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Review and Important Papers:

1.             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, 68:1014-1027.

2.             Wei W, Zhang Y, Lv H, Li D, Wang L, Zhang X: Association analysis for quality traits in a diverse panel of Chinese sesame (Sesamum indicum L.) germplasm.J Integr Plant Biol 2013.

3.             Ke t, Mao H, Hui FL, Dong CH, Chai GH, Liu SY: Bioinformatics analysis and functional annotation of complete expressed sequence tag collection for oil crops.China Journal of Bioinformatics 2010:165-170.

4.             Johnson LA, Suleiman TM, Lusas EW: Sesame protein: a review and prospectus.J Am Oil Chem Soc 1979, 56:463-468.

5.             Uzun B, Arslan C, Furat S: Variation in Fatty Acid Compositions, Oil Content and Oil Yield in a Germplasm Collection of Sesame (Sesamum indicum L.).J Am Oil Chem Soc 2008, 85:1135-1142.

6.             Miyake Y, Fukumoto S, Okada M, Sakaida K, Nakamura Y, Osawa T: Antioxidative catechol lignans converted from sesamin and sesaminol triglucoside by culturing with Aspergillus.J Agric Food Chem 2005, 53:22-27.

7.             Budowski P, Menezes FGT, Dollear FG: Sesame oil. V. The stability of sesame oil.J Am Oil Chem Soc 1950, 27:377-380.

8.             Hirata F, Fujita K, Ishikura Y, Hosoda K, Ishikawa T, Nakamura H: Hypocholesterolemic effect of sesame lignan in humans.Atherosclerosis 1996, 122:135-136.

9.             Tsai CM, Chen PR, Chien KL, Su TC, Chang CJ, Liu TL, Cheng HC: Dietary sesame reduces serum cholesterol and enhances antioxidant capacity in hypercholesterolemia.Nutr Res 2005, 25:559-567.

10.          Angiosperm Phylogeny Website. [http://www.mobot.org/MOBOT/research/APweb/.]

11.          Li Y, Hu Y, Bolund L, Wang J: State of the art de novo assembly of human genomes from massively parallel sequencing data.Hum Genomics 2010, 4:271-277.

12.          Zhang H, Miao H, Wang L, Qu L, Liu H, Wang Q, Yue M: Genome sequencing of the important oilseed crop Sesamum indicum L.Genome Biol 2013, 14:401.

13.          Suh MC, Kim MJ, Hur CG, Bae JM, Park YI, Chung CH, Kang CW, Ohlrogge JB: Comparative analysis of expressed sequence tags from Sesamum indicum and Arabidopsis thaliana developing seeds.Plant Mol Biol 2003, 52:1107-1123.

14.          Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X: Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers.BMC Genomics 2011, 12:451.

15.          Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.Nature 2007, 449:463-U465.

16.          The Tomato Genome Consortium: The tomato genome sequence provides insights into fleshy fruit evolution.Nature 2012, 485:635-641.

17.          Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, et al: Genome sequence and analysis of the tuber crop potato.Nature 2011, 475:189-195.

18.          Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA, Shoemaker RC, Ma J: Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison.The Plant Journal 2010, 63:584-598.

19.          The Angiosperm Phylogeny G: An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III.Bot J Linn Soc 2009, 161:105-121.

20.          Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, et al: The genome of the mesopolyploid crop species Brassica rapa.Nat Genet 2011, 43:1035-1039.

21.          Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND: Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily.Plant J 1999, 20:317-332.

22.          Tarr DE, Alexander HM: TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders.BMC Res Notes 2009, 2:197.

23.          Tian Y, Fan L, Thurau T, Jung C, Cai D: The absence of TIR-type resistance gene analogues in the sugar beet (Beta vulgaris L.) genome.Journal of Molecular Evolution 2004, 58:40-53.

24.          Yue JX, Meyers BC, Chen JQ, Tian D, Yang S: Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes.New Phytol 2012, 193:1049-1063.

25.          Kader JC: Lipid-Transfer Proteins in Plants.Annu Rev Plant Physiol Plant Mol Biol 1996, 47:627-654.

26.          Thompson JE, Froese CD, Madey E, Smith MD, Hong Y: Lipid metabolism during plant senescence.Prog Lipid Res 1998, 37:119-141.

27.          Feussner I, Kuhn H, Wasternack C: Lipoxygenase-dependent degradation of storage lipids.Trends Plant Sci 2001, 6:268-273.

28.          Lu C, Xin Z, Ren Z, Miquel M, Browse J: An enzyme regulating triacylglycerol composition is encoded by the ROD1 gene of Arabidopsis.Proc Natl Acad Sci U S A 2009, 106:18837-18842.

