An integrated bioinformatics analysis reveals divergent evolutionary pattern of oil biosynthesis in high- and low-oil plants

PLoS ONE

Volumn 11, Issue 5, 2016, Pages

  Zhang, Li ^a   Wang, Shi Bo ^a,b   Li, Qi Gang ^c   Song, Jian ^a   Hao, Yu Qi ^a   Zhou, Ling ^a,d   Zheng, Huan Quan ^e   Dunwell, Jim M ^f   Zhang, Yuan Ming ^a,b  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^c KUNMING INSTITUTE OF ZOOLOGY   (China)

^d INSTITUTE OF PLANT PROTECTION   (China)

^e MCGILL UNIVERSITY   (Canada)

^f UNIVERSITY OF READING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE OIL;

ACCASE GENE; ARTICLE; BIOACCUMULATION; BIOINFORMATICS; BIOSYNTHESIS; COMPARATIVE STUDY; CONTROLLED STUDY; DGAT1 GENE; FATTY ACID SYNTHESIS; GENE DUPLICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOSS; GENE ONTOLOGY; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; LIPID ANALYSIS; LIPID METABOLISM; MOLECULAR EVOLUTION; NONHUMAN; OLES GENE; PDAT1 GENE; PHYLOGENY; PLANT GENE; PP GENE; SEED DEVELOPMENT; STEROS GENE; UPREGULATION; BIOLOGY; METABOLISM; PLANT;

COMPUTATIONAL BIOLOGY; LIPID METABOLISM; PHYLOGENY; PLANT OILS; PLANTS;

EID: 84969792734     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0154882     Document Type: Article

References (110)

1. Scotland RW, Wortley AH. How many species of seed plants are there? Taxon. 2003; 52(1):101.
2. Raven P, Johnson G, Mason K, Losos J, Singer S. Biology: McGraw-Hill Education, 2010.
3. Bao X, Focke M, Pollard M, Ohlrogge J. Understanding in vivo carbon precursor supply for fatty acid synthesis in leaf tissue. Plant J. 2000; 22(1):39-50. PMID: 10792819
4. Rawsthorne S. Carbon flux and fatty acid synthesis in plants. Prog Lipid Res. 2002; 41(2):182-96. PMID: 11755683
5. Li Y, Han D, Hu G, Sommerfeld M, Hu Q. Inhibition of starch synthesis results in overproduction of lipids in Chlamydomonas reinhardtii. Biotechnol Bioengineer. 2010; 107(2):258-68.
6. Weselake RJ, Taylor DC, Rahman MH, Shah S, Laroche A, McVetty PB et al. Increasing the flow of carbon into seed oil. Biotechnol Adv. 2009; 27(6):866-78. doi: 10.1016/j.biotechadv.2009.07.001 PMID: 19625012
7. Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD et al. Acyl-lipid metabolism. The Arabidopsis book / American Society of Plant Biologists. 2013; 11:e0161. doi: 10.1199/tab.0161 PMID: 23505340
8. Beisson F, Koo AJ, Ruuska S, Schwender J, Pollard M, Thelen JJ et al. Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. Plant Physiol. 2003; 132(2):681-97. PMID: 12805597
9. Klaus D, Ohlrogge JB, Neuhaus HE, Dormann P. Increased fatty acid production in potato by engineering of acetyl-CoA carboxylase. Planta. 2004; 219(3):389-96. PMID: 15014998
10. Roesler K, Shintani D, Savage L, Boddupalli S, Ohlrogge J. Targeting of the Arabidopsis homomeric acetyl-coenzyme A carboxylase to plastids of rapeseeds. Plant Physiol. 1997; 113(1):75-81. PMID: 9008389
11. Davis MS, Solbiati J, Cronan JE Jr. Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J Biol Chem. 2000; 275(37):28593-8. PMID: 10893421
12. Vigeolas H, Waldeck P, Zank T, Geigenberger P. Increasing seed oil content in oil-seed rape (Brassica napus L.) by over-expression of a yeast glycerol-3-phosphate dehydrogenase under the control of a seed-specific promoter. Plant Biotechnol J. 2007; 5(3):431-41. PMID: 17430545
13. Jain RK, Coffey M, Lai K, Kumar A, MacKenzie SL. Enhancement of seed oil content by expression of glycerol-3-phosphate acyItransferase genes. Biochem Soc Trans. 2000; 28:958-61. PMID: 11171271
14. Maisonneuve S, Bessoule JJ, Lessire R, Delseny M, Roscoe TJ. Expression of rapeseed microsomal lysophosphatidic acid acyltransferase isozymes enhances seed oil content in Arabidopsis. Plant Physiol. 2010; 152(2):670-84. doi: 10.1104/pp.109.148247 PMID: 19965969
15. Jako C, Kumar A, Wei Y, Zou J, Barton DL, Giblin EM et al. Seed-specific over-expression of an Arabidopsis cDNA encoding a diacylglycerol acyltransferase enhances seed oil content and seed weight. Plant Physiol. 2001; 126(2):861-74. PMID: 11402213
16. Kim H, Kim HU, Suh MC. Efficiency for increasing seed oil content using WRINKLED1 and DGAT1 under the control of two seed-specific promoters, FAE1 and Napin. J Plant Biotechnol. 2012; 39 (4):242-52.
