메뉴 건너뛰기




Volumn 5, Issue 1, 2012, Pages 218-230

Dynamic intra-japonica subspecies variation and resource application

Author keywords

BAC; comparative genomics; Japonica; Oryza; Physical map; rice

Indexed keywords

JAPONICA; ORYZA; ORYZA SATIVA;

EID: 84863065036     PISSN: 16742052     EISSN: 17529867     Source Type: Journal    
DOI: 10.1093/mp/ssr085     Document Type: Article
Times cited : (20)

References (47)
  • 3
    • 27744525806 scopus 로고    scopus 로고
    • Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: Sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome
    • DOI 10.1007/s00122-005-0091-3
    • Ammiraju, J.S., et al. (2005). Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: Sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. Theor. Appl. Genet. 111, 1596-1607. (Pubitemid 41618661)
    • (2005) Theoretical and Applied Genetics , vol.111 , Issue.8 , pp. 1596-1607
    • Ammiraju, J.S.S.1    Yu, Y.2    Luo, M.3    Kudrna, D.4    Kim, H.5    Goicoechea, J.L.6    Katayose, Y.7    Matsumoto, T.8    Wu, J.9    Sasaki, T.10    Wing, R.A.11
  • 5
    • 62549137865 scopus 로고    scopus 로고
    • Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set
    • Ammiraju, J.S., et al. (2008). Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell. 20, 3191-3209.
    • (2008) Plant Cell. , vol.20 , pp. 3191-3209
    • Ammiraju, J.S.1
  • 6
    • 77954893229 scopus 로고    scopus 로고
    • Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza
    • Ammiraju, J.S., et al. (2010). Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant J. 63, 430-442.
    • (2010) Plant J. , vol.63 , pp. 430-442
    • Ammiraju, J.S.1
  • 7
    • 45249111400 scopus 로고    scopus 로고
    • Establishing a gene trap system mediated by T-DNA(GUS) in rice
    • DOI 10.1111/j.1744-7909.2007.00611.x
    • Chen, S.Y., Wang, A.M., Li, W., Wang, Z.Y., and Cai, X.L. (2008). Establishing a gene trap system mediated by T-DNA(GUS). in rice. J. Integr. Plant Biol. 50, 742-751. (Pubitemid 351837104)
    • (2008) Journal of Integrative Plant Biology , vol.50 , Issue.6 , pp. 742-751
    • Chen, S.-Y.1    Wang, A.-M.2    Li, W.3    Wang, Z.-Y.4    Cai, X.-L.5
  • 8
    • 0036137277 scopus 로고    scopus 로고
    • DNA sequence quality trimming and vector removal
    • Chou, H.H., and Holmes, M.H. (2001). DNA sequence quality trimming and vector removal. Bioinformatics. 17, 1093-1104. (Pubitemid 33735335)
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1093-1104
    • Chou, H.-H.1    Holmes, M.H.2
  • 9
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing, B., and Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194. (Pubitemid 28177230)
    • (1998) Genome Research , vol.8 , Issue.3 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 10
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing, B., Hillier, L., Wendl, M.C., and Green, P. (1998). Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185. (Pubitemid 28177229)
    • (1998) Genome Research , vol.8 , Issue.3 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 11
    • 70449678714 scopus 로고    scopus 로고
    • Analysis of collinear regions of Oryza AA and CC genomes
    • Feng, Q., Huang, T., Zhao, Q., Zhu, J., Lin, Z., and Han, B. (2009). Analysis of collinear regions of Oryza AA and CC genomes. J. Genet. Genomics. 36, 667-677.
    • (2009) J. Genet. Genomics. , vol.36 , pp. 667-677
    • Feng, Q.1    Huang, T.2    Zhao, Q.3    Zhu, J.4    Lin, Z.5    Han, B.6
  • 16
    • 0037394626 scopus 로고    scopus 로고
    • Genome-wide intraspecific DNA-sequence variations in rice
    • DOI 10.1016/S1369-5266(03)00004-9
    • Han, B., and Xue, Y. (2003). Genome-wide intraspecific DNA-sequence variations in rice. Curr. Opin. Plant Biol. 6, 134-138. (Pubitemid 36463287)
    • (2003) Current Opinion in Plant Biology , vol.6 , Issue.2 , pp. 134-138
