The first insight into the Taxus genome via fosmid library construction and end sequencing

Molecular Genetics and Genomics

Volumn 285, Issue 3, 2011, Pages 197-205

  Hao, Dacheng ^a   Yang, Ling ^b   Xiao, Peigen ^c  

^a DALIAN JIAOTONG UNIVERSITY   (China)

^b DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

^c INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

Author keywords

Comparative genomics; Fosmid end sequences; Fosmid genomic library; Repetitive sequences; Taxus mairei

Indexed keywords

ARTICLE; CHROMOSOME SATELLITE; CONTROLLED STUDY; DNA SEQUENCE; FOSMID END SEQUENCE; FOSMID LIBRARY; GENE LIBRARY; GENE SEQUENCE; GENOME ANALYSIS; GENOMIC INSTABILITY; GYMNOSPERM; LOBLOLLY PINE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PRIORITY JOURNAL; RETROPOSON; SEQUENCE ANALYSIS; SIMPLE SEQUENCE REPEAT; TAXUS; TAXUS MAIREI; TRANSPOSON; WHITE SPRUCE;

BASE SEQUENCE; CHINA; COMPUTATIONAL BIOLOGY; DNA PRIMERS; ENDANGERED SPECIES; GENE LIBRARY; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PLANTS, MEDICINAL; PLASMIDS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TAXUS;

DICOTYLEDONEAE; GYMNOSPERMAE; PICEA; PICEA GLAUCA; PINUS TAEDA; TAXUS; TAXUS WALLICHIANA VAR. MAIREI; TETRA;

EID: 79952988820     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-010-0598-4     Document Type: Article

References (34)