17. Lardizabal K, Effertz R, Levering C, Mai J, Pedroso MC, Jury T et al. Expression of Umbelopsis ramanniana DGAT2A in seed increases oil in soybean. Plant Physiol. 2008; 148(1):89-96. doi: 10.1104/pp.108.123042 PMID: 18633120
18. Weselake RJ, Shah S, Tang M, Quant PA, Snyder CL, Furukawa-Stoffer TL et al. Metabolic control analysis is helpful for informed genetic manipulation of oilseed rape (Brassica napus) to increase seed oil content. J Exp Bot. 2008; 59(13):3543-9. doi: 10.1093/jxb/ern206 PMID: 18703491
19. Zheng P, Allen WB, Roesler K, Williams ME, Zhang S, Li J et al. A phenylalanine in DGAT is a key determinant of oil content and composition in maize. Nat Genet. 2008; 40(3):367-72. doi: 10.1038/ng.85 PMID: 18278045
20. Baud S, Wuilleme S, To A, Rochat C, Lepiniec L. Role of WRINKLED1 in the transcriptional regulation of glycolytic and fatty acid biosynthetic genes in Arabidopsis. Plant J. 2009; 60(6):933-47. doi: 10.1111/j.1365-313X.2009.04011.x PMID: 19719479
21. Mu JY, Tan HL, Zheng Q, Fu FY, Liang Y, Zhang JA et al. LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis. Plant Physiol. 2008; 148(2):1042-54. doi: 10.1104/pp.108.126342 PMID: 18689444
22. Tan H, Yang X, Zhang F, Zheng X, Qu C, Mu J et al. Enhanced seed oil production in canola by conditional expression of Brassica napus LEAFY COTYLEDON1 and LEC1-LIKE in developing seeds. Plant Physiol. 2011; 156(3):1577-88. doi: 10.1104/pp.111.175000 PMID: 21562329
23. Baud S, Mendoza MS, To A, Harscoet E, Lepiniec L, Dubreucq B. WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis. Plant J. 2007; 50(5):825-38. PMID: 17419836
24. Wang H, Guo J, Lambert KN, Lin Y. Developmental control of Arabidopsis seed oil biosynthesis. Planta. 2007; 226(3):773-83. PMID: 17522888
25. Song QX, Li QT, Liu YF, Zhang FX, Ma B, Zhang WK et al. Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants. J Exp Bot. 2013; 64(14): 4329-41. doi: 10.1093/jxb/ert238 PMID: 23963672
26. Liu YF, Li QT, Lu X, Song QX, Lam SM, Zhang WK et al. Soybean GmMYB73 promotes lipid accumulation in transgenic plants. BMC Plant Biol. 2014; 14:73. doi: 10.1186/1471-2229-14-73 PMID: 24655684
27. Crowe AJ, Abenes M, Plant A, Moloney MM. The seed-specific transactivator, ABI3, induces oleosin gene expression. Plant Sci. 2000; 151(2):171-81. PMID: 10808073
