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Volumn 551, Issue 1, 2014, Pages 39-48

De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.)

Author keywords

Brassicaceae family; Chloroplast genome; Next generation sequencing; Raphanus sativus; Simple sequence repeat

Indexed keywords

RIBOSOME RNA; TRANSFER RNA; MICROSATELLITE DNA; VEGETABLE PROTEIN;

EID: 84907513004     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.08.038     Document Type: Article
Times cited : (33)

References (48)
  • 2
    • 84866266717 scopus 로고    scopus 로고
    • Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
    • Chaisson M.J., Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 2012, 13:238.
    • (2012) BMC Bioinformatics , vol.13 , pp. 238
    • Chaisson, M.J.1    Tesler, G.2
  • 3
    • 84869094459 scopus 로고    scopus 로고
    • Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding
    • Dong W., Liu J., Yu J., Wang L., Zhou S. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 2012, 7:e35071.
    • (2012) PLoS One , vol.7 , pp. e35071
    • Dong, W.1    Liu, J.2    Yu, J.3    Wang, L.4    Zhou, S.5
  • 4
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 7
    • 77953826984 scopus 로고    scopus 로고
    • Computer Science and Engineering, The Pennsylvania State University, State College
    • Harris R.S. Improved Pairwise Alignment of Genomic DNA 2007, Computer Science and Engineering, The Pennsylvania State University, State College.
    • (2007) Improved Pairwise Alignment of Genomic DNA
    • Harris, R.S.1
  • 9
    • 79960719599 scopus 로고    scopus 로고
    • Complete chloroplast genome sequence of rapeseed (Brassica napus L.) and its evolutionary implications
    • Hu Z.-Y., Hua W., Huang S.-M., Wang H.-Z. Complete chloroplast genome sequence of rapeseed (Brassica napus L.) and its evolutionary implications. Genet. Resour. Crop. Evol. 2011, 58:875-887.
    • (2011) Genet. Resour. Crop. Evol. , vol.58 , pp. 875-887
    • Hu, Z.-Y.1    Hua, W.2    Huang, S.-M.3    Wang, H.-Z.4
  • 10
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 2002, 12:656-664.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 11
    • 11144284040 scopus 로고    scopus 로고
    • Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants
    • Kim K.J., Lee H.L. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 2004, 11:247-261.
    • (2004) DNA Res. , vol.11 , pp. 247-261
    • Kim, K.J.1    Lee, H.L.2
  • 12
    • 67349123718 scopus 로고    scopus 로고
    • Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.)
    • Kim S., Lee Y.P., Lim H., Ahn Y., Sung S.K. Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.). Theor. Appl. Genet. 2009, 119:189-198.
    • (2009) Theor. Appl. Genet. , vol.119 , pp. 189-198
    • Kim, S.1    Lee, Y.P.2    Lim, H.3    Ahn, Y.4    Sung, S.K.5
  • 14
    • 0023657387 scopus 로고
    • Evidence for in vivo trans splicing of pre-mRNAs in tobacco chloroplasts
    • Koller B., Fromm H., Galun E., Edelman M. Evidence for in vivo trans splicing of pre-mRNAs in tobacco chloroplasts. Cell 1987, 48:111-119.
    • (1987) Cell , vol.48 , pp. 111-119
    • Koller, B.1    Fromm, H.2    Galun, E.3    Edelman, M.4
  • 16
    • 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 2009, 25:1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 17
    • 84875546384 scopus 로고    scopus 로고
    • CISA: contig integrator for sequence assembly of bacterial genomes
    • Lin S.H., Liao Y.C. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 2013, 8:e60843.