1. JS Ammiraju Y Yu M Luo D Kudrna H Kim JL Goicoechea Y Katayose T Matsumoto J Wu T Sasaki RA Wing 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 1:CAS:528:DC%2BD2MXht1SqtLnM 10.1007/s00122-005-0091-3 16200416 (Pubitemid 41618661)
2. T Barbará C Palma-Silva GM Paggi F Bered MF Fay C Lexer 2007 Cross-species transfer of nuclear microsatellite markers: potential and limitations Mol Ecol 16 3759 3767 10.1111/j.1365-294X.2007.03439.x 17850543 (Pubitemid 47397325)
3. PF Cavagnaro SM Chung M Szklarczyk D Grzebelus D Senalik AE Atkins PW Simon 2009 Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences Mol Genet Genomics 281 273 288 1:CAS:528:DC%2BD1MXit1OksLk%3D 10.1007/s00438-008-0411-9 19104839
4. Y Cheng RG Nicolson K Tripp SM Chaw 2000 Phylogeny of Taxaceae and Cephalotaxaceae genera inferred from chloroplast matK gene and nuclear rDNA ITS region Molec Phylogenet Evol 14 353 365 1:CAS:528:DC%2BD3cXhsFyltrk%3D 10.1006/mpev.1999.0710 10712841 (Pubitemid 30181319)
5. TM Davis ME Shields Q Zhang D Tombolato-Terzić JL Bennetzen AC Pontaroli H Wang Q Yao P SanMiguel KM Folta 2010 An examination of targeted gene neighborhoods in strawberry BMC Plant Biol 10 81 10.1186/1471-2229-10-81 20441596
6. B Hamberger D Hall M Yuen C Oddy B Hamberger CI Keeling C Ritland K Ritland J Bohlmann 2009 Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome BMC Plant Biol 9 106 10.1186/1471-2229-9-106 19656416
7. Y Han SS Korban 2008 An overview of the apple genome through BAC end sequence analysis Plant Mol Biol 67 581 588 1:CAS:528:DC%2BD1cXnslKmtro%3D 10.1007/s11103-008-9321-9 18521706
8. DC Hao L Yang B Huang 2009 Molecular evolution of paclitaxel biosynthetic genes TS and DBAT of Taxus species Genetica 135 123 135 1:CAS:528: DC%2BD1MXhtlKltLo%3D 10.1007/s10709-008-9257-7
9. DC Hao PG Xiao B Huang GB Ge L Yang 2008 Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences Plant Syst Evol 276 89 104 1:CAS:528:DC%2BD1cXhtlKrtL3F 10.1007/s00606-008-0069-0
10. DC Hao B Huang L Yang 2008 Phylogenetic relationships of the genus Taxus inferred from chloroplast intergenic spacer and nuclear coding DNA Biol Pharm Bull 31 260 265 1:CAS:528:DC%2BD1cXmtlaks7g%3D 10.1248/bpb.31.260 (Pubitemid 351198402)
11. V Hemleben A Kovarik RA Torres-Ruiz RA Volkov T Beridze 2007 Plant highly repeated satellite DNA: molecular evolution, distribution and use for identification of hybrids Syst Biodiversity 5 277 289 10.1017/S147720000700240X (Pubitemid 47172732)
12. DR Hoen KC Park N Elrouby Z Yu N Mohabir RK Cowan TE Bureau 2006 Transposon-mediated expansion and diversification of a family of ULP-like genes Mol Biol Evol 23 1254 1268 1:CAS:528:DC%2BD28XlsVGqurY%3D 10.1093/molbev/msk015 16581939 (Pubitemid 43781599)
13. CP Hong P Plaha DH Koo TJ Yang SR Choi YK Lee T Uhm JW Bang D Edwards I Bancroft BS Park J Lee YP Lim 2006 A survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana Mol Cells 22 300 307 17202858 (Pubitemid 46062294)
14. N Huo GR Lazo JP Vogel FM You Y Ma DM Hayden D Coleman-Derr TA Hill J Dvorak OD Anderson MC Luo YQ Gu 2008 The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences Funct Integr Genomics 8 135 147 1:CAS:528:DC%2BD1cXjsFGis74%3D 10.1007/s10142-007-0062-7 17985162
15. O Jaillon JM Aury B Noel A Policriti C Clepet A Casagrande, et al. 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 463 467 1:CAS:528:DC%2BD2sXhtV2is7%2FF 10.1038/nature06148 17721507 (Pubitemid 47509545)
16. CI Keeling HK Dullat M Yuen SG Ralph S Jancsik J Bohlmann 2010 Identification and functional characterization of monofunctional ent-copalyl diphosphate and ent-kaurene synthases in white spruce reveal different patterns for diterpene synthase evolution for primary and secondary metabolism in gymnosperms Plant Physiol 152 1197 1208 1:CAS:528:DC%2BC3cXmsF2ls7k%3D 10.1104/pp.109.151456 20044448
17. UJ Kim H Shizuya PJ de Jong B Birren MI Simon 1992 Stable propagation of cosmid sized human DNA inserts in an F factor based vector Nucleic Acids Res 20 1083 1085 1:CAS:528:DyaK38XitVyrt7g%3D 10.1093/nar/20.5.1083 1549470
