LOCUS FX173436 476 bp mRNA linear TSA 23-MAY-2012 DEFINITION TSA: Pandanus boninensis mRNA, contig: Pb_c11686. ACCESSION FX173436 VERSION FX173436.1 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 476) 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TITLE Development of EST-SSR markers from cDNA library of Pandanus boninensis Warburg (Pandanaceae) JOURNAL Unpublished (2011) COMMENT Several-year-old seedlings of Pandanus boninensis naturally grown in Bonin Island were used for RNA extraction.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..476 /db_xref="taxon:1035881" /dev_stage="several year old seedlings" /mol_type="mRNA" /note="contig: Pb_c11686" /organism="Pandanus boninensis" /tissue_type="mixture of inner bark, current year twigs and terminal buds" BASE COUNT 102 a 134 c 150 g 89 t ORIGIN 1 gagtacctcc gccgcgccga ggagatccgc gccgtcctcg acgacggtgg caccggcccc 61 gccgccaacg gggacgccgc ggtcgccacc cggcccaaga ccaagyccaa ggatggggat 121 ggggatgggg aggaccccga gcaggctaag ctgcggtcgg ggctcagctc cgctatcatc 181 cgggagaagc ccaacgtgaa gtggaatgat gtcgccgggc tcgagagcgc caagcaggcg 241 ctgcaggagg ctgtgatcct gcccgtcaac gttcccgcag ttcttcacta ggaaagcgaa 301 ggccatggag agcatttctt ttgtatggtc cgcctggaac tgggaagtca tacttggcca 361 aggctgttgc aacagaagca gaatcgactt tcttcagcat ctcttcatca gaccttgttt 421 ctaagtggat gggtgaaagt gaaagctagt atctaatctg ttccaaatgg ctcgtg //