    • Han, B.1    Xue, Y.2
  • 17
    • 78049332150 scopus 로고    scopus 로고
    • Genome-wide association studies of 14 agronomic traits in rice landraces
    • Huang, X., et al. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961-967.
    • (2010) Nat. Genet. , Issue.42 , pp. 961-967
    • Huang, X.1
  • 18
    • 0141853948 scopus 로고    scopus 로고
    • PCAP: A whole-genome assembly program
    • DOI 10.1101/gr.1390403
    • Huang, X., Wang, J., Aluru, S., Yang, S.P., and Hillier, L. (2003). PCAP: A whole-genome assembly program. Genome Res. 13, 2164-2170. (Pubitemid 37161773)
    • (2003) Genome Research , vol.13 , Issue.9 , pp. 2164-2170
    • Huang, X.1    Wang, J.2    Aluru, S.3    Yang, S.-P.4    Hillier, L.5
  • 19
    • 77956828564 scopus 로고    scopus 로고
    • Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza
    • Hurwitz, B.L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S.A., Ware, D., Wing, R.A., and Stein, L. (2010). Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J. 63, 990-1003.
    • (2010) Plant J. , vol.63 , pp. 990-1003
    • Hurwitz, B.L.1    Kudrna, D.2    Yu, Y.3    Sebastian, A.4    Zuccolo, A.5    Jackson, S.A.6    Ware, D.7    Wing, R.A.8    Stein, L.9
  • 20
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project (IRGSP)
    • International Rice Genome Sequencing Project (IRGSP) (2005). The map-based sequence of the rice genome. Nature. 436, 793-800.
    • (2005) Nature. , vol.436 , pp. 793-800
  • 21
    • 0036226603 scopus 로고    scopus 로고
    • Blat-The blast-like alignment tool
    • Kent, W.J. (2002). BLAT-The BLAST-LIKE Alignment Tool. Genome Res. 12, 656-664.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 22
    • 43549125262 scopus 로고    scopus 로고
    • Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of genus Oryza
    • Kim, H., et al. (2008). Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of genus Oryza. Genome Biol. 9, 45-59.
    • (2008) Genome Biol. , vol.9 , pp. 45-59
    • Kim, H.1
  • 23
    • 34548588693 scopus 로고    scopus 로고
    • Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type)
    • DOI 10.1534/genetics.106.068783
    • Kim, H., San Miguel, P., Nelson, W., Collura, K., Wissotski, M., Walling, J.G., Kim, J.P., Jackson, S.A., Soderlund, C., and Wing, R.A. (2007). Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics. 176, 379-390. (Pubitemid 350021033)
    • (2007) Genetics , vol.176 , Issue.1 , pp. 379-390
    • Kim, H.1    San Miguel, P.2    Nelson, W.3    Collura, K.4    Wissotski, M.5    Walling, J.G.6    Jun, P.K.7    Jackson, S.A.8    Soderlund, C.9    Wing, R.A.10
  • 24
    • 58449093788 scopus 로고    scopus 로고
    • Mutant resources in rice for functional genomics of the grasses
    • Krishnan, A., et al. (2009). Mutant resources in rice for functional genomics of the grasses. Plant Physiol. 149, 165-170.
    • (2009) Plant Physiol. , vol.149 , pp. 165-170
    • Krishnan, A.1
  • 25
    • 60549104200 scopus 로고    scopus 로고
    • Comparative sequence analysis of MONOCULM1- orthologous regions in 14 Oryza genomes
    • Lu, F., et al. (2009). Comparative sequence analysis of MONOCULM1- orthologous regions in 14 Oryza genomes. Proc. Natl Acad. Sci. U S A. 106, 2071-2076.
    • (2009) Proc. Natl Acad. Sci. U S A. , vol.106 , pp. 2071-2076
    • Lu, F.1
  • 26
    • 1542548246 scopus 로고    scopus 로고
    • An improved method for plant BAC library construction
    • Luo, M., and Wing, R.A. (2003). An improved method for plant BAC library construction. Methods Mol. Biol. 236, 3-20.
    • (2003) Methods Mol. Biol. , vol.236 , pp. 3-20
    • Luo, M.1    Wing, R.A.2
  • 27
    • 33746366455 scopus 로고    scopus 로고
    • Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey
    • Luo, M., et al. (2006). Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. BMC Genomics. 7, 106.
