. Genet. , vol.44 , pp. 803-807
    • Chia, J.M.1
  • 17
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
    • Cingolani, P., Platts, A., Wang, L., Coon, M., Nguyen, T., Wang, L., Land, S.J., Lu, X., and Ruden, D.M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6: 80-92.
    • (2012) Fly (Austin) , vol.6 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    Wang, L.3    Coon, M.4    Nguyen, T.5    Wang, L.6    Land, S.J.7    Lu, X.8    Ruden, D.M.9
  • 18
    • 84870253624 scopus 로고    scopus 로고
    • Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean
    • Cook, D.E., et al. (2012). Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338: 1206-1209.
    • (2012) Science , vol.338 , pp. 1206-1209
    • Cook, D.E.1
  • 19
    • 0347432399 scopus 로고    scopus 로고
    • PlantGDB, plant genome database and analysis tools
    • Dong, Q., Schlueter, S.D., and Brendel, V. (2004). PlantGDB, plant genome database and analysis tools. Nucleic Acids Res. 32: D354-D359.
    • (2004) Nucleic Acids Res. , vol.32 , pp. D354-D359
    • Dong, Q.1    Schlueter, S.D.2    Brendel, V.3
  • 20
    • 77954299992 scopus 로고    scopus 로고
    • AgriGO: A GO analysis toolkit for the agricultural community
    • Du, Z., Zhou, X., Ling, Y., Zhang, Z., and Su, Z. (2010). agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38: W64-W70.
    • (2010) Nucleic Acids Res. , vol.38 , pp. W64-W70
    • Du, Z.1    Zhou, X.2    Ling, Y.3    Zhang, Z.4    Su, Z.5
  • 21
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • Eddy, S.R. (2011). Accelerated Profile HMM Searches. PLOS Comput. Biol. 7: e1002195.
    • (2011) PLOS Comput. Biol. , vol.7
    • Eddy, S.R.1
  • 23
    • 62549098614 scopus 로고    scopus 로고
    • Quantitative measures for the management and comparison of annotated genomes
    • Eilbeck, K., Moore, B., Holt, C., and Yandell, M. (2009). Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 10: 67.
    • (2009) BMC Bioinformatics , vol.10 , pp. 67
    • Eilbeck, K.1    Moore, B.2    Holt, C.3    Yandell, M.4
  • 24
    • 84891782659 scopus 로고    scopus 로고
    • Pfam: The protein families database
    • Finn, R.D., et al. (2014). Pfam: the protein families database. Nucleic Acids Res. 42: D222-D230.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D222-D230
    • Finn, R.D.1
  • 25
    • 0037047037 scopus 로고    scopus 로고
    • Intraspecific violation of genetic colinearity and its implications in maize
    • Fu, H., and Dooner, H.K. (2002). Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. USA 99: 9573-9578.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 9573-9578
    • Fu, H.1    Dooner, H.K.2
  • 26
    • 77949890871 scopus 로고    scopus 로고
    • Gene amplification confers glyphosate resistance in Amaranthus palmeri
    • Gaines, T.A., et al. (2010). Gene amplification confers glyphosate resistance in Amaranthus palmeri. Proc. Natl. Acad. Sci. USA 107: 1029-1034.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 1029-1034
    • Gaines, T.A.1
  • 27
    • 80053132716 scopus 로고    scopus 로고
    • Multiple reference genomes and transcriptomes for Arabidopsis thaliana
    • Gan, X., et al. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419-423.
    • (2011) Nature , vol.477 , pp. 419-423
    • Gan, X.1
  • 28
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R.C., et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5: R80.
    • (2004) Genome Biol. , vol.5 , pp. R80
    • Gentleman, R.C.1
  • 31
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr, M.G., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29: 644-652.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 644-652
    • Grabherr, M.G.1
  • 33
    • 84960361852 scopus 로고    scopus 로고
    • Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum
    • Hardigan, M.A., et al. (2016). Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. Plant Cell 28: 388-405.
    • (2016) Plant Cell , vol.28 , pp. 388-405
    • Hardigan, M.A.1
  • 34
    • 84928410357 scopus 로고    scopus 로고
    • Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H
    • Hirakawa, H., et al. (2015). Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Res. 22: 171-179.
    • (2015) B. K.) G. Don. DNA Res. , vol.22 , pp. 171-179
    • Hirakawa, H.1
  • 35
    • 84944876337 scopus 로고    scopus 로고
    • Genomic limitations to RNA sequencing expression profiling
    • Hirsch, C.D., Springer, N.M., and Hirsch, C.N. (2015). Genomic limitations to RNA sequencing expression profiling. Plant J. 84: 491-503.
