메뉴 건너뛰기




Volumn 75, Issue 1, 2013, Pages 146-156

Whole-exome targeted sequencing of the uncharacterized pine genome

Author keywords

conifers; genome complexity reduction; genome de novo assembly; Pinus elliottii; Pinus taeda; sequence capture; target enrichment; technical advance

Indexed keywords

COMPLEXITY REDUCTION; CONIFERS; DE NOVO ASSEMBLIES; PINUS ELLIOTTII; PINUS TAEDA; SEQUENCE CAPTURES; TECHNICAL ADVANCES;

EID: 84879233990     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12193     Document Type: Article
Times cited : (107)

References (32)
  • 1
    • 35748951614 scopus 로고    scopus 로고
    • Direct selection of human genomic loci by microarray hybridization
    • Albert, T.J., Molla, M.N., Muzny, D.M., et al. (2007) Direct selection of human genomic loci by microarray hybridization. Nat. Methods, 4, 903-905.
    • (2007) Nat. Methods , vol.4 , pp. 903-905
    • Albert, T.J.1    Molla, M.N.2    Muzny, D.M.3
  • 2
    • 84859178440 scopus 로고    scopus 로고
    • De novo genome assembly: What every biologist should know
    • Baker, M., (2012) De novo genome assembly: what every biologist should know. Nat. Methods, 9, 333-337.
    • (2012) Nat. Methods , vol.9 , pp. 333-337
    • Baker, M.1
  • 3
    • 79953325544 scopus 로고    scopus 로고
    • Efficient and cost effective population resequencing by pooling and in-solution hybridization
    • Bansal, V., Tewhey, R., Leproust, E.M., and, Schork, N.J., (2011) Efficient and cost effective population resequencing by pooling and in-solution hybridization. PLoS ONE, 6, e18353.
    • (2011) PLoS ONE , vol.6
    • Bansal, V.1    Tewhey, R.2    Leproust, E.M.3    Schork, N.J.4
  • 4
    • 24644437451 scopus 로고    scopus 로고
    • Reduced representation sequencing: A success in maize and a promise for other plant genomes
    • Barbazuk, W.B., Bedell, J.A., and, Rabinowicz, P.D., (2005) Reduced representation sequencing: a success in maize and a promise for other plant genomes. BioEssays, 27, 839-848.
    • (2005) BioEssays , vol.27 , pp. 839-848
    • Barbazuk, W.B.1    Bedell, J.A.2    Rabinowicz, P.D.3
  • 5
    • 79958151996 scopus 로고    scopus 로고
    • BamTools: A C++ API and toolkit for analyzing and managing BAM files
    • Barnett, D., Garrison, E., Quinlan, A., Stromberg, M., and, Marth, G., (2011) BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27, 1691-1692.
    • (2011) Bioinformatics , vol.27 , pp. 1691-1692
    • Barnett, D.1    Garrison, E.2    Quinlan, A.3    Stromberg, M.4    Marth, G.5
  • 6
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1    Balasubramanian, S.2    Swerdlow, H.P.3
  • 8
    • 84863597153 scopus 로고    scopus 로고
    • Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant
    • Bundock, P.C., Casu, R.E., and, Henry, R.J., (2012) Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant. Plant Biotechnol. J. 10, 657-667.
    • (2012) Plant Biotechnol. J. , vol.10 , pp. 657-667
    • Bundock, P.C.1    Casu, R.E.2    Henry, R.J.3
  • 9
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., and, Robles, M., (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5    Robles, M.6
  • 11
    • 78349251346 scopus 로고    scopus 로고
    • Combining target enrichment with barcode multiplexing for high throughput SNP discovery
    • Cummings, N., King, R., Rickers, A., Kaspi, A., Lunke, S., Haviv, I., and, Jowett, J.B., (2010) Combining target enrichment with barcode multiplexing for high throughput SNP discovery. BMC Genomics, 11, 641.
    • (2010) BMC Genomics , vol.11 , pp. 641
    • Cummings, N.1    King, R.2    Rickers, A.3    Kaspi, A.4    Lunke, S.5    Haviv, I.6    Jowett, J.B.7
  • 12
    • 77952865614 scopus 로고    scopus 로고
    • Repeat subtraction-mediated sequence capture from a complex genome
    • Fu, Y., Springer, N.M., Gerhardt, D.J., et al,. (2010) Repeat subtraction-mediated sequence capture from a complex genome. Plant J. 62, 898-909.
    • (2010) Plant J. , vol.62 , pp. 898-909
    • Fu, Y.1    Springer, N.M.2    Gerhardt, D.J.3
  • 14
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke, A., Melnikov, A., Maguire, J., et al,. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182-189.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 182-189
    • Gnirke, A.1    Melnikov, A.2    Maguire, J.3
  • 15
    • 33750962013 scopus 로고    scopus 로고
    • Intron size, abundance, and distribution within untranslated regions of genes