    • (2006) BMC Genomics. , vol.7 , pp. 106
    • Luo, M.1
  • 28
    • 0035056110 scopus 로고    scopus 로고
    • Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2)
    • DOI 10.1139/gen-44-2-154
    • Luo, M., Wang, Y.H., Frisch, D., Joobeur, T., Wing, R.A., and Dean, R.A. (2001). Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2). Genome. 44, 154-162. (Pubitemid 32333529)
    • (2001) Genome , vol.44 , Issue.2 , pp. 154-162
    • Luo, M.1    Wang, Y.-H.2    Frisch, D.3    Joobeur, T.4    Wing, R.A.5    Dean, R.A.6
  • 29
    • 12444325815 scopus 로고    scopus 로고
    • High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis
    • DOI 10.1016/S0888-7543(03)00128-9
    • Luo, M.C., Thomas, C., You, F.M., Hsiao, J., Ouyang, S., Buell, C.R., Malandro, M., McGuire, P.E., Anderson, O.D., and Dvorak, J. (2003). High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics. 82, 378-389. (Pubitemid 36952308)
    • (2003) Genomics , vol.82 , Issue.3 , pp. 378-389
    • Luo, M.-C.1    Thomas, C.2    You, F.M.3    Hsiao, J.4    Ouyang, S.5    Buell, C.R.6    Malandro, M.7    McGuire, P.E.8    Anderson, O.D.9    Dvorak, J.10
  • 31
    • 2342466982 scopus 로고    scopus 로고
    • Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice
    • DOI 10.1101/gr.1466204
    • Ma, J., Devos, K.M., and Bennetzen, J.L. (2004). Analyses of LTRretrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14, 860-869. (Pubitemid 38660503)
    • (2004) Genome Research , vol.14 , Issue.5 , pp. 860-869
    • Ma, J.1    Devos, K.M.2    Bennetzen, J.L.3
  • 32
    • 68149145780 scopus 로고    scopus 로고
    • Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
    • McNally, K.L., et al. (2009). Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl Acad. Sci. U S A. 106, 12273-12278.
    • (2009) Proc. Natl Acad. Sci. U S A. , vol.106 , pp. 12273-12278
    • McNally, K.L.1
  • 34
    • 0033674122 scopus 로고    scopus 로고
    • Contigs built with fingerprints, markers, and FPC V4.7
    • Soderlund, C., Humphray, S., Dunham, A., and French, L. (2000). Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10, 1772-1787.
    • (2000) Genome Res. , vol.10 , pp. 1772-1787
    • Soderlund, C.1    Humphray, S.2    Dunham, A.3    French, L.4
  • 35
    • 0030690108 scopus 로고    scopus 로고
    • FPC: A system for building contigs from restriction fingerprinted clones
    • Soderlund, C., Longden, I., and Mott, R. (1997). FPC: A system for building contigs form restriction fingerprinted clones. Comput Appl. Biosci. 13, 523-535. (Pubitemid 27480212)
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.5 , pp. 523-535
    • Soderlund, C.1    Longden, I.2    Mott, R.3
  • 36
    • 33748260755 scopus 로고    scopus 로고
    • SyMAP: A system for discovering and viewing syntenic regions of FPC maps
    • DOI 10.1101/gr.5396706
    • Soderlund, C., Nelson, W., Shoemaker, A., and Paterson, A. (2006). SyMAP: A systeming for discovering and viewing sytenic regions of FPC maps. Genome Res. 16, 1159-1168. (Pubitemid 44320403)
    • (2006) Genome Research , vol.16 , Issue.9 , pp. 1159-1168
    • Soderlund, C.1    Nelson, W.2    Shoemaker, A.3    Paterson, A.4
  • 37
    • 76249106402 scopus 로고    scopus 로고
    • Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
    • Tang, H., Bowers, J.E., Wang, X., and Paterson, A.H. (2010). Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc. Natl Acad. Sci. U S A. 107, 472-477.
    • (2010) Proc. Natl Acad. Sci. U S A. , vol.107 , pp. 472-477
    • Tang, H.1    Bowers, J.E.2    Wang, X.3    Paterson, A.H.4
  • 38
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994). CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680. (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 40
    • 12444307483 scopus 로고    scopus 로고
