title: Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation.
abstract: BACKGROUND
  Duckweed can thrive on anthropogenic wastewater and produce tremendous biomass production. Due to its relatively high starch and low lignin percentage, duckweed is a good candidate for bioethanol fermentation. Previous studies have observed that water devoid of nutrients is good for starch accumulation, but its molecular mechanism remains unrevealed.
  
  
  RESULTS
  This study globally analyzed the response to nutrient starvation in order to investigate the starch accumulation in duckweed (Landoltia punctata). L. punctata was transferred from nutrient-rich solution to distilled water and sampled at different time points. Physiological measurements demonstrated that the activity of ADP-glucose pyrophosphorylase, the key enzyme of starch synthesis, as well as the starch percentage in duckweed, increased continuously under nutrient starvation. Samples collected at 0 h, 2 h and 24 h time points respectively were used for comparative gene expression analysis using RNA-Seq. A comprehensive transcriptome, comprising of 74,797 contigs, was constructed by a de novo assembly of the RNA-Seq reads. Gene expression profiling results showed that the expression of some transcripts encoding key enzymes involved in starch biosynthesis was up-regulated, while the expression of transcripts encoding enzymes involved in starch consumption were down-regulated, the expression of some photosynthesis-related transcripts were down-regulated during the first 24 h, and the expression of some transporter transcripts were up-regulated within the first 2 h. Very interestingly, most transcripts encoding key enzymes involved in flavonoid biosynthesis were highly expressed regardless of starvation, while transcripts encoding laccase, the last rate-limiting enzyme of lignifications, exhibited very low expression abundance in all three samples.
  
  
  CONCLUSIONS
  Our study provides a comprehensive expression profiling of L. punctata under nutrient starvation, which indicates that nutrient starvation down-regulated the global metabolic status, redirects metabolic flux of fixed CO2 into starch synthesis branch resulting in starch accumulation in L. punctata.
authors: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.|College of Life Sciences, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, Sichuan, 610064, China.
authors: Xiang
authors: X
authors: Tao
authors: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.
authors: Yang
authors: Y
authors: Fang
authors: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.
authors: Yao
authors: Y
authors: Xiao
authors: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.
authors: Yan-Ling
authors: YL
authors: Jin
authors: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.
authors: Xin-Rong
authors: XR
authors: Ma
authors: College of Life Sciences, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, Sichuan, 610064, China.
authors: Yun
authors: Y
authors: Zhao
authors: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.
authors: Kai-Ze
authors: KZ
authors: He
authors: Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China.
authors: Hai
authors: H
authors: Zhao
authors: College of Life Sciences, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, Sichuan, 610064, China.
authors: Hai-Yan
authors: HY
authors: Wang
references: Int J Plant Genomics. 2008;2008:619832
references: 18483572
references: Plant Mol Biol. 2012 Apr;78(6):627-32
references: 22318677
references: Nat Biotechnol. 2011 May 15;29(7):644-52
references: 21572440
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references: 16845012
references: Biochem J. 1998 Mar 15;330 ( Pt 3):1189-95
references: 9494084
references: Plant Cell Environ. 2006 Jan;29(1):115-25
references: 17086758
references: PLoS One. 2011;6(9):e24670
references: 21931804
references: J Environ Qual. 2003 Sep-Oct;32(5):1583-90
references: 14535298
references: Plant Cell. 2007 Jan;19(1):148-62
references: 17237352
references: Photochem Photobiol. 1976 Jun;23(6):425-44
references: 781695
references: BMC Genomics. 2011 Feb 28;12:131
references: 21356090
references: Adv Exp Med Biol. 2002;505:95-111
references: 12083471
references: Plant Physiol. 1978 Oct;62(4):629-35
references: 16660573
references: Bioresour Technol. 2010 Jan;101 Suppl 1:S112-8
references: 19766487
references: Plant Mol Biol. 2009 Mar;69(4):361-73
references: 18688730
references: Science. 1963 Jun 28;140(3574):1397-8
references: 17799843
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Planta. 1970 Dec;90(4):349-59
references: 24499946
references: Trends Genet. 2000 Jun;16(6):276-7
references: 10827456
references: Plant Physiol. 1989 Aug;90(4):1275-8
references: 16666922
references: Biochimie. 2011 Jul;93(7):1179-86
references: 21536093
references: Plant Physiol. 1980 May;65(5):906-12
references: 16661306
references: Physiol Plant. 2008 Nov;134(3):508-21
references: 18785901
references: J Mol Evol. 2008 Jun;66(6):555-64
references: 18463914
references: Nat Genet. 2000 May;25(1):25-9
references: 10802651
references: Bioresour Technol. 2008 Sep;99(13):5270-95
references: 18158236
references: Bioresour Technol. 2007 Mar;98(4):798-807
references: 16713255
references: Genome Biol. 2010;11(8):R86
references: 20738864
references: Plant Physiol. 1970 Oct;46(4):609-13
references: 16657514
references: Plant Physiol. 1981 Jun;67(6):1078-83
references: 16661813
references: Trends Plant Sci. 2006 Dec;11(12):610-7
references: 17092760
references: Bioresour Technol. 2011 Jan;102(2):848-53
references: 20869239
references: Curr Opin Plant Biol. 2003 Jun;6(3):280-7
references: 12753979
references: Nucleic Acids Res. 2008 Dec;36(21):e141
references: 18927111
references: Nat Rev Genet. 2009 Jan;10(1):57-63
references: 19015660
references: Nat Genet. 2007 Jun;39(6):792-6
references: 17496893
references: Bioinformatics. 2010 Jan 1;26(1):139-40
references: 19910308
references: Science. 2006 Jan 27;311(5760):484-9
references: 16439654
references: BMC Genomics. 2009 May 12;10:219
references: 19435504
references: Bioinformatics. 2005 Sep 15;21(18):3674-6
references: 16081474
references: Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6300-5
references: 21444820
references: Annu Rev Plant Biol. 2007;58:47-69
references: 17067284
references: Planta. 2013 Jan;237(1):1-13
references: 23053544
references: Am J Bot. 2012 Feb;99(2):175-85
references: 22312116
references: Mol Ecol. 2008 Apr;17(7):1636-47
references: 18266620
references: Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21
references: 20069535
references: Planta. 2010 Aug;232(3):609-19
references: 20526614
references: Bioresour Technol. 2002 Jan;81(1):81-5
references: 11708759
references: Brief Funct Genomics. 2010 Mar;9(2):118-28
references: 20130067
references: Plant Physiol. 1991 Apr;95(4):1203-8
references: 16668112
references: J Biol Chem. 1984 Oct 25;259(20):12481-8
references: 6548473
references: BMC Plant Biol. 2010 Sep 16;10:205
references: 20846439