LOCUS FX173158 712 bp mRNA linear TSA 23-MAY-2012 DEFINITION TSA: Pandanus boninensis mRNA, contig: Pb_c11408. ACCESSION FX173158 VERSION FX173158.1 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 712) 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TITLE Development of EST-SSR markers from cDNA library of Pandanus boninensis Warburg (Pandanaceae) JOURNAL Unpublished (2011) COMMENT Several-year-old seedlings of Pandanus boninensis naturally grown in Bonin Island were used for RNA extraction.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..712 /db_xref="taxon:1035881" /dev_stage="several year old seedlings" /mol_type="mRNA" /note="contig: Pb_c11408" /organism="Pandanus boninensis" /tissue_type="mixture of inner bark, current year twigs and terminal buds" BASE COUNT 196 a 134 c 169 g 213 t ORIGIN 1 caggtgacca taaaatgtta ccatttcctg cagtgcgagc caaagtttgt tggcctcgta 61 ggcctagcag gggtgttgcc cttgtttcat gcttaaagga ggatgctgac catattgtcc 121 aggaactaga ctatcaactg gaggttggtg gaaggtatgt caattgtgaa gttagcacca 181 agtacatcaa ctgtattttt gtaactggaa ttccaaggga tgttgcagaa ccagagttat 241 atgatgcatt tcaaagtgtg acaaagcgga aaatccttgg tattcatatc ttgagaggag 301 aagcaatcaa caacatttca cgtgctgctt gtgcagaaat gcttgttaga gaaatcactc 361 cctttatgcc taacaagcat gtccctagcc ataattttca ggttgaagtg ttcaaccccc 421 gaaccgaagg attatatgat gaaagctatg atcacttttt gatggaagtt tacatttgga 481 ggcagcaaag gctttggatc acatccaggg gaaagtgctt cctggcttcc tttcatggca 541 aaggatacaa tgccaacata tgtttcacag ctcagtttct tgctctggtc gtgttttttc 601 tgttatcagg aagcaacttg attctctact tggaagcttc aagcatcgga aaggtgtgct 661 ttgtaagctt gagaggaatg ataatggctc ttttagtgta aagatacgtg cc //