    • (2015) Plant J. , vol.84 , pp. 491-503
    • Hirsch, C.D.1    Springer, N.M.2    Hirsch, C.N.3
  • 36
    • 84896808010 scopus 로고    scopus 로고
    • Insights into the maize pan-genome and pan-transcriptome
    • Hirsch, C.N., et al. (2014). Insights into the maize pan-genome and pan-transcriptome. Plant Cell 26: 121-135.
    • (2014) Plant Cell , vol.26 , pp. 121-135
    • Hirsch, C.N.1
  • 37
    • 76749150030 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the model grass Brachypodium distachyon
    • International Brachypodium Initiative (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
    • (2010) Nature , vol.463 , pp. 763-768
  • 38
    • 84907150192 scopus 로고    scopus 로고
    • The mapbased sequence of the rice genome
    • International Rice Genome Sequencing Project (2005). The mapbased sequence of the rice genome. Nature 436: 793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 39
    • 84885960825 scopus 로고    scopus 로고
    • Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
    • Kawahara, Y., et al. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N. Y.) 6: 4.
    • (2013) Rice (N. Y.) , vol.6 , pp. 4
    • Kawahara, Y.1
  • 40
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and Salzberg, S.L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14: R36.
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 41
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf, I. (2004). Gene finding in novel genomes. BMC Bioinformatics 5: 59.
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 43
    • 78049338441 scopus 로고    scopus 로고
    • Genome-wide patterns of genetic variation among elite maize inbred lines
    • Lai, J., et al. (2010). Genome-wide patterns of genetic variation among elite maize inbred lines. Nat. Genet. 42: 1027-1030.
    • (2010) Nat. Genet. , vol.42 , pp. 1027-1030
    • Lai, J.1
  • 44
    • 84862234802 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools
    • Lamesch, P., et al. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40: D1202-D1210.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D1202-D1210
    • Lamesch, P.1
  • 45
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9: 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 46
    • 84920188663 scopus 로고    scopus 로고
    • Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes
    • Law, M., et al. (2015). Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiol. 167: 25-39.
    • (2015) Plant Physiol. , vol.167 , pp. 25-39
    • Law, M.1
  • 47
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 49
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • Li, L., Stoeckert, C.J., Jr., and Roos, D.S. (2003). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13: 2178-2189.
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 50
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M.I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15: 550.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 51
    • 84928018963 scopus 로고    scopus 로고
    • High-resolution genetic mapping of maize pangenome sequence anchors
    • Lu, F., et al. (2015). High-resolution genetic mapping of maize pangenome sequence anchors. Nat. Commun. 6: 6914.
    • (2015) Nat. Commun. , vol.6 , pp. 6914
    • Lu, F.1
  • 52
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory- efficient short-read de novo assembler
    • Luo, R., et al. (2012). SOAPdenovo2: an empirically improved memory- efficient short-read de novo assembler. Gigascience 1: 18.
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1
  • 53
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: Fast length adjustment of short reads to improve genome assemblies
    • Magoč, T., and Salzberg, S.L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27: 2957-2963.
    • (2011) Bioinformatics , vol.27 , pp. 2957-2963
    • Magoč, T.1    Salzberg, S.L.2
  • 54
    • 84875508685 scopus 로고    scopus 로고
    • Aluminum tolerance in maize is associated with higher MATE1 gene copy number
    • Maron, L.G., et al. (2013). Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc. Natl. Acad. Sci. USA 110: 5241-5246.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 5241-5246
    • Maron, L.G.1
  • 55
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from highthroughput sequencing reads
    • Martin, M. (2011). Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet.journal 17: 10-12.
    • (2011) EMBnet.journal , vol.17 , pp. 10-12
    • Martin, M.1
  • 56
    • 79952483763 scopus 로고    scopus 로고
    • Genetic composition of contemporary U.S commercial dent corn germplasm
    • Mikel, M.A. (2011). Genetic composition of contemporary U.S. commercial dent corn germplasm. Crop Sci. 51: 592-599.
