LOCUS FX175460 878 bp mRNA linear TSA 23-MAY-2012 DEFINITION TSA: Pandanus boninensis mRNA, contig: Pb_c13710. ACCESSION FX175460 VERSION FX175460.1 DBLINK BioProject:PRJDA67377 Sequence Read Archive:DRR001102 BioSample:SAMD00011606 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Pandanus boninensis ORGANISM Pandanus boninensis Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Pandanales; Pandanaceae; Pandanus. REFERENCE 1 (bases 1 to 878) AUTHORS Yoshimaru,H. and Suzuki,S. TITLE Direct Submission JOURNAL Submitted (30-MAY-2011) to the DDBJ/EMBL/GenBank databases. Contact:Hiroshi Yoshimaru Forestry and Forest Products Research Institute, Department of Forest Genetics; 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan REFERENCE 2 AUTHORS Setsuko,S., Uchiyama,K., Sugai,K. and Yoshimaru,H. TITLE Development of EST-SSR markers from cDNA library of Pandanus boninensis Warburg (Pandanaceae) JOURNAL Unpublished (2011) COMMENT Several-year-old seedlings of Pandanus boninensis naturally grown in Bonin Island were used for RNA extraction. About 3 g of inner bark was cut and frozen in liquid nitrogen, ground using mortar and pestle. Total RNA was extracted by the CTAB method (Le Provost et al., 2007), and contaminated DNA was removed by SV total RNA isolation system (Promega, Madison, WI). The cDNA library construction and next generation sequencing by Roche 454 GS FLX sequencer with titanium chemistry were carried out by the Hokkaido System Science Co., Ltd. (Hokkaido, Japan). To remove polyA and adapter sequences from the cDNA sequences, the Program cross_match (http://bozeman.mbt.washington.edu/phrap.docs/phrap.html) and TIGR SeqClean sequence trimming pipeline (http://compbio.dfci.harvard.edu/tgi/software/) was used prior to further analyses. We used a EST sequence assembler MIRA (Chevreux et al., 2004) to run de novo assemblies. FEATURES Location/Qualifiers source 1..878 /db_xref="taxon:1035881" /dev_stage="several year old seedlings" /mol_type="mRNA" /note="contig: Pb_c13710" /organism="Pandanus boninensis" /tissue_type="mixture of inner bark, current year twigs and terminal buds" BASE COUNT 327 a 164 c 146 g 239 t ORIGIN 1 tgcccttgaa gttaattagg tacaaagaca tgtgaaanac taactacaaa caaattacca 61 taaattaaga tataacacac acaagctcaa ccaagagaaa aaggaaccac atgatggatg 121 cattaacatt gcactttggt tgctcatgca tagaagtagg aaatagaacg caatacttct 181 cttggatggt gtgtttccat attttccaga aatgaaaagg aggatagacc taccactgta 241 acaatgttac aagaatatcg ttcacatact tccgtagttc aaaaccatta ccatcatcat 301 tatgcatgca atcatcaaca tcctaaatgc ctagtaaaag atcctaaaaa ttgtagtgtt 361 caaaattttt gactctcaat gatttaatca tgaaggcttt aggaacaaac tatacttctg 421 atcccaagca gaaggtaatg gtcaataaca gtcaaaatgt tsaaatactt agttaaatac 481 atgatattga agctctcctc aggctatgca cggctctttc catcaacata tgcaaggatg 541 tggatctcaa tgaggatgtt ccaaaaaaac aaagaaaaat gaagggaaaa ggctgttctt 601 tcaaacctga aacaggtctc gtaccatgca ccttttttta gacatgattt ttgtcaagca 661 tccaaggaaa tccatgttta ccatcttctg gacagagtaa gttgaacagc taatcatctg 721 caaccaagag aatgggtata tcaatatgca atagactata caagaataat aagagtgtcg 781 tcgatcaatc agtaaggtat ccctaacaca tcccaactat attttacaat tgaattgtac 841 aggcttctat gcaagggaag acaagaatga tatattac //