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

Yao, Lina; Tan, Tin Wee; Ng, Yi-Kai; Ban, Kenneth Hon Kim; Shen, Hui; Lin, Huixin; Lee, Yuan Kun

doi:10.1186/s13068-015-0382-0

Biotechnology for Biofuels and Bioproducts

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	*

BlastX with C. reinhardtii using cut-off value at E-value ≤10⁻⁶ for this comparison
The one in italic font was chosen in the database optimization for each gene
+, the NCBI nucleotide was chosen for the corresponding gene, but it was elongated by part of the sequence from Bag2D
*, 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)

Back to article page

ISSN: 2731-3654

Contact us

General enquiries: journalsubmissions@springernature.com