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Volumn 540, Issue 2, 2014, Pages 201-209

The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): Loss of an inverted repeat region and comparative analysis with related species

Author keywords

Chloroplast genome; IR loss; Large inversion; SSRs; Taxus chinensis var. mairei

Indexed keywords

ANGIOSPERM; ARTICLE; CHLOROPLAST GENOME; CONTROLLED STUDY; CYCAS; CYCAS REVOLUTA; EMBRYOPHYTA; FERN; GENE LOCUS; GENE LOSS; GENE ORDER; GENE REARRANGEMENT; GENE SEQUENCE; GENE STRUCTURE; GINKGO BILOBA; GYMNOSPERM; INVERTED REPEAT; LIVERWORT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT LEAF; PRIORITY JOURNAL; SIMPLE SEQUENCE REPEAT; TAXUS WALLICHIANA VAR. MAIREI;

EID: 84896546442     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.02.037     Document Type: Article
Times cited : (65)

References (32)
  • 2
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data
    • Cox M.P., Peterson D.A., Biggs P.J. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010, 11:485.
    • (2010) BMC Bioinformatics , vol.11 , pp. 485
    • Cox, M.P.1    Peterson, D.A.2    Biggs, P.J.3
  • 3
    • 34248662670 scopus 로고    scopus 로고
    • When gene marriages don't work out: divorce by subfunctionalization
    • Cusack B.P., Wolfe K.H. When gene marriages don't work out: divorce by subfunctionalization. Trends in Genetics 2007, 23:270-272.
    • (2007) Trends in Genetics , vol.23 , pp. 270-272
    • Cusack, B.P.1    Wolfe, K.H.2
  • 4
    • 46649088563 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species
    • Hirao T., Watanabe A., Kurita M., Kondo T., Takata K. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biology 2008, 8:70.
    • (2008) BMC Plant Biology , vol.8 , pp. 70
    • Hirao, T.1    Watanabe, A.2    Kurita, M.3    Kondo, T.4    Takata, K.5
  • 5
    • 37649007931 scopus 로고    scopus 로고
    • Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
    • Jansen R.K., et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:19369-19374.
    • (2007) Proceedings of the National Academy of Sciences of the United States of America , vol.104 , pp. 19369-19374
    • Jansen, R.K.1
  • 6
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent W.James BLAT-the BLAST-like alignment tool. Genome Research 2002, 12:656-664.
    • (2002) Genome Research , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 7
    • 0033030789 scopus 로고    scopus 로고
    • Efficient extraction of paclitaxel and related taxoids from leaf tissue of Taxus using a potable solvent system
    • Ketchum R.E., Luong J.V., Gibson D.M. Efficient extraction of paclitaxel and related taxoids from leaf tissue of Taxus using a potable solvent system. Journal of Liquid Chromatography & Related Technologies 1999, 22:1715-1732.
    • (1999) Journal of Liquid Chromatography & Related Technologies , vol.22 , pp. 1715-1732
    • Ketchum, R.E.1    Luong, J.V.2    Gibson, D.M.3
  • 9
    • 84913590878 scopus 로고    scopus 로고
    • Construction of DNA fingerprinting and analysis of genetic diversity with SSR markers for cotton major cultivars in China
    • Kuang M., et al. Construction of DNA fingerprinting and analysis of genetic diversity with SSR markers for cotton major cultivars in China. Scientia Agricultura Sinica 2011, 44(1):32-36.
    • (2011) Scientia Agricultura Sinica , vol.44 , Issue.1 , pp. 32-36
    • Kuang, M.1
  • 11
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0
    • Larkin M.A., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 12
    • 84863206928 scopus 로고    scopus 로고
    • The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction
    • Lin C.P., Wu C.S., Huang Y.Y., Chaw S.M. The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction. Genome Biology and Evolution 2012, 4:374-381.
    • (2012) Genome Biology and Evolution , vol.4 , pp. 374-381
    • Lin, C.P.1    Wu, C.S.2    Huang, Y.Y.3    Chaw, S.M.4
  • 13
    • 36048989002 scopus 로고    scopus 로고
    • Organellar Genome DRAW (OGDRAW) - a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes
    • Lohse M., Drechsel O., Bock R. Organellar Genome DRAW (OGDRAW) - a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics 2007, 52:267-274.
    • (2007) Current Genetics , vol.52 , pp. 267-274
    • Lohse, M.1    Drechsel, O.2    Bock, R.3
  • 14
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 1997, 25:955-964.
    • (1997) Nucleic Acids Research , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 15