    • (2013) PLoS One , vol.8 , pp. e60843
    • Lin, S.H.1    Liao, Y.C.2
  • 18
    • 42049117340 scopus 로고    scopus 로고
    • Genetic diversity of cultivated and wild radish and phylogenetic relationships among Raphanus and Brassica species revealed by the analysis of trnK/matK sequence
    • Lü N., Yamane K., Ohnishi O. Genetic diversity of cultivated and wild radish and phylogenetic relationships among Raphanus and Brassica species revealed by the analysis of trnK/matK sequence. Breed. Sci. 2008, 58:15-22.
    • (2008) Breed. Sci. , vol.58 , pp. 15-22
    • Lü, N.1    Yamane, K.2    Ohnishi, O.3
  • 21
    • 84903648903 scopus 로고    scopus 로고
    • Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species
    • Moghe G.D., Hufnagel D.E., Tang H., Xiao Y., Dworkin I., Town C.D., Conner J.K., Shiu S.H. Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species. Plant Cell 2014, 26:1925-1937.
    • (2014) Plant Cell , vol.26 , pp. 1925-1937
    • Moghe, G.D.1    Hufnagel, D.E.2    Tang, H.3    Xiao, Y.4    Dworkin, I.5    Town, C.D.6    Conner, J.K.7    Shiu, S.H.8
  • 22
    • 84869136099 scopus 로고    scopus 로고
    • Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis
    • Pang X., Liu C., Shi L., Liu R., Liang D., Li H., Cherny S.S., Chen S. Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis. PLoS One 2012, 7:e48833.
    • (2012) PLoS One , vol.7 , pp. e48833
    • Pang, X.1    Liu, C.2    Shi, L.3    Liu, R.4    Liang, D.5    Li, H.6    Cherny, S.S.7    Chen, S.8
  • 23
    • 57349177509 scopus 로고    scopus 로고
    • Bidirectional history of hybridization in California wild radish, Raphanus sativus (Brassicaceae), as revealed by chloroplast DNA
    • Ridley C.E., Kim S.C., Ellstrand N.C. Bidirectional history of hybridization in California wild radish, Raphanus sativus (Brassicaceae), as revealed by chloroplast DNA. Am. J. Bot. 2008, 95:1437-1442.
    • (2008) Am. J. Bot. , vol.95 , pp. 1437-1442
    • Ridley, C.E.1    Kim, S.C.2    Ellstrand, N.C.3
  • 24
    • 34547793573 scopus 로고    scopus 로고
    • Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes
    • Saski C., Lee S.B., Fjellheim S., Guda C., Jansen R.K., Luo H., Tomkins J., Rognli O.A., Daniell H., Clarke J.L. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor. Appl. Genet. 2007, 115:571-590.
    • (2007) Theor. Appl. Genet. , vol.115 , pp. 571-590
    • Saski, C.1    Lee, S.B.2    Fjellheim, S.3    Guda, C.4    Jansen, R.K.5    Luo, H.6    Tomkins, J.7    Rognli, O.A.8    Daniell, H.9    Clarke, J.L.10
  • 25
    • 0033615372 scopus 로고    scopus 로고
    • Complete structure of the chloroplast genome of Arabidopsis thaliana
    • Sato S., Nakamura Y., Kaneko T., Asamizu E., Tabata S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 1999, 6:283-290.
    • (1999) DNA Res , vol.6 , pp. 283-290
    • Sato, S.1    Nakamura, Y.2    Kaneko, T.3    Asamizu, E.4    Tabata, S.5
  • 27
    • 0001282689 scopus 로고
    • Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 2. Preliminary analysis of subspecies within B. rapa (syn. campestris) and B. oleracea
    • Song K.M., Osborn T.C., Williams P.H. Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 2. Preliminary analysis of subspecies within B. rapa (syn. campestris) and B. oleracea. Theor. Appl. Genet. 1988, 76:593-600.
    • (1988) Theor. Appl. Genet. , vol.76 , pp. 593-600
    • Song, K.M.1    Osborn, T.C.2    Williams, P.H.3
  • 28
    • 34249960658 scopus 로고
    • Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 3. Genome relationships in Brassica and related genera and the origin of B. oleracea and B. rapa (syn. campestris)
    • Song K., Osborn T.C., Williams P.H. Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs): 3. Genome relationships in Brassica and related genera and the origin of B. oleracea and B. rapa (syn. campestris). Theor. Appl. Genet. 1990, 79:497-506.
    • (1990) Theor. Appl. Genet. , vol.79 , pp. 497-506
    • Song, K.1    Osborn, T.C.2    Williams, P.H.3
  • 29
    • 14644438364 scopus 로고    scopus 로고
    • Circular genome visualization and exploration using CGView
    • Stothard P., Wishart D.S. Circular genome visualization and exploration using CGView. Bioinformatics 2005, 21:537-539.
    • (2005) Bioinformatics , vol.21 , pp. 537-539
    • Stothard, P.1    Wishart, D.S.2
  • 30
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56:564-577.
    • (2007) Syst. Biol. , vol.56 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 31
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 32
    • 0034882994 scopus 로고    scopus 로고
    • Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential
    • Temnykh S., DeClerck G., Lukashova A., Lipovich L., Cartinhour S., McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 2001, 11:1441-1452.
    • (2001) Genome Res. , vol.11 , pp. 1441-1452
    • Temnykh, S.1    DeClerck, G.2    Lukashova, A.3    Lipovich, L.4    Cartinhour, S.5    McCouch, S.6
  • 33
    • 0028050863 scopus 로고
    • Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species
    • Thormann C.E., Ferreira M.E., Camargo L.E., Tivang J.G., Osborn T.C. Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species. Theor. Appl. Genet. 1994, 88:973-980.
    • (1994) Theor. Appl. Genet. , vol.88 , pp. 973-980
    • Thormann, C.E.1    Ferreira, M.E.2    Camargo, L.E.3    Tivang, J.G.4    Osborn, T.C.5
  • 34
    • 23944474868 scopus 로고    scopus 로고
    • Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences
    • Wang A., Yang M., Liu J. Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences. Ann. Bot. 2005, 96:489-498.
    • (2005) Ann. Bot. , vol.96 , pp. 489-498
    • Wang, A.1    Yang, M.2    Liu, J.3
  • 35
    • 0002427832 scopus 로고
    • Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae)-chloroplast genome and cytodeme congruence
    • Warwick S.I., Black L.D. Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae)-chloroplast genome and cytodeme congruence. Theor. Appl. Genet. 1991, 82:81-92.
    • (1991) Theor. Appl. Genet. , vol.82 , pp. 81-92
    • Warwick, S.I.1    Black, L.D.2
  • 36
    • 0030967445 scopus 로고    scopus 로고
    • Phylogenetic implications of chloroplast DNA restriction site variation in subtribes Raphaninae and Cakilinae (Brassicaceae, tribe Brassiceae)
    • Warwick S.I., Black L.D. Phylogenetic implications of chloroplast DNA restriction site variation in subtribes Raphaninae and Cakilinae (Brassicaceae, tribe Brassiceae). Can. J. Bot. 1997, 75:960-973.
    • (1997) Can. J. Bot. , vol.75 , pp. 960-973
    • Warwick, S.I.1    Black, L.D.2
  • 38
    • 0023462635 scopus 로고
    • Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
    • Wolfe K.H., Li W.H., Sharp P.M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:9054-9058.
    • (1987) Proc. Natl. Acad. Sci. U. S. A. , vol.84 , pp. 9054-9058
    • Wolfe, K.H.1    Li, W.H.2    Sharp, P.M.3
  • 39
    • 84892516697 scopus 로고    scopus 로고
    • Sequencing of chloroplast genome using whole cellular DNA and solexa sequencing technology