28. Monke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hahnel U et al. Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res. 2012; 40(17):8240-54. PMID: 22730287
29. Smooker AM, Wells R, Morgan C, Beaudoin F, Cho K, Fraser F et al. The identification and mapping of candidate genes and QTL involved in the fatty acid desaturation pathway in Brassica napus. Theor Appl Genet. 2011; 122(6):1075-90. doi: 10.1007/s00122-010-1512-5 PMID: 21184048
30. Ying JZ, Shan JX, Gao JP, Zhu MZ, Shi M, Lin HX. Identification of quantitative trait loci for lipid metabolism in rice seeds. Mol Plant. 2012; 5(4):865-75. doi: 10.1093/mp/ssr100 PMID: 22147755
31. Schwender J, Hay JO. Predictive modeling of biomass component tradeoffs in Brassica napus developing oilseeds based on in silico manipulation of storage metabolism. Plant Physiol. 2012; 160 (3):1218-36. doi: 10.1104/pp.112.203927 PMID: 22984123
32. van Erp H, Kelly AA, Menard G, Eastmond PJ. Multigene engineering of triacylglycerol metabolism boosts seed oil content in Arabidopsis. Plant Physiol. 2014; 165(1):30-6. doi: 10.1104/pp.114.236430 PMID: 24696520
33. Andre C, Froehlich JE, Moll MR, Benning C. A heteromeric plastidic pyruvate kinase complex involved in seed oil biosynthesis in Arabidopsis. Plant Cell. 2007; 19(6):2006-22. PMID: 17557808
34. Andriotis VM, Kruger NJ, Pike MJ, Smith AM. Plastidial glycolysis in developing Arabidopsis embryos. The New Phytologist. 2010; 185(3):649-62. doi: 10.1111/j.1469-8137.2009.03113.x PMID: 20002588
35. Allen DK, Young JD. Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos. Plant Physiol. 2013; 161(3):1458-75. doi: 10.1104/pp.112.203299 PMID: 23314943
36. Wakao S, Andre C, Benning C. Functional analyses of cytosolic glucose-6-phosphate dehydrogenases and their contribution to seed oil accumulation in Arabidopsis. Plant Physiol. 2008; 146(1):277-88. PMID: 17993547
37. Sanjaya, Durrett TP, Weise SE, Benning C. Increasing the energy density of vegetative tissues by diverting carbon from starch to oil biosynthesis in transgenic Arabidopsis. Plant Biotechnol J. 2011; 9 (8):874-83. PMID: 22003502
38. Meyer K, Stecca KL, Ewell-Hicks K, Allen SM, Everard JD. Oil and protein accumulation in developing seeds is influenced by the expression of a cytosolic pyrophosphatase in Arabidopsis. Plant Physiol. 2012; 159(3):1221-34. doi: 10.1104/pp.112.198309 PMID: 22566496