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
    • Luo, et al.
    • Luo, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012, 1:18.
    • (2012) GigaScience , vol.1 , pp. 18
  • 19
    • 0034020416 scopus 로고    scopus 로고
    • PipMaker-a web server for aligning two genomic DNA sequences
    • Schwartz S., et al. PipMaker-a web server for aligning two genomic DNA sequences. Genome Research 2000, 10:577-586.
    • (2000) Genome Research , vol.10 , pp. 577-586
    • Schwartz, S.1
  • 20
    • 84968989005 scopus 로고
    • The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression
    • Shinozaki K., et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. The EMBO Journal 1986, 5:2043.
    • (1986) The EMBO Journal , vol.5 , pp. 2043
    • Shinozaki, K.1
  • 21
    • 0036211065 scopus 로고    scopus 로고
    • GRIMM: genome rearrangements web server
    • Tesler G. GRIMM: genome rearrangements web server. Bioinformatics 2002, 18:492-493.
    • (2002) Bioinformatics , vol.18 , pp. 492-493
    • Tesler, G.1
  • 22
    • 0037854629 scopus 로고    scopus 로고
    • Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
    • Thiel T., Michalek W., Varshney R.K., Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 2003, 106:411-422.
    • (2003) Theoretical and Applied Genetics , vol.106 , pp. 411-422
    • Thiel, T.1    Michalek, W.2    Varshney, R.K.3    Graner, A.4
  • 23
    • 0026506180 scopus 로고
    • Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16
    • Tsudzuki J., et al. Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16. Molecular and General Genetics MGG 1992, 232:206-214.
    • (1992) Molecular and General Genetics MGG , vol.232 , pp. 206-214
    • Tsudzuki, J.1
  • 24
    • 0033621040 scopus 로고    scopus 로고
    • The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes
    • Turmel M., Otis C., Lemieux C. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proceedings of the National Academy of Sciences 1999, 96:10248-10253.
    • (1999) Proceedings of the National Academy of Sciences , vol.96 , pp. 10248-10253
    • Turmel, M.1    Otis, C.2    Lemieux, C.3
  • 25
    • 34548661941 scopus 로고    scopus 로고
    • Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus
    • Ueda M., Fujimoto M., Arimura S.I., Murata J., Tsutsumi N., Kadowaki K.I. Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. Gene 2007, 402:51-56.
    • (2007) Gene , vol.402 , pp. 51-56
    • Ueda, M.1    Fujimoto, M.2    Arimura, S.I.3    Murata, J.4    Tsutsumi, N.5    Kadowaki, K.I.6
  • 27
    • 34548108492 scopus 로고    scopus 로고
    • Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants
    • Wu C.S., Wang Y.N., Liu S.M., Chaw S.M. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Molecular Biology and Evolution 2007, 24:1366-1379.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1366-1379
    • Wu, C.S.1    Wang, Y.N.2    Liu, S.M.3    Chaw, S.M.4
  • 28
    • 84855848337 scopus 로고    scopus 로고
    • Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny
    • Wu C.S., Wang Y.N., Hsu C.Y., Lin C.P., Chaw S.M. Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biology and Evolution 2011, 3:1284.
    • (2011) Genome Biology and Evolution , vol.3 , pp. 1284
    • Wu, C.S.1    Wang, Y.N.2    Hsu, C.Y.3    Lin, C.P.4    Chaw, S.M.5
  • 29
    • 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
  • 30
    • 56249103747 scopus 로고    scopus 로고
    • Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences
    • Xiao P.G., Huang B., Ge G.B., Yang L. Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences. Plant Systematics and Evolution 2008, 276:89-104.
    • (2008) Plant Systematics and Evolution , vol.276 , pp. 89-104
    • Xiao, P.G.1    Huang, B.2    Ge, G.B.3    Yang, L.4
  • 31
    • 77958527485 scopus 로고    scopus 로고
    • The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.)
    • Yang M., et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 2010, 5:e12762.
    • (2010) PLoS One , vol.5
    • Yang, M.1
  • 32
    • 84876540601 scopus 로고    scopus 로고
    • The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms
    • Yi X., Gao L., Wang B., Su Y.J., Wang T. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms. Genome Biology and Evolution 2013, 5:688-698.
    • (2013) Genome Biology and Evolution , vol.5 , pp. 688-698
    • Yi, X.1    Gao, L.2    Wang, B.3    Su, Y.J.4    Wang, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.