18. A Kovach JL Wegrzyn G Parra C Holt GE Bruening CA Loopstra J Hartigan M Yandell CH Langley I Korf DB Neale 2010 The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences BMC Genomics 11 420 10.1186/1471-2164-11-420 20609256
19. C Lange D Holtgräwe B Schulz B Weisshaar H Himmelbauer 2008 Construction and characterization of a sugar beet (Beta vulgaris) fosmid library Genome 51 948 951 1:CAS:528:DC%2BD1cXht12ns7bO 10.1139/G08-071 18956027
20. IJ Leitch L Hanson 2001 Nuclear DNA C-values complete familial representation in gymnosperms Ann Bot 88 843 849 1:CAS:528:DC%2BD3MXnslCktbk%3D 10.1006/anbo.2001.1521 (Pubitemid 33124592)
21. G Luikart PR England D Tallmon S Jordan P Taberlet 2003 The power and promise of population genomics: from genotyping to genome typing Nat Rev Genet 4 981 994 1:CAS:528:DC%2BD3sXptFait7k%3D 10.1038/nrg1226 14631358 (Pubitemid 37474645)
22. WS Martins DC Lucas KF Neves DJ Bertioli 2009 WebSat-a web software for microsatellite marker development Bioinformation 3 282 283 19255650
23. JD Meyer W Deleu J Garcia-Mas MJ Havey 2008 Construction of a fosmid library of cucumber (Cucumis sativus) and comparative analyses of the eIF4E and eIF(iso)4E regions from cucumber and melon (Cucumis melo) Mol Genet Genomics 279 473 480 1:CAS:528:DC%2BD1cXkvFWksr4%3D 10.1007/s00438-008-0326-5 18273646
24. M Morgante M Hanafey W Powell 2002 Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes Nat Genet 30 194 200 1:CAS:528:DC%2BD38XhtFWltLs%3D 10.1038/ng822 11799393
25. AM Morse DG Peterson MN Islam-Faridi KE Smith Z Magbanua SA Garcia TL Kubisiak HV Amerson JE Carlson CD Nelson JM Davis 2009 Evolution of genome size and complexity in Pinus PLoS One 4 e4332 10.1371/journal.pone.0004332 19194510
26. TL Newman E Tuzun VA Morrison KE Hayden M Ventura SD McGrath M Rocchi EE Eichler 2005 A genome-wide survey of structural variation between human and chimpanzee Genome Res 15 1344 1356 1:CAS:528:DC%2BD2MXhtFajurjJ 10.1101/gr.4338005 16169929 (Pubitemid 41400900)
27. E Tuzun AJ Sharp JA Bailey R Kaul VA Morrison LM Pertz E Haugen H Hayden D Albertson D Pinkel MV Olson EE Eichler 2005 Fine-scale structural variation of the human genome Nat Genet 37 727 732 1:CAS:528:DC%2BD2MXlslWhsrk%3D 10.1038/ng1562 15895083 (Pubitemid 41754889)
28. T Ujino-Ihara H Kanamori H Yamane Y Taguchi N Namiki Y Mukai K Yoshimura Y Tsumura 2005 Comparative analysis of expressed sequence tags of conifers and angiosperms reveals sequences specifically conserved in conifers Plant Mol Biol 59 895 907 1:CAS:528:DC%2BD2MXht1Cqt7nM 10.1007/s11103-005-2080-y 16307365 (Pubitemid 41677675)
29. EL van Rozendaal GP Lelyveld TA van Beek 2000 Screening of the needles of different yew species and cultivars for paclitaxel and related taxoids Phytochemistry 53 383 389 10.1016/S0031-9422(99)00094-1 10703062 (Pubitemid 30096921)
30. X Xia Z Xie WH Li 2003 Effects of GC content and mutational pressure on the lengths of exons and coding sequences J Mol Evol 56 362 370 1:CAS:528:DC%2BD3sXhslWhsrk%3D 10.1007/s00239-002-2406-1 12612839 (Pubitemid 36279040)
31. X Wang Q Zhang X Sun 2009 Fosmid library construction and initial analysis of end sequences in female half-smooth tongue sole (Cynoglossus semilaevis) Mar Biotechnol 11 236 242 1:CAS:528:DC%2BD1MXitFKhsb4%3D 10.1007/s10126-008-9137-2 18763017
32. T Wicker B Keller 2007 Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families Genome Res 17 1072 1081 1:CAS:528:DC%2BD2sXnvVWkurk%3D 10.1101/gr.6214107 17556529 (Pubitemid 47026354)
33. F Zakrzewski T Wenke D Holtgräwe B Weisshaar T Schmidt 2010 Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris BMC Plant Biol 10 8 10.1186/1471-2229-10-8 20064260
34. L Zhang Z Bao J Cheng H Li X Huang S Wang C Zhang J Hu 2007 Fosmid library construction and initial analysis of end sequences in zhikong scallop (Chlamys farreri) Mar Biotechnol 9 606 612 1:CAS:528:DC%2BD2sXhtFylu7zL 10.1007/s10126-007-9014-4 17605073 (Pubitemid 47599034)