39. Pedersen P, Elbert B. Soybean growth and development. Iowa State University, University Extension Ames, IA; 2004.
40. Li L, Stoeckert CJ Jr., Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMID: 12952885
41. Jones SI, Vodkin LO. Using RNA-Seq to profile soybean seed development from fertilization to maturity. PLoS ONE. 2013; 8(3):e59270. doi: 10.1371/journal.pone.0059270 PMID: 23555009
42. Theocharidis A, van Dongen S, Enright AJ, Freeman TC. Network visualization and analysis of gene expression data using BioLayout Express(3D). Nature Protocols. 2009; 4(10):1535-50. doi: 10.1038/nprot.2009.177 PMID: 19798086
43. Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP et al. Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol. 2006; 142(2):762-74. PMID: 16920875
44. Mochida K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K. Global landscape of a coexpressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol. 2011; 52(5):785-803. doi: 10.1093/pcp/pcr035 PMID: 21441235
45. Guo K, Zou W, Feng Y, Zhang M, Zhang J, Tu F et al. An integrated genomic and metabolomic framework for cell wall biology in rice. BMC Genomics. 2014; 15:596. doi: 10.1186/1471-2164-15-596 PMID: 25023612
46. Fu FF, Xue HW. Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. Plant Physiol. 2010; 154(2):927-38. doi: 10.1104/pp.110.159517 PMID: 20713616
47. Baud S, Lepiniec L. Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis. Plant Physiol Biochem. 2009; 47(6):448-55. doi: 10.1016/j.plaphy.2008.12.006 PMID: 19136270
48. Banas W, Sanchez Garcia A, Banas A, Stymne S. Activities of acyl-CoA:diacylglycerol acyltransferase (DGAT) and phospholipid:diacylglycerol acyltransferase (PDAT) in microsomal preparations of developing sunflower and safflower seeds. Planta. 2013; 237(6):1627-36. doi: 10.1007/s00425-013-1870-8 PMID: 23539042
49. Kim HU, Hsieh K, Ratnayake C, Huang AH. A novel group of oleosins is present inside the pollen of Arabidopsis. J Biol Chem. 2002; 277(25):22677-84. PMID: 11929861
50. Liu WX, Liu HL, Qu le Q. Embryo-specific expression of soybean oleosin altered oil body morphogenesis and increased lipid content in transgenic rice seeds. Theor Appl Genet. 2013; 126(9):2289-97. doi: 10.1007/s00122-013-2135-4 PMID: 23748707
51. Miquel M, Trigui G, d'Andrea S, Kelemen Z, Baud S, Berger A et al. Specialization of oleosins in oil body dynamics during seed development in Arabidopsis seeds. Plant Physiol. 2014; 164(4):1866-78. doi: 10.1104/pp.113.233262 PMID: 24515832
52. Wang HW, Zhang B, Hao YJ, Huang J, Tian AG, Liao Y et al. The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant J. 2007; 52(4):716-29. PMID: 17877700
53. Maeo K, Tokuda T, Ayame A, Mitsui N, Kawai T, Tsukagoshi H et al. An AP2-type transcription factor, WRINKLED1, of Arabidopsis thaliana binds to the AW-box sequence conserved among proximal upstream regions of genes involved in fatty acid synthesis. Plant J. 2009; 60(3):476-87. doi: 10.1111/j.1365-313X.2009.03967.x PMID: 19594710
54. Jin J, Zhang H, Kong L, Gao G, Luo J. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 2014; 42:D1182-7. doi: 10.1093/nar/gkt1016 PMID: 24174544
55. Jessen D, Roth C, Wiermer M, Fulda M. Two activities of long-chain acyl-coenzyme A synthetase are involved in lipid trafficking between the endoplasmic reticulum and the plastid in Arabidopsis. Plant Physiol. 2015; 167(2):351-66. doi: 10.1104/pp.114.250365 PMID: 25540329
56. Zhao L, Katavic V, Li F, Haughn GW, Kunst L. Insertional mutant analysis reveals that long-chain acyl-CoA synthetase 1 (LACS1), but not LACS8, functionally overlaps with LACS9 in Arabidopsis seed oil biosynthesis. Plant J. 2010; 64(6):1048-58. doi: 10.1111/j.1365-313X.2010.04396.x PMID: 21143684
57. Wu XL, Liu ZH, Hu ZH, Huang RZ. BnWRI1 coordinates fatty acid biosynthesis and photosynthesis pathways during oil accumulation in rapeseed. J Integr Plant Biol. 2014; 56(6):582-93. doi: 10.1111/jipb.12158 PMID: 24393360
58. Ma W, Kong Q, Arondel V, Kilaru A, Bates PD, Thrower NA et al. Wrinkled1, a ubiquitous regulator in oil accumulating tissues from Arabidopsis embryos to oil palm mesocarp. PLoS ONE. 2013; 8(7): e68887. doi: 10.1371/journal.pone.0068887 PMID: 23922666
59. Dussert S, Guerin C, Andersson M, Joet T, Tranbarger TJ, Pizot M et al. Comparative transcriptome analysis of three oil Palm fruit and seed tissues that differ in oil content and fatty acid composition. Plant Physiol. 2013; 162(3):1337-58. doi: 10.1104/pp.113.220525 PMID: 23735505
60. Shen B, Allen WB, Zheng P, Li C, Glassman K, Ranch J et al. Expression of ZmLEC1 and ZmWRI1 increases seed oil production in maize. Plant Physiol. 2010; 153(3):980-7. doi: 10.1104/pp.110.157537 PMID: 20488892
61. Sreenivasulu N, Wobus U. Seed-development programs: a systems biology-based comparison between dicots and monocots. Ann Rev Plant Biol. 2013; 64:189-217.
