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1. Durrett TP, Benning C, Ohlrogge J. Plant triacylglycerols as feedstocks for the production of biofuels. Plant J. 2008;54(4):593–607. 2. Horn PJ, Benning C. The plant lipidome in human and environmental health. Science. 2016;353(6305):1228–32. 3. Min CW, Gupta R, Kim SW, Lee SE, Kim YC, Bae DW, Han WY, Lee BW, Ko JM, Agrawal GK, Rakwal R, Kim ST. Comparative biochemical and proteomic analyses of soybean seed cultivars differing in protein and oil contents. J Agric Food Chem. 2015;63(32):7134–42. 4. Kennedy Y, Yokoi S, Sato T, Daimon H, Nishida I, Takahata Y. Genetic variation of storage compounds and seed weight in rapeseed (Brassica napus L.) germplasms. Breeding Sci. 2011;61(3):311–5. 5. Rawsthorne S. 2002 Carbon flux and fatty acid synthesis in plants. Prog Lipid Res. 2002;41(2):182–96. 6. Voelker T, Kinney AJ. Variations in the biosynthesis of seed-storage lipids. Annu Rev Plant Physiol Plant Mol Biol. 2001;52:335–61. 7. Thelen JJ, Ohlrogge JB. Metabolic engineering of fatty acid biosynthesis in plants. Metab Eng. 2002;4(1):12–21. 8. Weselake RJ, Taylor DC, Rahman MH, Shah S, Laroche A, McVetty PB, Harwood JL. Increasing the flow of carbon into seed oil. Biotechnol Adv. 2009;27(6):866–78. 9. Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Baud S, Bird D, Debono A, Durrett TP, Franke RB, Graham IA, Katayama K,Kelly AA, Larson T, Markham JE, Miquel M, Molina I, Nishida I, Rowland O, Samuels L, Schmid KM, Wada H, Welti R, Xu C, Zallot R, Ohlrogge J. Acyl-Lipid Metabolism. In: Rockville ed., the Arabidopsis book. MD: American Society of Plant Biologists. 2013;11:e0161. 10. Troncoso-Ponce MA, Kilaru A, Cao X, Durrett TP, Fan J, Jensen JK, Thrower NA, Pauly M, Wilkerson C, Ohlrogge JB. Comparative deep transcriptional profiling of four developing oilseeds. Plant J. 2011;68(6):1014–27. 11. McGlew K, Shaw V, Zhang M, Kim RJ, Yang W, Shorrosh B, Suh MC, Ohlrogge J. An annotated database of Arabidopsis mutants of acyl lipid metabolism. Plant Cell Rep. 2015;34(4):519–32. 12. Xu Z, Li J, Guo X, Jin S, Zhang X. Metabolic engineering of cottonseed oil biosynthesis pathway via RNA interference. Sci Rep. 2016;13(6):33342. 13. 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. 14. Klaus D, Ohlrogge JB, Neuhaus HE, Dörmann P. Increased fatty acid production in potato by engineering of acetyl-CoA carboxylase. Planta. 2004;219(3):389–96. 15. Murad AM, Vianna GR, Machado AM, da Cunha NB, Coelho CM, Lacerda VA, Coelho MC, Rech EL. Mass spectrometry characterisation of fatty acids from metabolically engineered soybean seeds. Anal Bioanal Chem. 2014;406: 2873–83. 16. Li M, Bahn SC, Fan C, Li J, Phan T, Ortiz M, Roth MR, Welti R, Jaworski J, Wang X. Patatin-related phospholipase pPLAIIIδ increases seed oil content with long-chain fatty acids in Arabidopsis. Plant Physiol. 2013;162(1):39–51. 17. 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. 18. Jain RK, Coffey M, Lai K, Kumar A, MacKenzie SL. Enhancement of seed oil content by expression of glycerol-3-phosphate acyltransferase genes. Biochem Soc Trans. 2000;28(6):958–61. 19. 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. 20. Wang N, Ma J, Pei W, Wu M, Li H, Li X, Yu S, Zhang J, Yu J. A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality. BMC Genomics. 2017;18(1):218. 21. Jako C, Kumar A, Wei Y, Zou J, Barton DL, Giblin EM, Covello PS, Taylor DC. 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. 22. Misra A, Khan K, Niranjan A, Nath P, Sane VA. Over-expression of JcDGAT1 from Jatropha curcas increases seed oil levels and alters oil quality in transgenic Arabidopsis thaliana. Phytochemistry. 