    • (2011) Crop Sci. , vol.51 , pp. 592-599
    • Mikel, M.A.1
  • 57
    • 84891793130 scopus 로고    scopus 로고
    • Gramene 2013: Comparative plant genomics resources
    • Monaco, M.K., et al. (2014). Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. 42: D1193-D1199.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D1193-D1199
    • Monaco, M.K.1
  • 59
    • 0019321718 scopus 로고
    • Rapid isolation of high molecular weight plant DNA
    • Murray, M.G., and Thompson, W.F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8: 4321-4325.
    • (1980) Nucleic Acids Res. , vol.8 , pp. 4321-4325
    • Murray, M.G.1    Thompson, W.F.2
  • 61
    • 33846101405 scopus 로고    scopus 로고
    • The TIGR Rice Genome Annotation Resource: Improvements and new features
    • Ouyang, S., et al. (2007). The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 35: D883-D887.
    • (2007) Nucleic Acids Res. , vol.35 , pp. D883-D887
    • Ouyang, S.1
  • 62
    • 84922538560 scopus 로고    scopus 로고
    • Optimization of crop productivity in tomato using induced mutations in the florigen pathway
    • Park, S.J., Jiang, K., Tal, L., Yichie, Y., Gar, O., Zamir, D., Eshed, Y., and Lippman, Z.B. (2014). Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nat. Genet. 46: 1337-1342.
    • (2014) Nat. Genet. , vol.46 , pp. 1337-1342
    • Park, S.J.1    Jiang, K.2    Tal, L.3    Yichie, Y.4    Gar, O.5    Zamir, D.6    Eshed, Y.7    Lippman, Z.B.8
  • 63
    • 34249848751 scopus 로고    scopus 로고
    • CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes
    • Parra, G., Bradnam, K., and Korf, I. (2007). CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23: 1061-1067.
    • (2007) Bioinformatics , vol.23 , pp. 1061-1067
    • Parra, G.1    Bradnam, K.2    Korf, I.3
  • 64
    • 58449137410 scopus 로고    scopus 로고
    • The Sorghum bicolor genome and the diversification of grasses
    • Paterson, A.H., et al. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
    • (2009) Nature , vol.457 , pp. 551-556
    • Paterson, A.H.1
  • 65
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 66
    • 79961135005 scopus 로고    scopus 로고
    • (Vienna, Austria: R Foundation for Statistical Computing)
    • R Development Core Team (2011). R: A Language and Environment for Statistical Computing. (Vienna, Austria: R Foundation for Statistical Computing).
    • (2011) R: A Language and Environment for Statistical Computing
  • 67
    • 84965187491 scopus 로고    scopus 로고
    • Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica
    • Schatz, M.C., et al. (2014). Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 15: 506.
    • (2014) Genome Biol. , vol.15 , pp. 506
    • Schatz, M.C.1
  • 68
    • 79952744855 scopus 로고    scopus 로고
    • Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
    • Schnable, J.C., Springer, N.M., and Freeling, M. (2011). Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108: 4069-4074.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 4069-4074
    • Schnable, J.C.1    Springer, N.M.2    Freeling, M.3
  • 69
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, and dynamics
    • Schnable, P.S., et al. (2009). The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
    • (2009) Science , vol.326 , pp. 1112-1115
    • Schnable, P.S.1
  • 70
    • 0042307299 scopus 로고    scopus 로고
    • Gene expression of a gene family in maize based on noncollinear haplotypes
    • Song, R., and Messing, J. (2003). Gene expression of a gene family in maize based on noncollinear haplotypes. Proc. Natl. Acad. Sci. USA 100: 9055-9060.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9055-9060
    • Song, R.1    Messing, J.2
  • 71
    • 33847701258 scopus 로고    scopus 로고
    • Allelic variation and heterosis in maize: How do two halves make more than a whole?
    • Springer, N.M., and Stupar, R.M. (2007). Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res. 17: 264-275.
    • (2007) Genome Res. , vol.17 , pp. 264-275
    • Springer, N.M.1    Stupar, R.M.2
  • 72
    • 73649121258 scopus 로고    scopus 로고
    • Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content
    • Springer, N.M., et al. (2009). Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 5: e1000734.
    • (2009) PLoS Genet. , vol.5
    • Springer, N.M.1
  • 73
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke, M., and Waack, S. (2003). Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 (suppl. 2): ii215-ii225.
    • (2003) Bioinformatics , vol.19 , pp. ii215-ii225
    • Stanke, M.1    Waack, S.2
  • 76
    • 34347388470 scopus 로고    scopus 로고
    • UniRef: Comprehensive and non-redundant UniProt reference clusters
    • Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R., and Wu, C.H. (2007). UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23: 1282-1288.