    • Development of enhancer trap lines for functional analysis of the rice genome
    • DOI 10.1046/j.1365-313X.2003.01808.x
    • Wu, C., Li, X., Yuan,W., Chen, G., Kilian, A., Li, J., Xu, C., Zhou, D.X., Wang, S., and Zhang, Q. (2003). Development of enhancer trap lines for functional analysis of the rice genome. Plant J. 35, 418-427. (Pubitemid 36990643)
    • (2003) Plant Journal , vol.35 , Issue.3 , pp. 418-427
    • Wu, C.1    Li, X.2    Yuan, W.3    Chen, G.4    Kilian, A.5    Li, J.6    Xu, C.7    Li, X.8    Zhou, D.-X.9    Wang, S.10    Zhang, Q.11
  • 41
    • 36249029898 scopus 로고    scopus 로고
    • Fine Mapping and Isolation of Bc7(t), Allelic to OsCesA4
    • DOI 10.1016/S1673-8527(07)60115-5, PII S1673852707601155
    • Yan, C., Yan, S., Zeng, X., Zhang, Z., and Gu, M. (2007). Fine mapping and isolation of Bc7(t), allelic to OsCesA4. J. Genet. Genomics. 34, 1019-1027. (Pubitemid 350123218)
    • (2007) Journal of Genetics and Genomics , vol.34 , Issue.11 , pp. 1019-1027
    • Yan, C.1    Yan, S.2    Zeng, X.3    Zhang, Z.4    Gu, M.5
  • 42
    • 20144366003 scopus 로고    scopus 로고
    • The genomes of Oryza sativa: A history of duplications
    • Yu, J., et al. (2005). The genomes of Oryza sativa: A history of duplications. PLoS Biol. 3, e38.
    • (2005) PLoS Biol. , vol.3
    • Yu, J.1
  • 43
    • 33746280756 scopus 로고    scopus 로고
    • Comparing the whole-genome-shotgun and map-based sequences of the rice genome
    • DOI 10.1016/j.tplants.2006.06.005, PII S1360138506001609
    • Yu, J., Ni, P., and Wong, G.K. (2006). Comparing the whole-genomeshotgun and map-based sequences of the rice genome. Trends Plant Sci. 11, 387-391. (Pubitemid 44108709)
    • (2006) Trends in Plant Science , vol.11 , Issue.8 , pp. 387-391
    • Yu, J.1    Ni, P.2    Wong, G.K.-S.3
  • 44
    • 33847120341 scopus 로고    scopus 로고
    • Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library
    • DOI 10.1111/j.1365-313X.2006.03001.x
    • Zhang, J., et al. (2007). Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancertrap mutant library. Plant J. 49, 947-959. (Pubitemid 46279276)
    • (2007) Plant Journal , vol.49 , Issue.5 , pp. 947-959
    • Zhang, J.1    Guo, D.2    Chang, Y.3    You, C.4    Li, X.5    Dai, X.6    Weng, Q.7    Zhang, J.8    Chen, G.9    Li, X.10    Liu, H.11    Han, B.12    Zhang, Q.13    Wu, C.14
  • 45
    • 20444502606 scopus 로고    scopus 로고
    • Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63
    • DOI 10.1111/j.1365-313X.2005.02408.x
    • Zhang, J., Feng, Q., Jin, C., Qiu, D., Zhang, L., Xie, K., Yuan, D., Han, B., Zhang, Q., and Wang, S. (2005). Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63. Plant J. 42, 772-780. (Pubitemid 40809893)
    • (2005) Plant Journal , vol.42 , Issue.5 , pp. 772-780
    • Zhang, J.1    Feng, Q.2    Jin, C.3    Qiu, D.4    Zhang, L.5    Xie, K.6    Yuan, D.7    Han, B.8    Zhang, Q.9    Wang, S.10
  • 46
    • 28244445008 scopus 로고    scopus 로고
    • RMD: A rice mutant database for funtional analysis of the rice genome
    • Zhang, J., Li, C.,Wu, C., Xiong, L., Chen, G., Zhang, Q., andWang, S. (2006). RMD: A rice mutant database for funtional analysis of the rice genome. Nucleic Acids Res. 34, 745-748.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 745-748
    • Zhang, J.1    Li, C.2    Wu, C.3    Xiong, L.4    Chen, G.5    Zhang, Q.6    Wang, S.7
  • 47
    • 1842681942 scopus 로고    scopus 로고
    • Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea
    • DOI 10.1073/pnas.0401243101
    • Zhang, X., and Wessler, S.R. (2004). Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc. Natl Acad. Sci. U S A. 101, 5589-5594. (Pubitemid 38481200)
    • (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , Issue.15 , pp. 5589-5594
    • Zhang, X.1    Wessler, S.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.