2013;96:37–45. 23. Zheng P, Allen WB, Roesler K, Williams ME, Zhang S, Li J, Glassman K, Ranch J, Nubel D, Solawetz W, Bhattramakki D, Llaca V, Deschamps S, Zhong GY, Tarczynski MC, Shen B. A phenylalanine in DGAT is a key determinant of oil contents and composition in maize. Nat Genet. 2008;40(3):367–72. 24. Weselake RJ, Shah S, Tang M, Quant PA, Snyder CL, Furukawa-Stoffer TL, Zhu W, Taylor DC, Zou J, Kumar A, Hall L, Laroche A, Rakow G, Raney P, Moloney MM, Harwood JL. 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. 25. Shimada TL, Hara-Nishimura I. Oil-body-membrane proteins and their physiological functions in plants. Biol Pharm Bull. 2010;33(3):360–3. 26. Ma W, Kong Q, Grix M, Mantyla JJ, Yang Y, Benning C, Ohlrogge JB. Deletion of a C-terminal intrinsically disordered region of WRINKLED1 affects its stability and enhances oil accumulation in Arabidopsis. Plant J. 2015;83(5): 864–74. 27. Mu J, Tan H, Zheng Q, Fu F, Liang Y, Zhang J, Yang X, Wang T, Chong K, Wang XJ, Zuo J. LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis. Plant Physiol. 2008;148(2):1042–54. 28. Tan H, Yang X, Zhang F, Zheng X, Qu C, Mu J, Fu F, Li J, Guan R, Zhang H, ang G, Zuo J. 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. 29. Baud S, Mendoza MS, To A, Harscoët 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. 30. Wang H, Guo J, Lambert KN, Lin Y. Developmental control of Arabidopsis seed oil biosynthesis. Planta. 2007;226(3):773–83. 31. Wang HW, Zhang B, Hao YJ, Huang J, Tian AG, Liao Y, Zhang JS, Chen SY. 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. 32. Song QX, Li QT, Liu YF, Zhang FX, Ma B, Zhang WK, Man WQ, Du WG, Wang GD, Chen SY, Zhang JS. Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants. J Exp Bot. 2013; 64(14):4329–41. 33. Liu YF, Li QT, Lu X, Song QX, Lam SM, Zhang WK, Ma B, Lin Q, Man WQ, Du WG, Shui GH, Chen SY, Zhang JS. Soybean GmMYB73 promotes lipid accumulation in transgenic plants. BMC Plant Biol. 2014;14:73. 34. Zhang YQ, Lu X, Zhao FY, Li QT, Niu SL, Wei W, Zhang WK, Ma B, Chen SY, Zhang JS. Soybean GmDREBL increases lipid content in seeds of transgenic Arabidopsis. Sci Rep. 2016;6:34307. 35. Lu X, Li QT, Xiong Q, Li W, Bi YD, Lai YC, Liu XL, Man WQ, Zhang WK, Ma B, Chen SY, Zhang JS. The transcriptomic signature of developing soybean seeds reveals genetic basis of seed trait adaptation during domestication. Plant J. 2016;86(6):530–44. 36. Li QT, Lu X, Song QX, Chen HW, Wei W, Tao JJ, Bian XH, Shen M, Ma B, Zhang WK, Bi YD, Li W, Lai YC, Lam SM, Shui GH, Chen SY, Zhang JS. Selection for a zinc-finger protein contributes to seed oil increase during soybean domestication. Plant Physiol. 2017;173(4):2208–24. 37. Crowe AJ, Abenes M, Plant A, Moloney MM. The seed-specific transactivator, ABI3, induces oleosin gene expression. Plant Sci. 2000;151(2):171–81. 38. Mönke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hähnel U, Junker A, Weisshaar B, Conrad U, Bäumlein H, Altschmied L. Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res. 2012;40(17):8240–54. 39. Jiang C, Shi J, Li R, Long Y, Wang H, Li D, Zhao J, Meng J. Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.). Theor Appl Genet. 2014;127(4):957–68. 40. Sun F, Liu J, Hua W, Sun X, Wang X, Wang H. Identification of stable QTLs for seed oil content by combined linkage and association mapping in Brassica napus. Plant Sci. 2016;252:388–99. 41. Sun M, Hua W, Liu J, Huang S, Wang X, Liu G, Wang H. Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar. PLoS One. 2012;7(10):e47037. 42. Hwang EY, Song Q, Jia G, Specht JE, Hyten DL, Costa J, Cregan PB. A genome-wide association study of seed protein and oil content in soybean. BMC Genomics. 