LOCUS FX085123 302 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 10881_Contig1, strain: BOT22. ACCESSION FX085123 VERSION FX085123.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 302) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..302 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to 3-hydroxyacyl-CoA dehydrogenase" /note="contig: 10881_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 72 a 67 c 77 g 86 t ORIGIN 1 gtaccggccc tgccccctcc ttatccagta tgtcgacgct ggctggcttg gaaagaaagc 61 gtctagagga gttttttcat acgattcctg agacatatgt agaagttttc acgttactcc 121 tgagcagtct gagctcgaga attagcaccc cattgactgt cagtaacttt tccacggcgt 181 tcatggttca gaaggatgct ggcttccaaa atcctcagtg tgttgtgtct gaagtgttca 241 agcaacagct ggggtactgg ggacatgctt tgaagatatt ggtaacagta gcctaagatt 301 ag // LOCUS FX085124 523 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 10001_Contig1, strain: BOT22. ACCESSION FX085124 VERSION FX085124.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 523) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..523 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to 3-ketoacyl-CoA synthase" /note="contig: 10001_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 137 a 115 c 120 g 151 t ORIGIN 1 attgatgagt tggaagagaa attgatgttg actccaaagc aggtccagcc ctcaaaggat 61 acactgtacc gctttggaaa cacatctgca gcatcaactt ggtacattct tgccaacatt 121 gaacatacca cagggattcg aaagggcgaa cgcatttggc agctgggctt tggtggaggt 181 ttcaaatgca acagcgcagt gtggaaggca cgaaggaatg tcaagcagtc acatacctgc 241 tgggactaga ttttctgaga cgtcagaact caactgtcat acaaacatca gcagtttgct 301 caccattagg acgtggtttg cagattttgc agacacccta attgttcgca acatttgtct 361 tagttatcgg tggcatacca tgctgtcctg ggtatttaac agtcaaatta aagatcaccc 421 atgccttggt gacagttttc agttctggta ttgtgacatt tcatgatttc agcttctggc 481 cgttttgctt tctgaccaca cctgcatcct agttttttca gtg // LOCUS FX085125 281 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 11709_Contig1, strain: BOT22. ACCESSION FX085125 VERSION FX085125.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 281) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..281 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to 3-ketoacyl-CoA synthase" /note="contig: 11709_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 67 a 64 c 72 g 78 t ORIGIN 1 ctcgggagga gtcggagctg gcactgtttg tatctattca agaagctcct aggacaaaac 61 tggcctgaaa gcaaaggata atagatggag ttatttgcca ttgtaccgcc ttcaatccag 121 tgccatctct gtctgcatcc gttgtccatc acttcaagat gcgttacgat gtgatgtcct 181 acaatctggc gggcatggga tgtgctgcat ccatcatcgc tgttgacttg gccaaggaaa 241 ttatttggaa tcaccctgag aaacgcattc ttgtgtgcgg g // LOCUS FX085126 249 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 13157_Contig1, strain: BOT22. ACCESSION FX085126 VERSION FX085126.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 249) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..249 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to 3-ketoacyl-CoA synthase" /note="contig: 13157_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 72 a 51 c 69 g 57 t ORIGIN 1 gcattgtgtg cggacacaca tggggtccag cgatgaaagc tatggatgca tatatcaatg 61 cgaagatgaa gctgggaaca ttggggtcca tttgtcaaag gatttaatga cagtggcggg 121 acgagccttg aagtcaaata taacagcgtt agggcccttg gtcctaccgt tttccgagca 181 gctgaagttc atggttacgc acatcaagcg gaaggtgctc aaaagcaaag ataaacccta 241 cttgccagt // LOCUS FX085127 257 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 13716_Contig1, strain: BOT22. ACCESSION FX085127 VERSION FX085127.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 257) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..257 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to 3-ketoacyl-CoA synthase" /note="contig: 13716_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 61 a 61 c 73 g 62 t ORIGIN 1 gcctttggct gcatgggcaa tggagaagat gccgaaggtg tcaagggggt tttcttgcgc 61 cgcaatgttg tgaatgtggc gggacgtgcc ctgaaataca atctgacgcg cctgggcccc 121 cttgttctgc catactccca gctgatgaaa tgctacatgg acaagaactt cactccagac 181 ttcaagacgg catttgacca cttcttgctg cacactggag gacgcgcagt cattgatgag 241 ttggaagaga aattgat // LOCUS FX085128 152 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 8047_Contig1, strain: BOT22. ACCESSION FX085128 VERSION FX085128.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 152) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..152 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to 3-ketoacyl-CoA synthase" /note="contig: 8047_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 49 a 39 c 32 g 32 t ORIGIN 1 cgcagagctc tccaagttgc agagcagcat ttaaagccag acccaaaacc cagttgccat 61 acccggtcgc ccttttttac atggtgattg gtctccacat atgaccatgc ataccaagtg 121 gagcaggatg aggtattgcc aaaaaaaaaa aa // LOCUS FX085129 255 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: FR19XNJ02JW0UI, strain: BOT22. ACCESSION FX085129 VERSION FX085129.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 255) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..255 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to 3-oxoacyl-[acyl-carrier-protein] reductase" /note="contig: FR19XNJ02JW0UI" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 64 a 70 c 76 g 45 t ORIGIN 1 gccatctccc ccggttggat aaacaccttc caggagcccg acgagatcac cgccgccgac 61 aaagactggc accttgtggg cagaagtggg caggaccaga ggacatagcg caggcagccc 121 tctttttggc agacagcgaa aaggctggct tcatcaccgg ccaggacctg gtggtggatg 181 gtggcgtctc cataaaaatg gtctacccgg aatagatgac gcctcgcatg tgctcacgaa 241 gtgaagaagt atagt // LOCUS FX085130 285 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 11030_Contig1, strain: BOT22. ACCESSION FX085130 VERSION FX085130.