    • Hong, X., Scofield, D.G., and, Lynch, M., (2006) Intron size, abundance, and distribution within untranslated regions of genes. Mol. Biol. Evol. 23, 2392-2404.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 2392-2404
    • Hong, X.1    Scofield, D.G.2    Lynch, M.3
  • 16
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang, X., and, Madan, A., (1999) CAP3: A DNA sequence assembly program. Genome Res. 9, 868-877.
    • (1999) Genome Res. , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 17
    • 17444388556 scopus 로고    scopus 로고
    • Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine
    • Kayihan, G.C., Huber, D.A., Morse, A.M., White, T.L., and, Davis, J.M., (2005) Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theor. Appl. Genet. 110, 948-958.
    • (2005) Theor. Appl. Genet. , vol.110 , pp. 948-958
    • Kayihan, G.C.1    Huber, D.A.2    Morse, A.M.3    White, T.L.4    Davis, J.M.5
  • 19
    • 0035198385 scopus 로고    scopus 로고
    • Nuclear DNA C-values complete familial representation in gymnosperms
    • Leitch, I.J., Hanson, L., Winfield, M., Parker, J., and, Bennett, M.D., (2001) Nuclear DNA C-values complete familial representation in gymnosperms. Ann. Bot. 88, 843-849.
    • (2001) Ann. Bot. , vol.88 , pp. 843-849
    • Leitch, I.J.1    Hanson, L.2    Winfield, M.3    Parker, J.4    Bennett, M.D.5
  • 20
    • 84865266483 scopus 로고    scopus 로고
    • Anchored hybrid enrichment for massively high-throughput phylogenomics
    • Lemmon, A.R., Emme, S., and, Lemmon, E.M., (2012) Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 61, 727-744.
    • (2012) Syst. Biol. , vol.61 , pp. 727-744
    • Lemmon, A.R.1    Emme, S.2    Lemmon, E.M.3
  • 21
    • 84887212567 scopus 로고    scopus 로고
    • Evolution of genome size and complexity in Pinus
    • Morse, A.M., Peterson, D.G., Islam-Faridi, M.N., et al. (2009) Evolution of genome size and complexity in Pinus. PLoS ONE, 4, e4332.
    • (2009) PLoS ONE , vol.4
    • Morse, A.M.1    Peterson, D.G.2    Islam-Faridi, M.N.3
  • 23
    • 84862214789 scopus 로고    scopus 로고
    • Creation and application of immortalized bait libraries for targeted enrichment and next-generation sequencing
    • Querfurth, R., Fischer, A., Schweiger, M.R., Lehrach, H., and, Mertes, F., (2012) Creation and application of immortalized bait libraries for targeted enrichment and next-generation sequencing. Biotechniques, 52, 375-380.
    • (2012) Biotechniques , vol.52 , pp. 375-380
    • Querfurth, R.1    Fischer, A.2    Schweiger, M.R.3    Lehrach, H.4    Mertes, F.5
  • 26
    • 80052831072 scopus 로고    scopus 로고
    • Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome
    • Saintenac, C., Jiang, D., and, Akhunov, E.D., (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol. 12, R88.
    • (2011) Genome Biol. , vol.12
    • Saintenac, C.1    Jiang, D.2    Akhunov, E.D.3
  • 27
    • 77956279237 scopus 로고    scopus 로고
    • Assembly of large genomes using second-generation sequencing
    • Schatz, M.C., Delcher, A.L., and, Salzberg, S.L., (2010) Assembly of large genomes using second-generation sequencing. Genome Res. 20, 1165-1173.
    • (2010) Genome Res. , vol.20 , pp. 1165-1173
    • Schatz, M.C.1    Delcher, A.L.2    Salzberg, S.L.3
  • 28
    • 0027137093 scopus 로고
    • Genome size and environmental factors in the genus Pinus
    • Wakamiya, I., Newton, R.J., Johnston, J.S., and, Price, H.J., (1993) Genome size and environmental factors in the genus Pinus. Am. J. Bot. 80, 1235-1241.
    • (1993) Am. J. Bot. , vol.80 , pp. 1235-1241
    • Wakamiya, I.1    Newton, R.J.2    Johnston, J.S.3    Price, H.J.4
  • 30
    • 0345731466 scopus 로고    scopus 로고
    • Enrichment of gene-coding sequences in maize by genome filtration
    • Whitelaw, C.A., Barbazuk, W.B., Pertea, G., et al. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science, 302, 2118-2120.
    • (2003) Science , vol.302 , pp. 2118-2120
    • Whitelaw, C.A.1    Barbazuk, W.B.2    Pertea, G.3
  • 31
    • 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
  • 32
    • 84870860897 scopus 로고    scopus 로고
    • Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
    • Zhou, L., and, Holliday, J.A., (2012) Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture. BMC Genomics, 13, 703.
    • (2012) BMC Genomics , vol.13 , pp. 703
    • Zhou, L.1    Holliday, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.