De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production.
BACKGROUND
Microalgae, which can absorb carbon dioxide and then transform it into lipid, are promising candidates to produce renewable energy, especially biodiesel. The paucity of genomic information, however, limits the development of genome-based genetic modification to improve lipid production in many microalgae. Here, we describe the de novo sequencing, transcriptome assembly, annotation and differential expression analysis for Chlorella sorokiniana cultivated in different conditions to reveal the change of genes expression associated with lipid accumulation and photosynthetic carbon fixation.


RESULTS
Six cultivation conditions were selected to cultivate C. sorokiniana. Lipid content of C. sorokiniana under nitrogen-limited condition was 2.96 times than that under nitrogen-replete condition. When cultivated in light with nitrogen-limited supply, C. sorokiniana can use carbon dioxide to accumulate lipid. Then, transcriptome of C. sorokiniana was sequenced using Illumina paired-end sequencing technology, and 244,291,069 raw reads with length of 100 bp were produced. After preprocessed, these reads were de novo assembled into 63,811 contigs among which 23,528 contigs were found homologous sequences in public databases through Blastx. Gene expression abundance under six conditions were quantified by calculating FPKM value. Ultimately, we found 385 genes at least 2-fold up-regulated while 71 genes at least 2-fold down-regulated in nitrogen-limited condition. Also, 204 genes were at least 2-fold up-regulated in light while 638 genes at least 2-fold down-regulated. Finally, 16 genes were selected to conduct RT-qPCR and 15 genes showed the similar results as those identified by transcriptomic analysis in term of differential expression.


CONCLUSIONS
De novo transcriptomic analyses have generated enormous information over C. sorokiniana, revealing a broad overview of genomic information related to lipid accumulation and photosynthetic carbon fixation. The genes with expression change under different conditions are highly likely the potential targets for genetic modification to improve lipid production and CO2fixation efficiency in oleaginous microalgae.
Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.
Lin
L
Li
Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.
Guoqiang
G
Zhang
Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China. wang_qh@tib.cas.cn.
Qinhong
Q
Wang
Chlorella sorokiniana; Lipid accumulation; Photosynthetic carbon fixation; RNA-seq; Transcriptome
Plant J. 2008 May;54(4):621-39
18476868
J Ind Microbiol Biotechnol. 2009 Feb;36(2):269-74
18982369
Genomics. 2013 Apr;101(4):229-37
23396177
BMC Genomics. 2013 Jul 01;14:434
23815514
Biotechnol Biofuels. 2013 Aug 23;6(1):118
23971877
Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
22080510
J Microbiol Methods. 2007 Mar;68(3):639-42
17189655
Bioresour Technol. 2011 Jan;102(1):123-9
20594832
Science. 1997 Oct 24;278(5338):631-7
9381173
BMC Bioinformatics. 2011 Aug 04;12:323
21816040
Plant Cell. 1998 Mar;10(3):383-98
9501112
PLoS One. 2012;7(7):e41286
22911771
Plant Cell. 2010 Sep;22(9):2943-55
20852019
Biochem J. 2007 Nov 15;408(1):61-8
17688423
Plant J. 2007 Nov;52(4):716-29
17877700
Environ Microbiol. 2015 Sep;17(9):3341-51
25684321
Gene. 2013 Jul 10;523(2):117-21
23603020
BMC Bioinformatics. 2007 Feb 07;8:42
17286856
Wei Sheng Wu Xue Bao. 2014 Sep 4;54(9):1010-21
25522590
Appl Microbiol Biotechnol. 2004 Nov;65(6):635-48
15300417
Plant Cell. 2004 Jun;16(6):1466-77
15155888
Nat Biotechnol. 2011 May 15;29(7):644-52
21572440
Plant Physiol. 2010 Oct;154(2):1001-11
20720172
PLoS One. 2011;6(10):e25851
22043295
Biochim Biophys Acta. 1956 Aug;21(2):376-7
13363921
J Biotechnol. 2014 Aug 20;184:27-38
24844864
Biotechnol Biofuels. 2012 Sep 24;5(1):74
23006831
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5
17526522
J Biotechnol. 2006 Dec 1;126(4):499-507
16772097
Plant Physiol. 2010 Dec;154(4):1737-52
20935180
Biotechnol Adv. 2012 Nov-Dec;30(6):1344-53
22361647
PLoS One. 2014 Dec 02;9(12):e114238
25461610
Bioresour Technol. 2006 Apr;97(6):841-6
15936938
J Mol Biol. 2004 Mar 12;337(1):49-63
15001351
J Biotechnol. 2009 Apr 20;141(1-2):31-41
19428728
BMC Genomics. 2011 Mar 14;12:148
21401935
Bioinformatics. 2010 Mar 1;26(5):680-2
20053844
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Methods. 2001 Dec;25(4):402-8
11846609
Nucleic Acids Res. 2000 Jan 1;28(1):33-6
10592175
J Biol Chem. 1950 Aug;185(2):781-7
14774424
Genetics. 2008 May;179(1):31-9
18493038
Biotechnol Adv. 2007 May-Jun;25(3):294-306
17350212