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 285) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..285 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to acyl-CoA dehydrogenase" /note="contig: 11030_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 59 a 66 c 100 g 60 t ORIGIN 1 gaacaagggt gtgtatgtgt tgatgtctgg cttggactat gagcggttgg ttttggcggc 61 tggcccggtc ggcattctgc aagcctgctt ggacaacgtt ctgccgtacg tcacgacccg 121 acagcagttt gggaggccga ttggggagtt tcagctggtg caaggcaaac tagcggacat 181 gtacgcaaca accgcagcgg cgcgagcact tgtgtactcc atagcggcaa aggcagacag 241 ggatgcgtac accaggaaag gtgagcgggc tcgggattgt gctgc // LOCUS FX085131 396 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: 8611_Contig1, strain: BOT22. ACCESSION FX085131 VERSION FX085131.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 396) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..396 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to beta-ketoacyl-acyl-carrier-protein synthase I" /note="contig: 8611_Contig1" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 104 a 108 c 97 g 87 t ORIGIN 1 gaactaacta ttaaatgcac atgacaacga gcaccttagt tggtgacatt gccgaggtaa 61 aggccatcaa gaatgtcttc tccgacagat cgcacatcaa gatgaatggc accaagtcga 121 tgattggaca ctgcttgggt gctgccgccg gcattgaggc tgttgccacc attaaagcca 181 tcgagactgg ctgggtccat cctaccatca accaggagaa ccaaatcgac gaggtggcag 241 acttcaacac tgtccccaac atcaagcagg agcacaaggt cactgccggt ctttccaact 301 cctttggatt tggtgggcac aactccgtag ttgtctttgg tccctatggc aacgggtccg 361 cataaaagca gccatggtgc ctgtccccaa tgactg // LOCUS FX085132 192 bp mRNA linear TSA 07-MAR-2012 DEFINITION TSA: Botryococcus braunii mRNA, contig: FR19XNJ02G52FD, strain: BOT22. ACCESSION FX085132 VERSION FX085132.1 DBLINK BioProject:PRJDA50789 Sequence Read Archive:DRR000584 BioSample:DRR000584 KEYWORDS TSA; Transcriptome Shotgun Assembly. SOURCE Botryococcus braunii ORGANISM Botryococcus braunii Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Trebouxiophyceae; Trebouxiophyceae incertae sedis; Elliptochloris clade; Botryococcus. REFERENCE 1 (bases 1 to 192) AUTHORS Baba,M., Ioki,M., Nakajima,N., Shiraiwa,Y. and Watanabe.M.M. TITLE Direct Submission JOURNAL Submitted (25-OCT-2010) to the DDBJ/EMBL/GenBank databases. Contact:Nobuyoshi Nakajima National Institute for Environmental Studies, Environmental Biology Division; Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan REFERENCE 2 AUTHORS Ioki,M., Baba,M., Nakajima,N., Shiraiwa,Y. and Watanabe,M.M. TITLE Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads JOURNAL Bioresour. Technol. 109, 292-296 (2012) REFERENCE 3 AUTHORS Ioki,M., Baba,M., Bidadi,H., Suzuki,I., Shiraiwa,Y., Watanabe,M.M. and Nakajima,N. TITLE Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii JOURNAL Bioresour. Technol. 109, 271-276 (2012) COMMENT This strain of Botryococcus braunii, isolated from the Kanna Dam in Okinawa, Japan on April 22nd, 2004, produces terpenoid-derived liquid hydrocarbons. We obtained partial mRNA sequences via 454 pyrosequencing. The cDNA reads were filtered, clustered and assembled using the Paracel TranscriptAssemblerTM Version 2.6 software (Paracel). In the filtering process, (i) poly A/T sequences detected in 5'- and 3'-ends of the cDNA reads by the HASTE algorithm and (ii) repetitive sequences detected by the DUST algorithm were marked not to be used in the clustering process. Terminal sequences with low quality values, the adaptor sequences, and short sequences of less than 50 bases were removed. The parameters used in the filtering process were as following: ATAIL (PolyDist=30, Threshold=8, Action=annot); DUST (Threshold=22, Action=annot); VECTOR (Reference file=SMART adaptor sequence, Threshold=20); QUALCLEAN (Threshold=15); MINLEN (Threshold=50). In the clustering process, the filtered sequences were grouped into clusters locally sharing common sequences detected by one-to-one comparisons. The parameters used in the clustering process were as following: compare_matrix=dna.p1m6.l.mat, WordLen=12, cluster_threshold=50. The sequences within each cluster were subjected to the assembling procedure to retrieve non-redundant sequences based on global similarity detected by the CAP4 algorithm. The parameters used in the assembling process were as following: InOverfhand=30, EndOverhang=30, ClipQual=10, QualSumLim=300, PenalizeN=0, IgnorePolyMaskChars=on, KeepDups=on. FEATURES Location/Qualifiers source 1..192 /db_xref="taxon:38881" /mol_type="mRNA" /note="Partial mRNA sequence for gene encoding protein similar to fructose-bisphosphatase" /note="contig: FR19XNJ02G52FD" /organism="Botryococcus braunii" /strain="BOT22" BASE COUNT 37 a 59 c 55 g 41 t ORIGIN 1 ttggccggct ggcttgcgaa cctacattga caccatccgg caaggcaagg ggcagtaccc 61 aaagcagtat tcggctcgat acatttgctc ccttgtggct gacctgcata ggacgctgct 121 gtacggggga gtggcaatga atccgcgctc gcacctgcgc cttgtctacg agggcaaccc 181 cctggccttc at //