2014;15:1. 43. Cao Y, Li S, Wang Z, Chang F, Kong J, Gai J, Zhao T. Identification of major quantitative trait loci for seed oil content in soybeans by combining linkage and genome-wide association mapping. Front Plant Sci. 2017;8:1222. 44. 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. 45. Li B, Fan S, Yu F, Chen Y, Zhang S, Han F, Yan S, Wang L, Sun J. High resolution mapping of QTL for fatty acid composition in soybean using specific-locus amplified fragment sequencing. Theor Appl Genet. 2017; 130(7):1467–79. 46. Li X, Mei D, Liu Q, Fan J, Singh S, Green A, Zhou XR, Zhu LH. Downregulation of crambe fatty acid desaturase and elongase in Arabidopsis and crambe resulted in significantly increased oleic acid content in seed oil. Plant Biotechnol J. 2016;14(1):323–31. 47. Liu F, Xia Y, Wu L, Fu D, Hayward A, Luo J, Yan X, Xiong X, Fu P, Wu G, Lu C. Enhanced seed oil content by overexpressing genes related to triacylglyceride synthesis. Gene. 2015;557(2):163–71. 48. Yu J, Zhang Z, Wei J, Ling Y, Xu W, Su Z. SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. BMC Genomics. 2014;15:271. 49. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178–83. 50. Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le CI, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 2014;345(6199):950–3. 51. Wang L, Yu S, Tong C, Zhao Y, Liu Y, Song C, Zhang Y, Zhang X, Wang Y, Hua W, Li D, Li D, Li F, Yu J, Xu C, Han X, Huang S, Tai S, Wang J, Xu X, Li Y, Liu S, Varshney RK, Wang J, Zhang X. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol. 2014;15(2):R39. 52. Chen X, Li H, Pandey MK, Yang Q, Wang X, Garg V, Li H, Chi X, Doddamani D, Hong Y, Upadhyaya H, Guo H, Khan AW, Zhu F, Zhang X, Pan L, Pierce GJ, Zhou G, Krishnamohan KA, Chen M, Zhong N, Agarwal G, Li S, Chitikineni A, Zhang GQ, Sharma S, Chen N, Liu H, Janila P, Li S, Wang M, Wang T, Sun J, Li X, Li C, Wang M, Yu L, Wen S, Singh S, Yang Z, Zhao J, Zhang C, Yu Y, Bi J, Zhang X, Liu ZJ, Paterson AH, Wang S, Liang X, Varshney RK, Yu S. Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proc Natl Acad Sci U S A. 2016;113(24):6785–90. 53. Niu J, Chen Y, An J, Hou X, Cai J, Wang J, Zhang Z, Lin S. Integrated transcriptome sequencing and dynamic analysis reveal carbon source partitioning between terpenoid and oil accumulation in developing Lindera glauca fruits. Sci Rep. 2015;5:15017. 54. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel RJ, Percy RG, Yu JZ, Zhu YX, Wang J, Yu S. The draft genome of a diploid cotton Gossypium raimondii. Nat Genet. 2012; 44(10):1098–103. 55. Zhang L, Wang SB, Li QG, Song J, Hao YQ, Zhou L, Zheng HQ, Dunwell JM, Zhang YM. An integrated bioinformatics analysis reveals divergent evolutionary pattern of oil biosynthesis in high- and low-oil plants. PLoS One. 2016;11(5):e0154882. 56. Ernst J, Bar-Joseph ZSTEM. A tool for the analysis of short time series gene expression data. BMC Bioinformatics. 2006;7:191. 57. Wan H, Cui Y, Ding Y, Mei J, Dong H, Zhang W, Wu S, Liang Y, Zhang C, Li J, Xiong Q, Qian W. Time-series analyses of transcriptomes and proteomes reveal molecular networks underlying oil accumulation in canola. Front Plant Sci. 2017;7:2007. 58. Jones SI, Vodkin LO. Using RNA-Seq to profile soybean seed development from fertilization to maturity. PLoS One. 2013;8(3):e59270. 59. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011;39(Web Server issue):W316–22. 60. Ohlrogge J, Browse J. Lipid biosynthesis. Plant Cell. 1995;7(7):957–70. 61. 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(Database issue):D1182–7. 62. Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017;45(D1):D1040–5. 