29.          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, 43:413-417.

30.          Cases S, Stone SJ, Zhou P, Yen E, Tow B, Lardizabal KD, Voelker T, Farese RV, Jr.: Cloning of DGAT2, a second mammalian diacylglycerol acyltransferase, and related family members.J Biol Chem 2001, 276:38870-38876.

31.          Dahlqvist A, Stahl U, Lenman M, Banas A, Lee M, Sandager L, Ronne H, Stymne S: Phospholipid:diacylglycerol acyltransferase: an enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants.Proc Natl Acad Sci U S A 2000, 97:6487-6492.

32.          Ratnayake C, Huang AH: Oleosins and oil bodies in plant seeds have postulated structures.Biochem J 1996, 317 ( Pt 3):956-958.

33.          Jolivet P, Roux E, D'Andrea S, Davanture M, Negroni L, Zivy M, Chardot T: Protein composition of oil bodies in Arabidopsis thaliana ecotype WS.Plant Physiol Biochem 2004, 42:501-509.

34.          Holman TJ, Jones PD, Russell L, Medhurst A, Ubeda Tomas S, Talloji P, Marquez J, Schmuths H, Tung SA, Taylor I, et al: The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis.Proc Natl Acad Sci U S A 2009, 106:4549-4554.

35.          Crowe AJ, Abenes M, Plant A, Moloney MM: The seed-specific transactivator, ABI3, induces oleosin gene expression.Plant Sci 2000, 151:171-181.

36.          Li H, Peng Z, Yang X, Wang W, Fu J, Wang J, Han Y, Chai Y, Guo T, Yang N, et al: Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels.Nat Genet 2013, 45:43-50.

37.          Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, et al: Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.Nat Biotechnol 2012, 30:105-111.

38.          Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, et al: Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.Nat Biotechnol 2013, 31:240-246.

39.          Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L, Ren Y, Wang Z, et al: The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions.Nat Genet 2012, 45:51-58.

40.          Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, et al: Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.Nat Genet 2010, 42:1053-1059.

41.          Zhang X, Li P, Wang X, Wang X: Studies on relationship among lignans, oil and protein content in sesame seed.Chinese journal of oil crop sciences 2005, 27:88-90.

42.          Kim HJ, Ono E, Morimoto K, Yamagaki T, Okazawa A, Kobayashi A, Satake H: Metabolic engineering of lignan biosynthesis in Forsythia cell culture.Plant Cell Physiol 2009, 50:2200-2209.

43.          Doyle JJ, Doyle JL: Isolation of plant DNA from fresh tissue.Focus 1990:13-15.

44.          Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, et al: De novo assembly of human genomes with massively parallel short read sequencing.Genome Res 2010, 20:265-272.

45.          Dolezel J, Greilhuber J, Suda J: Estimation of nuclear DNA content in plants using flow cytometry.Nat Protocols 2007, 2:2233-2244.

46.          Dolezel J, Bartos J, Voglmayr H, Greilhuber J: Nuclear DNA content and genome size of trout and human.Cytometry A 2003, 51:127-128; author reply 129.

47.          Birney E, Durbin R: Using GeneWise in the Drosophila annotation experiment.Genome Res 2000, 10:547-548.

48.          Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B: AUGUSTUS: ab initio prediction of alternative transcripts.Nucleic Acids Res 2006, 34:W435-439.

49.          Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq.Bioinformatics 2009, 25:1105-1111.

50.          McCarthy EM, McDonald JF: LTR_STRUC: a novel search and identification program for LTR retrotransposons.Bioinformatics 2003, 19:362-367.

51.          Labbe J, Murat C, Morin E, Tuskan GA, Le Tacon F, Martin F: Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.PLoS One 2012, 7:e40197.

52.          Li L, Stoeckert CJ, Jr., Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes.Genome Res 2003, 13:2178-2189.

53.          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, 59:307-321.

54.          Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.J Mol Evol 1985, 22:160-174.

55.          Yang Z: PAML 4: phylogenetic analysis by maximum likelihood.Mol Biol Evol 2007, 24:1586-1591.

56.          Delorenzi M, Speed T: An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.Bioinformatics 2002, 18:617-625.

57.          McDonnell AV, Jiang T, Keating AE, Berger B: Paircoil2: improved prediction of coiled coils from sequence.Bioinformatics 2006, 22:356-358.

58.          Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics 2009, 25:1754-1760.

59.          Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools.Bioinformatics 2009, 25:2078-2079.

 


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