    • Wu J., Liu B., Cheng F., Ramchiary N., Choi S.R., Lim Y.P., Wang X.W. Sequencing of chloroplast genome using whole cellular DNA and solexa sequencing technology. Front. Plant Sci. 2012, 3:243.
    • (2012) Front. Plant Sci. , vol.3 , pp. 243
    • Wu, J.1    Liu, B.2    Cheng, F.3    Ramchiary, N.4    Choi, S.R.5    Lim, Y.P.6    Wang, X.W.7
  • 40
    • 10244240599 scopus 로고    scopus 로고
    • Automatic annotation of organellar genomes with DOGMA
    • Wyman S.K., Jansen R.K., Boore J.L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 2004, 20:3252-3255.
    • (2004) Bioinformatics , vol.20 , pp. 3252-3255
    • Wyman, S.K.1    Jansen, R.K.2    Boore, J.L.3
  • 41
    • 63849142518 scopus 로고    scopus 로고
    • Inter- and intraspecific sequence variations of the chloroplast genome in wild and cultivated Raphanus
    • Yamagishi H., Terachi T., Ozaki A., Ishibashi A. Inter- and intraspecific sequence variations of the chloroplast genome in wild and cultivated Raphanus. Plant Breed. 2009, 128:172-177.
    • (2009) Plant Breed. , vol.128 , pp. 172-177
    • Yamagishi, H.1    Terachi, T.2    Ozaki, A.3    Ishibashi, A.4
  • 42
    • 12744274680 scopus 로고    scopus 로고
    • Chloroplast DNA variations of cultivated radish and its wild relatives
    • Yamane K., Lü N., Ohnishi O. Chloroplast DNA variations of cultivated radish and its wild relatives. Plant Sci. 2005, 168:627-634.
    • (2005) Plant Sci. , vol.168 , pp. 627-634
    • Yamane, K.1    Lü, N.2    Ohnishi, O.3
  • 43
    • 62249205058 scopus 로고    scopus 로고
    • Multiple origins and high genetic diversity of cultivated radish inferred from polymorphism in chloroplast simple sequence repeats
    • Yamane K., Lü N., Ohnishi O. Multiple origins and high genetic diversity of cultivated radish inferred from polymorphism in chloroplast simple sequence repeats. Breed. Sci. 2009, 59:55-65.
    • (2009) Breed. Sci. , vol.59 , pp. 55-65
    • Yamane, K.1    Lü, N.2    Ohnishi, O.3
  • 44
    • 0033257252 scopus 로고    scopus 로고
    • Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA
    • Yang Y.W., Lai K.N., Tai P.Y., Ma D.P., Li W.H. Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA. Mol. Phylogenet. Evol. 1999, 13:455-462.
    • (1999) Mol. Phylogenet. Evol. , vol.13 , pp. 455-462
    • Yang, Y.W.1    Lai, K.N.2    Tai, P.Y.3    Ma, D.P.4    Li, W.H.5
  • 45
    • 0035983979 scopus 로고    scopus 로고
    • A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA
    • Yang Y.W., Tai P.Y., Chen Y., Li W.H. A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA. Mol. Phylogenet. Evol. 2002, 23:268-275.
    • (2002) Mol. Phylogenet. Evol. , vol.23 , pp. 268-275
    • Yang, Y.W.1    Tai, P.Y.2    Chen, Y.3    Li, W.H.4
  • 47
    • 84856082699 scopus 로고    scopus 로고
    • The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes
    • Zhang T., Fang Y., Wang X., Deng X., Zhang X., Hu S., Yu J. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes. PLoS One 2012, 7:e30531.
    • (2012) PLoS One , vol.7 , pp. e30531
    • Zhang, T.1    Fang, Y.2    Wang, X.3    Deng, X.4    Zhang, X.5    Hu, S.6    Yu, J.7
  • 48
    • 84896707642 scopus 로고    scopus 로고
    • Insights from the complete chloroplast genome into the evolution of Sesamum indicum L
    • Zhang H., Li C., Miao H., Xiong S. Insights from the complete chloroplast genome into the evolution of Sesamum indicum L. PLoS One 2013, 8:e80508.
    • (2013) PLoS One , vol.8 , pp. e80508
    • Zhang, H.1    Li, C.2    Miao, H.3    Xiong, S.4


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