63. Loic L, Jean V, Raymond C, Pierre G, Claude C. Phosphoenolpyruvate carboxylase: structure, regulation and evolution. Plant Sci. 1994;99(2):111–24. 64. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server):W202–8. 65. Gargouri M, Park JJ, Holguin FO, Kim MJ, Wang H, Deshpande RR, Shachar-Hill Y, Hicks LM, Gang DR. Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii. J Exp Bot. 2015; 66(15):4551–66. 66. Lin H, Yu J, Pearce SP, Zhang D, Wilson ZA. RiceAntherNet: a gene coexpression network for identifying anther and pollen development genes. Plant J. 2017;92(6):1076–91. 67. Chung KO, Kim BY, Lee MH, Kim YR, Chung HY, Park JH, Moon JO. In-vitro and in-vivo anti- inflammatory effect of oxyresveratrol from Morus alba L. J Pharm Pharmacol. 2003;55(12):1695–700. 68. Cober ER, Voldenga HD. Developing high-protein, high-yield soybean populations and lines. Crop Sci. 2000;40(1):39–42. 69. Hu ZY, Hua W, Zhang L, Deng LB, Wang XF, Liu GH, Hao WJ, Wang HZ. Seed structure characteristics to form ultrahigh oil content in rapeseed. PLoS One. 2013;8(4):e62099. 70. Uhrig RG, O'Leary B, Spang HE, MacDonald JA, She YM, Plaxton WC. Coimmunopurification of phosphorylated bacterial- and plant-type phosphoenolpyruvate carboxylases with the plastidial pyruvate dehydrogenase complex from developing castor oil seeds. Plant Physiol. 2008;146(3):1346–57. 71. Gennidakis S, Rao S, Greenham K, Uhrig RG, O'Leary B, Snedden WA, Lu C, Plaxton WC. Bacterial- and plant-type phosphoenolpyruvate carboxylase polypeptides interact in the hetero-oligomeric Class-2 PEPC complex of developing castor oil seeds. Plant J. 2007;52(5):839–49. 72. Wang FL, Liu RH, Wu GT, Lang CX, Chen JQ, Shi CH. Specific down regulation of the bacterial-type PEPC gene by artificial microRNA improves salt tolerance in Arabidopsis. Plant Mol Biol Rep. 2012;30(5):1080–7. 73. O'Leary B, Rao SK, Kim J, Plaxton WC. Bacterial-type phosphoenolpyruvate carboxylase (PEPC) functions as a catalytic and regulatory subunit of the novel class-2 PEPC complex of vascular plants. J Biol Chem. 2009;284(37): 24797–805. 74. Angelovici R, Lipka AE, Deason N, Gonzalez-Jorge S, Lin H, Cepela J, Buell R, Gore MA, Dellapenna D. Genome-wide analysis of branched-chain amino acid levels in Arabidopsis seeds. Plant Cell. 2013;25(12):4827–43. 75. Zhou M, Wang W, Karapetyan S, Mwimba M, Marqués J, Buchler NE, Dong X. Redox rhythm reinforces the circadian clock to gate immune response. Nature. 2015;523(7561):472–6. 76. Graf A, Schlereth A, Stitt M, Smith AM. Circadian control of carbohydrate availability for growth in Arabidopsis plants at night. Proc Natl Acad Sci U S A. 2010;107(20):9458–63. 77. Hsiao AS, Haslam RP, Michaelson LV, Liao P, Napier JA, Chye ML. Gene expression in plant lipid metabolism in Arabidopsis seedlings. PLoS One. 2014;9(9):e107372. 78. Yang J, Yang MF, Wang D, Chen F, Shen SH. JcDof1, a Dof transcription factor gene, is associated with the light-mediated circadian clock in Jatropha curcas. Physiol Plant. 2010;139(3):324–34. 79. Oishi K, Miyazaki K, Kadota K, Kikuno R, Nagase T, Atsumi G, Ohkura N, Azama T, Mesaki M, Yukimasa S, Kobayashi H, Iitaka C, Umehara T, Horikoshi M, Kudo T, Shimizu Y, Yano M, Monden M, Machida K, Matsuda J, Horie S, Todo T, Ishida N. Genome-wide expression analysis of mouse liver reveals clock-regulated circadian output genes. J Biol Chem. 2003;278(42):41519–27. 80. Daniel X, Sugano S, Tobin EM. CK2 phosphorylation of CCA1 is necessary for its circadian oscillator function in Arabidopsis. Proc Natl Acad Sci U S A. 2004;101(9):3292–7. 81. Madoka YK, Ken-Ichi T, Junya M, Ikuo N, Yukio N, Yukiko S. Chloroplast transformation with modified accD operon increases acetyl-CoA carboxylase and causes extension of leaf longevity and increase in seed yield in tobacco. Plant Cell Physiol. 