62. Yamamoto A, Kagaya Y, Usui H, Hobo T, Takeda S, Hattori T. Diverse roles and mechanisms of gene regulation by the Arabidopsis seed maturation master regulator FUS3 revealed by microarray analysis. Plant Cell Physiol. 2010; 51(12):2031-46. doi: 10.1093/pcp/pcq162 PMID: 21045071
63. Pouvreau B, Baud S, Vernoud V, Morin V, Py C, Gendrot G et al. Duplicate maize Wrinkled1 transcription factors activate target genes involved in seed oil biosynthesis. Plant Physiol. 2011; 156(2):674-86. doi: 10.1104/pp.111.173641 PMID: 21474435
64. Wang L, Yu S, Tong C, Zhao Y, Liu Y, Song C et al. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol. 2014; 15(2):R39. doi: 10.1186/gb-2014-15-2-r39 PMID: 24576357
65. Mhaske V, Beldjilali K, Ohlrogge J, Pollard M. Isolation and characterization of an Arabidopsis thaliana knockout line for phospholipid: diacylglycerol transacylase gene (At5g13640). Plant Physiol Biochem. 2005; 43(4):413-7. PMID: 15907694
66. van Erp H, Bates PD, Burgal J, Shockey J, Browse J. Castor phospholipid:diacylglycerol acyltransferase facilitates efficient metabolism of hydroxy fatty acids in transgenic Arabidopsis. Plant Physiol. 2011; 155(2):683-93. doi: 10.1104/pp.110.167239 PMID: 21173026
67. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY et al. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2015; 43:D222-6. doi: 10.1093/nar/gku1221 PMID: 25414356
68. Christiansen C, Abou Hachem M, Janecek S, Vikso-Nielsen A, Blennow A, Svensson B. The carbohydrate-binding module family 20 - diversity, structure, and function. The FEBS Journal. 2009; 276 (18):5006-29. doi: 10.1111/j.1742-4658.2009.07221.x PMID: 19682075
69. Rodriguez-Sanoja R, Oviedo N, Sanchez S. Microbial starch-binding domain. Curr Opinion Microbiol. 2005; 8(3):260-7.
70. Southall SM, Simpson PJ, Gilbert HJ, Williamson G, Williamson MP. The starch-binding domain from glucoamylase disrupts the structure of starch. FEBS Letters. 1999; 447(1):58-60. PMID: 10218582
71. Kammerer B, Fischer K, Hilpert B, Schubert S, Gutensohn M, Weber A et al. Molecular characterization of a carbon transporter in plastids from heterotrophic tissues: the glucose 6-phosphate/phosphate antiporter. Plant Cell. 1998; 10(1):105-17. PMID: 9477574
72. Fischer K. The import and export business in plastids: transport processes across the inner envelope membrane. Plant Physiol. 2011; 155(4):1511-9. doi: 10.1104/pp.110.170241 PMID: 21263040
73. Andriotis VME, Pike MJ, Bunnewell S, Hills MJ, Smith AM. The plastidial glucose-6-phosphate/phosphate antiporter GPT1 is essential for morphogenesis in Arabidopsis embryos. Plant J. 2010; 64(1): 128-39. doi: 10.1111/j.1365-313X.2010.04313.x PMID: 20659277
74. Niewiadomski P, Knappe S, Geimer S, Fischer K, Schulz B, Unte US et al. The Arabidopsis plastidic glucose 6-phosphate/phosphate translocator GPT1 is essential for pollen maturation and embryo sac development. Plant Cell. 2005; 17(3):760-75. PMID: 15722468
75. Kunz HH, Hausler RE, Fettke J, Herbst K, Niewiadomski P, Gierth M et al. The role of plastidial glucose-6-phosphate/phosphate translocators in vegetative tissues of Arabidopsis thaliana mutants impaired in starch biosynthesis. Plant Biol. 2010; 12 Suppl 1:115-28. doi: 10.1111/j.1438-8677.2010.00349.x PMID: 20712627
76. Dyson BC, Allwood JW, Feil R, Xu Y, Miller M, Bowsher CG et al. Acclimation of metabolism to light in Arabidopsis thaliana: the glucose 6-phosphate/phosphate translocator GPT2 directs metabolic acclimation. Plant Cell Environ. 2015; 38(7):1404-17. doi: 10.1111/pce.12495 PMID: 25474495
77. Bourgis F, Kilaru A, Cao X, Ngando-Ebongue GF, Drira N, Ohlrogge JB et al. Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning. Proc Natl Acad Sci U S A. 2011; 108(30):12527-32. doi: 10.1073/pnas.1106502108 PMID: 21709233
78. Ohlrogge JB, Jaworski JG. Regulation of Fatty Acid Synthesis. Annual Review of Plant Physiology and Plant Mol Biol. 1997; 48:109-36.
