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Table 4 Comparison studies of transcripts from Bag2D program and NCBI

From: RNA-Seq transcriptomic analysis with Bag2D software identifies key pathways enhancing lipid yield in a high lipid-producing mutant of the non-model green alga Dunaliella tertiolecta

D. tertiolecta transcripts from Bag2D E-value Length (bps) D. tertiolecta nucleotide from NCBI E-value Length (bps) Aligned score Elongated
>Locus_1123_4Transcript_1/2_Confidence_0.800_Length_1500 0 1500 >gi|46981381|gb|AY575952.1| Dunaliella tertiolecta assimilatory nitrate reductase (nar) gene, partial cds 2e−18 1313  
   >gi|311818483|emb|HH768845.1| Sequence 5032 from Patent EP2221382 0 2531 90.6  
   >gi|18913154|gb|AY078279.1| Dunaliella tertiolecta assimilatory nitrate reductase (nar) mRNA, complete cds 0 3447 90.6 +
>Locus_96_4Transcript_1/1_Confidence_1.000_Length_1881 0 1881 >gi|3869303|gb|AF065142.1| Dunaliella tertiolecta glutamine synthetase mRNA, partial cds 2e−109 601 92.8453  
>Locus_797_6Transcript_1/1_Confidence_1.000_Length_1463 1e−144 1463 >gi|2645974|gb|AF034201.1| Dunaliella tertiolecta proliferating cell nuclear antigen (PCNA) mRNA, partial cds 7e−122 616 97.8896  
>Locus_6018_7Transcript_2/2_Confidence_0.667_Length_959 2e−115 959 >gi|12232559|gb|AF036312.2| Dunaliella tertiolecta mitotic cyclin mRNA, partial cds 6e−47 490 96.1224 +
>Locus_1375_7Transcript_7/9_Confidence_0.632_Length_1220 1e−132 1220 >gi|167984|gb|M60049.1|DUNCAB D.tertiolecta 28.5-kDa LHCII apoprotein mRNA, complete cds 2e−132 1041 91.0663  
>Locus_169_2Transcript_3/5_Confidence_0.632_Length_1062 3e−122 1062 >gi|225322931|gb|FJ769282.1| Dunaliella tertiolecta ascorbate peroxidase mRNA, partial cds 1e−72 546 87.5458  
>Locus_1725_6Transcript_1/1_Confidence_1.000_Length_1811 0 1811 >gi|585087513|gb|KF193066.1| Dunaliella tertiolecta sedoheptulose-1,7-bisphosphatase (SBP) mRNA, complete cds 2e−180 1631 97.9767  
>Locus_613_6Transcript_1/1_Confidence_1.000_Length_1405 0 1405 >gi|682124627|gb|KJ930518.1| Dunaliella tertiolecta mitogen-activated protein kinase (MAPK) mRNA, complete cds 0 1687 90.3915 +
>Locus_284_4Transcript_1/1_Confidence_1.000_Length_1355 2e−16 1355 >gi|371532816|gb|JQ039042.1| Dunaliella tertiolecta ATP-dependent Clp protease proteolytic subunit (clpP) mRNA, complete cds; plastid 2e−16 1560 98.2288  
>Locus_17606_9Transcript_1/1_Confidence_1.000_Length_2042 0 2042 >gi|682124625|gb|KJ930517.1| Dunaliella tertiolecta phosphofructokinase (PFK) mRNA, complete cds 0 2049 99.3144  
>Locus_979_2Transcript_1/2_Confidence_0.833_Length_2662 4e−139 2662 >gi|144601644|gb|EF471039.1| Dunaliella tertiolecta isolate 1 NRT2 (Nrt2) gene, partial cds 5e−50 644 94.4099  
>Locus_1062_4Transcript_1/1_Confidence_1.000_Length_630 2e−82 630 >gi|19879329|gb|AY032598.1| Dunaliella tertiolecta nucleoside diphosphate kinase mRNA, complete cds 7e−57 840 42.5397 *
>Locus_2576_1Transcript_1/1_Confidence_1.000_Length_1955 0 1955 >gi|459938225|gb|KC572136.1| UNVERIFIED: Dunaliella tertiolecta isolate PL1 acetyl-CoA carboxylase beta subunit-like (accD) gene, partial sequence; chloroplast 1e−42 925 44.973  
>Locus_468_7Transcript_1/1_Confidence_1.000_Length_1448 0 1448 >gi|4165328|gb|AF038570.1| Dunaliella tertiolecta cyclin-dependent kinase 1 (DUNCDC2) mRNA, complete cds 0 1061 99.7172  
>Locus_652_4Transcript_1/1_Confidence_1.000_Length_2435 0 2435 >gi|371532796|gb|JQ039032.1| Dunaliella tertiolecta ATP synthase CF1 alpha subunit (atpA) mRNA, complete cds; plastid 0 1515 42.8383 *
>Locus_7608_9Transcript_1/1_Confidence_1.000_Length_2170 0 2170 >gi|371532798|gb|JQ039033.1| Dunaliella tertiolecta ATP synthase CF1 beta subunit (atpB) mRNA, partial cds; plastid 5e−177 1167 46.8723 *
>Locus_3958_1Transcript_1/1_Confidence_1.000_Length_2042 0 2042 >gi|371532912|gb|JQ039091.1| Dunaliella tertiolecta elongation factor Tu (tufA) mRNA, complete cds; plastid 8e−154 1257 47.494  
>Locus_3579_4Transcript_1/1_Confidence_1.000_Length_943 1e−64 943 >gi|371532800|gb|JQ039034.1| Dunaliella tertiolecta ATP synthase CF1 epsilon subunit (atpE) mRNA, complete cds; plastid 3e−07 408 26.4706 *
>Locus_6870_1Transcript_3/3_Confidence_0.778_Length_1870 1e−117 1870 >gi|761262915|gb|KJ930371.1| Dunaliella tertiolectaglucose-6-phosphate dehydrogenase (G6PDH) mRNA, complete cds;chloroplast 3e−72 3246 34.6524 *
  1. BlastX with C. reinhardtii using cut-off value at E-value ≤10−6 for this comparison
  2. The one in italic font was chosen in the database optimization for each gene
  3. +, the NCBI nucleotide was chosen for the corresponding gene, but it was elongated by part of the sequence from Bag2D
  4. *, the two nucleotides did not quite match from the two methods, which may have been caused by the existence of isoforms or errors of the one from NCBI (determined by E-value and analyses of the sequences)