2002;43(12):1518–25. 82. Konishi T, Shinohara K, Yamada K, Sasaki 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. 83. Davis MS, Solbiati J, Cronan JE. Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J Biol Chem. 2000;275(37):28593–8. 84. Li X, Ilarslan H, Brachova L, Qian HR, Li L, Che P, Wurtele ES, Nikolau BJ. Reverse-genetic analysis of the two biotin-containing subunit genes of the heteromeric acetyl-coenzyme a carboxylase in Arabidopsis indicates a unidirectional functional redundancy. Plant Physiol. 2011;155(1):293–314. 85. Schwender J, König C, Klapperstück M, Heinzel N, Munz E, Hebbelmann I, Hay JO, Denolf P, De Bodt S, Redestig H, Caestecker E, Jakob PM, Borisjuk L, Rolletschek H. Transcript abundance on its own cannot be used to infer fluxes in central metabolism. Front Plant Sci. 2014;5:668. 86. Gidda SK, Watt S, Collins-Silva J, Kilaru A, Arondel V, Yurchenko O, Horn PJ, James CN, Shintani D, Ohlrogge JB, Chapman KD, Mullen RT, Dyer JM. Lipid droplet-associated proteins (LDAPs) are involved in the compartmentalization of lipophilic compounds in plant cells. Plant Signal Behav. 2013;8(11):e27141. 87. Miquel M, Trigui G, d'Andréa S, Kelemen Z, Baud S, Berger A, Deruyffelaere C, Trubuil A, Lepiniec L, Dubreucq B. Specialization of oleosins in oil body dynamics during seed development in Arabidopsis seeds. Plant Physiol. 2014;164(4):1866–78. 88. Roos-Mattjus P, Sistonen L. The ubiquitin-proteasome pathway. Ann Med. 2004;36(4):285–95. 89. Thrower JS, Hoffman L, Rechsteiner M, Pickart CM. Recognition of the polyubiquitin proteolytic signal. EMBO J. 2000;19(1):94–102. 90. Xu HM, Kong XD, Chen F, Huang JX, Lou XY, Zhao JY. Transcriptome analysis of Brassica napus pod using RNA-seq and identification of lipidrelated candidate genes. BMC Genomics. 2015;16:858. 91. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28(1):33–6. 92. Ritchie SW, Hanway JJ, Thompson HE, Benson GO. How a soybean plant develops. Iowa State University: Cooperative Extension Service; 1985. p. 1–20. 93. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106. 94. Li L, Christian JS, David SR. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178–89. 95. Van Dongen S. “Graph clustering by flow simulation.” Ph.D thesis. Utrecht: University of Utrecht; 2000. 96. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-) orthologs in large-scale analysis. BMC Bioinformatics. 2011;12:124. 97. Sonnhammer EL, Östlund G. InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 2015;43(Database issue): D234–9. 98. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995;57(1):289–300. 99. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. 100. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016; 33(7):1870–4. 101. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307–21. 102. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008; 25(7):1253–6. 103. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44(W1):W242–5. 104. Yang Z. PAML. 4: a program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–91. 105. Yang Z, Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 1998;46(4):409–18. 106. Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014; 42(Database issue):D68–73. 107. Dai X. Zhao PX. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 2011;39(Web Server issue):W155–9. 108. Wong N, Wang X. miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 2015;43(D1): D146–52. 109. Killcoyne S, Carter GW, Smith J, Boyle J. Cytoscape: a community-based framework for network modeling. Methods Mol Biol. 2009;563:219–39.