79. Konishi T, Shinohara K, Yamada K, Sasak Y. Acetyl-CoA carboxylase in higher plants: most plants other than Gramineae have both the prokaryotic and the eukaryotic forms of this enzyme. Plant Cell Physiol. 1996; 37(2):117-22. PMID: 8665091
80. Cernac A, Benning C. WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. Plant J. 2004; 40(4):575-85. PMID: 15500472
81. Girke T, Todd J, Ruuska S, White J, Benning C, Ohlrogge J. Microarray analysis of developing Arabidopsis seeds. Plant Physiol. 2000; 124(4):1570-81. PMID: 11115875
82. Ke J, Behal RH, Back SL, Nikolau BJ, Wurtele ES, Oliver DJ. The role of pyruvate dehydrogenase and acetyl-coenzyme A synthetase in fatty acid synthesis in developing Arabidopsis seeds. Plant Physiol. 2000; 123(2):497-508. PMID: 10859180
83. Chen M, Mooney BP, Hajduch M, Joshi T, Zhou M, Xu D et al. System analysis of an Arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolism. Plant Physiol. 2009; 150(1):27-41. doi: 10.1104/pp.108.134882 PMID: 19279196
84. Hayden DM, Rolletschek H, Borisjuk L, Corwin J, Kliebenstein DJ, Grimberg A et al. Cofactome analyses reveal enhanced flux of carbon into oil for potential biofuel production. Plant J. 2011; 67(6):1018-28. doi: 10.1111/j.1365-313X.2011.04654.x PMID: 21615570
85. Branen JK, Chiou TJ, Engeseth NJ. Overexpression of acyl carrier protein-1 alters fatty acid composition of leaf tissue in Arabidopsis. Plant Physiol. 2001; 127(1):222-9. PMID: 11553750
86. Shockey JM, Fulda MS, Browse JA. Arabidopsis contains nine long-chain acyl-coenzyme a synthetase genes that participate in fatty acid and glycerolipid metabolism. Plant Physiol. 2002; 129 (4):1710-22. PMID: 12177484
87. Tjellstrom H, Strawsine M, Ohlrogge JB. Tracking synthesis and turnover of triacylglycerol in leaves. J Exp Bot. 2015; 66(5):1453-61. doi: 10.1093/jxb/eru500 PMID: 25609824
88. Vanhercke T, El Tahchy A, Shrestha P, Zhou XR, Singh SP, Petrie JR. Synergistic effect of WRI1 and DGAT1 coexpression on triacylglycerol biosynthesis in plants. FEBS Letters. 2013; 587(4):364-9. doi: 10.1016/j.febslet.2012.12.018 PMID: 23313251
89. Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 2014; 345(6199):950-3. doi: 10.1126/science.1253435 PMID: 25146293
90. Siloto RM, Findlay K, Lopez-Villalobos A, Yeung EC, Nykiforuk CL, Moloney MM. The accumulation of oleosins determines the size of seed oilbodies in Arabidopsis. Plant Cell. 2006; 18(8):1961-74. PMID: 16877495
91. Wang X, Devaiah SP, Zhang W, Welti R. Signaling functions of phosphatidic acid. Prog Lipid Res. 2006; 45(3):250-78. PMID: 16574237
92. Lee J, Welti R, Schapaugh WT, Trick HN. Phospholipid and triacylglycerol profiles modified by PLD suppression in soybean seed. Plant Biotechnol J. 2011; 9(3):359-72. doi: 10.1111/j.1467-7652.2010.00562.x PMID: 20796246
93. Lu S, Bahn SC, Qu G, Qin H, Hong Y, Xu Q et al. Increased expression of phospholipase Dα1 in guard cells decreases water loss with improved seed production under drought in Brassica napus. Plant Biotechnol J. 2013; 11(3):380-9. doi: 10.1111/pbi.12028 PMID: 23279050