    • (2007) Bioinformatics , vol.23 , pp. 1282-1288
    • Suzek, B.E.1    Huang, H.2    McGarvey, P.3    Mazumder, R.4    Wu, C.H.5
  • 77
    • 78549273825 scopus 로고    scopus 로고
    • Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
    • Swanson-Wagner, R.A., Eichten, S.R., Kumari, S., Tiffin, P., Stein, J.C., Ware, D., and Springer, N.M. (2010). Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 20: 1689-1699.
    • (2010) Genome Res. , vol.20 , pp. 1689-1699
    • Swanson-Wagner, R.A.1    Eichten, S.R.2    Kumari, S.3    Tiffin, P.4    Stein, J.C.5    Ware, D.6    Springer, N.M.7
  • 79
    • 0033012987 scopus 로고    scopus 로고
    • Background of U.S hybrid corn
    • Troyer, A.F. (1999). Background of U.S. hybrid corn. Crop Sci. 39: 601-626.
    • (1999) Crop Sci. , vol.39 , pp. 601-626
    • Troyer, A.F.1
  • 80
    • 33644988504 scopus 로고    scopus 로고
    • Adaptedness and heterosis in corn and mule hybrids
    • Troyer, A.F. (2006). Adaptedness and heterosis in corn and mule hybrids. Crop Sci. 46: 528-543.
    • (2006) Crop Sci. , vol.46 , pp. 528-543
    • Troyer, A.F.1
  • 81
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the Universal Protein Resource (UniProt)
    • UniProt Consortium (2014). Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 42: D191-D198.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D191-D198
  • 82
    • 84938287602 scopus 로고    scopus 로고
    • Copy number variation at the GL7 locus contributes to grain size diversity in rice
    • Wang, Y., et al. (2015). Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat. Genet. 47: 944-948.
    • (2015) Nat. Genet. , vol.47 , pp. 944-948
    • Wang, Y.1
  • 83
    • 84988715280 scopus 로고    scopus 로고
    • Expression of an osmotin-like protein from Solanum nigrum confers drought tolerance in transgenic soybean
    • Weber, R.L., et al. (2014). Expression of an osmotin-like protein from Solanum nigrum confers drought tolerance in transgenic soybean. BMC Plant Biol. 14: 343.
    • (2014) BMC Plant Biol. , vol.14 , pp. 343
    • Weber, R.L.1
  • 84
    • 68249140383 scopus 로고    scopus 로고
    • The 1001 genomes project for Arabidopsis thaliana
    • Weigel, D., and Mott, R. (2009). The 1001 genomes project for Arabidopsis thaliana. Genome Biol. 10: 107.
    • (2009) Genome Biol. , vol.10 , pp. 107
    • Weigel, D.1    Mott, R.2
  • 85
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: A genomic mapping and alignment program for mRNA and EST sequences
    • Wu, T.D., and Watanabe, C.K. (2005). GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859-1875.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 86
    • 84871457328 scopus 로고    scopus 로고
    • FastUniq: A fast de novo duplicates removal tool for paired short reads
    • Xu, H., Luo, X., Qian, J., Pang, X., Song, J., Qian, G., Chen, J., and Chen, S. (2012). FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS One 7: e52249.
    • (2012) PLoS One , vol.7
    • Xu, H.1    Luo, X.2    Qian, J.3    Pang, X.4    Song, J.5    Qian, G.6    Chen, J.7    Chen, S.8
  • 87
    • 84859898660 scopus 로고    scopus 로고
    • A beginner’s guide to eukaryotic genome annotation
    • Yandell, M., and Ence, D. (2012). A beginner’s guide to eukaryotic genome annotation. Nat. Rev. Genet. 13: 329-342.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 329-342
    • Yandell, M.1    Ence, D.2
  • 89
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan-an integration platform for the signature-recognition methods in InterPro
    • Zdobnov, E.M., and Apweiler, R. (2001). InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
    • (2001) Bioinformatics , vol.17 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 90
    • 84897373336 scopus 로고    scopus 로고
    • CrossMap: A versatile tool for coordinate conversion between genome assemblies
    • Zhao, H., Sun, Z., Wang, J., Huang, H., Kocher, J.P., and Wang, L. (2014). CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30: 1006-1007.
    • (2014) Bioinformatics , vol.30 , pp. 1006-1007
    • Zhao, H.1    Sun, Z.2    Wang, J.3    Huang, H.4    Kocher, J.P.5    Wang, L.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.