94. Reyes JC, Muro-Pastor MI, Florencio FJ. The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol. 2004; 134(4):1718-32. PMID: 15084732
95. Velmurugan N, Sung M, Yim SS, Park MS, Yang JW, Jeong KJ. Systematically programmed adaptive evolution reveals potential role of carbon and nitrogen pathways during lipid accumulation in Chlamydomonas reinhardtii. Biotechnol Biofuels. 2014; 7(1):117. doi: 10.1186/s13068-014-0117-7 PMID: 25258645
96. Bi YM, Zhang Y, Signorelli T, Zhao R, Zhu T, Rothstein S. Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll synthesis and glucose sensitivity. Plant J. 2005; 44(4):680-92. PMID: 16262716
97. Aubert D, Chevillard M, Dorne A, Arlaud G, Herzog M. Expression patterns of GASA genes in Arabidopsis thaliana: the GASA4 gene is up-regulated by gibberellins in meristematic regions. Plant Mol Biol. 1998; 36(6):871-83. PMID: 9520278
98. Chen M, Du X, Zhu Y, Wang Z, Hua S, Li Z et al. Seed fatty acid reducer acts downstream of gibberellin signalling pathway to lower seed fatty acid storage in Arabidopsis. Plant Cell Environ. 2012; 35 (12): 2155-69. doi: 10.1111/j.1365-3040.2012.02546.x PMID: 22632271
99. Pinot F, Beisson F. Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles. FEBS J. 2011; 278(2):195-205. doi: 10.1111/j.1742-4658.2010.07948.x PMID: 21156024
100. Sun L, Zhu L, Xu L, Yuan D, Min L, Zhang X. Cotton cytochrome P450 CYP82D regulates systemic cell death by modulating the octadecanoid pathway. Nature Commun. 2014; 5:5372.
101. Kim JS, Kim HJ, Lee IA, Lim JS, Seo JY. Regulation of adipocyte differentiation by glyceollins. Faseb J. 2009; 23:712.6.
102. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012; 40:D1178-86. doi: 10.1093/nar/gkr944 PMID: 22110026
103. McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB et al. AgBase: a functional genomics resource for agriculture. BMC Genomics. 2006; 7:229. PMID: 16961921
104. Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics. 2007; 23(2):257-8. PMID: 17098774
105. Van Dongen S. Graph Clustering by Flow Simulation [Ph D thesis]. The Netherlands: University of Utrecht; 2000.
106. Aoki K, Ogata Y, Shibata D. Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol. 2007; 48(3):381-90. PMID: 17251202
107. Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD et al. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 2010; 10:160. doi: 10.1186/1471-2229-10-160 PMID: 20687943
108. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008; 5(7):621-8. doi: 10.1038/nmeth.1226 PMID: 18516045
109. Wang L, Feng Z, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 2010; 26(1):136-8. doi: 10.1093/bioinformatics/btp612 PMID: 19855105
110. Fukuda N, Ikawa Y, Aoyagi T, Kozaki A. Expression of the genes coding for plastidic acetyl-CoA carboxylase subunits is regulated by a location-sensitive transcription factor binding site. Plant Mol Biol. 2013; 82(4-5):473-83. doi: 10.1007/s11103-013-0075-7 PMID: 23733600