Transcriptomic analysis revealed the mechanism of oil dynamic accumulation during developing Siberian apricot (Prunus sibirica L.) seed kernels for the development of woody biodiesel

Biotechnology for Biofuels

Jun Niu²  Jiyong An²  Libing Wang⁴  Chengliang Fang³  Denglong Ha³  Chengyu Fu¹  Lin Qiu³  Haiyan Yu⁴  Haiyan Zhao³  Xinyu Hou²  Zheng Xiang²  Sufan Zhou²  Zhixiang Zhang²  Xinyi Feng²  Shanzhi Lin² 

[1] Liaocheng Food and Drug Administration, Liaocheng 252000, Shandong, China

[2] College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing 10083, China

[3] Jigongshan National Nature Reserve, Xingyang 464133, China

[4] Research Institute of Forestry, Chinese Academy of Forestry, Beijing 10091, China

关键词: Oil accumulation mechanism;    Differential expression;    Transcriptome sequencing;    Woody biodiesel;    Siberian apricot;   

Others  :  1177299
DOI  :  10.1186/s13068-015-0213-3

 received in 2014-09-01, accepted in 2015-01-27,  发布年份 2015

【 摘 要 】

Background

Siberian apricot (Prunus sibirica L.) has emerged as a novel potential source of biodiesel in China, but the molecular regulatory mechanism of oil accumulation in Siberian apricot seed kernels (SASK) is still unknown at present. To better develop SASK oil as woody biodiesel, it is essential to profile transcriptome and to identify the full repertoire of potential unigenes involved in the formation and accumulation of oil SASK during the different developing stages.

Results

We firstly detected the temporal patterns for oil content and fatty acid (FA) compositions of SASK in 7 different developing stages. The best time for obtaining the high quality and quantity of SASK oil was characterized at 60 days after flowering (DAF), and the representative periods (10, 30, 50, 60, and 70 DAF) were selected for transcriptomic analysis. By Illumina/Solexa sequencings, approximately 65 million short reads (average length = 96 bp) were obtained, and then assembled into 124,070 unigenes by Trinity strategy (mean size = 829.62 bp). A total of 3,000, 2,781, 2,620, and 2,675 differentially expressed unigenes were identified at 30, 50, 60, and 70 DAF (10 DAF as the control) by DESeq method, respectively. The relationship between the unigene transcriptional profiles and the oil dynamic patterns in developing SASK was comparatively analyzed, and the specific unigenes encoding some known enzymes and transcription factors involved in acetyl-coenzyme A (acetyl-CoA) formation and oil accumulation were determined. Additionally, 5 key metabolic genes implicated in SASK oil accumulation were experimentally validated by quantitative real-time PCR (qRT-PCR). Our findings could help to construction of oil accumulated pathway and to elucidate the molecular regulatory mechanism of increased oil production in developing SASK.

Conclusions

This is the first study of oil temporal patterns, transcriptome sequencings, and differential profiles in developing SASK. All our results will serve as the important foundation to further deeply explore the regulatory mechanism of SASK high-quality oil accumulation, and may also provide some reference for researching the woody biodiesel plants.

【 授权许可】

   
2015 Niu et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

Figure 8.

【 参考文献 】

• [1]Ghadge SV, Raheman H: Biodiesel production from mahua (Madhuca indica) oil having high free fatty acids. Biomass Bioenergy 2005, 28:601-5.
• [2]Lin SF, Shen Y: Thinking about the wood-oil biodiesel industry. Issues of Forestry Econ 2010, 30:131-5.
• [3]Wang LB, Yu HY, He XH, Liu RY: Influence of fatty acid composition of woody biodiesel plants on the fuel properties. J Fuel Chem Technol 2012, 40:397-404.
• [4]Wang LB: Resource investigation and distribute regular of three Armeniaca species. Forest Resource Manage 2011, 5:65-70.
• [5]Zhang JY, Wei ZZ, Zhao HL: Determination of ability of several arbor and shrub species to endure and survive extreme aridity with limited-areas methods under field conditions in Horqin Sandy Land. Acta Ecol Sin 2006, 26:467-74.
• [6]Wang LB: Geographic distribution and botanical characters of 3 Armeniaca plant in China. For Res 2010, 3:435-9.
• [7]Wang LB: Properties of Manchurian apricot (Prunus mandshurica Skv.) and Siberian apricot (Prunus sibirica L.) seed kernel oils and evaluation as biodiesel feedstocks. Ind Crop Prod 2013, 50:838-43.
• [8]Zhang JY: Chinese Fruit Species. Volume apricot. China Forestry Publishing House, Beijng; 2003.
• [9]Wang LB: Evaluation of Siberian Apricot (Prunus sibirica L.) germplasm variability for biodiesel properties. J Am Oil Chem Soc 2012, 89:1743-7.
• [10]Wang LB, Yu HY: Biodiesel from Siberian apricot (Prunus sibirica L.) seed kernel oil. Bioresour Technol 2012, 112:355-8.
• [11]Wang LB, Chu J: Optimization of biodiesel production from Siberian Apricot (Prunus sibirica L.) oil using response surface methodology. Asian J Chem 2013, 25:2577-82.
• [12]Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, et al.: A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform 2012, 14:671-83.
• [13]Huang JY, Jie ZJ, Wang LJ, Yan XH, Wei WH: Analysis of the differential expression of the genes related to Brassica napus seed development. Mol Biol Rep 2011, 38:1055-61.
• [14]Chen H, Wang FW, Dong YY, Wang N, Sun YP, Li XY, et al.: Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during soybean seed development. BMC Plant Biol 2012, 12:122. BioMed Central Full Text
• [15]Yin DM, Wang Y, Zhang XG, Li HM, Lu X, Zhang JS, et al.: De novo assembly of the peanut (Arachis hypogaea L.) seed transcriptome revealed candidate unigenes for oil accumulation pathways. PLoS ONE 2013, 8:e73767.
• [16]Troncoso-Ponce MA, Kilaru A, Cao X, Durrett TP, Fan J, Jensen JK, et al.: Comparative deep transcriptional profiling of four developing oilseeds. Plant J 2011, 68:1014-27.
• [17]Kroon J, Wei W, Simon WJ, Slabas AR: Identification and functional expression of a type 2 acyl-CoA: diacylglycerol acyltransferase (DGAT2) in developing castor bean seeds which has high homology to the major triglyceride biosynthetic enzyme of fungi and animals. Phytochemistry 2006, 67:2541-9.
• [18]Tao X, Fang Y, Xiao Y, Jin YL, Ma XR, Zhao Y, et al.: Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation. Biotechnol Biofuels 2013, 6:72. BioMed Central Full Text
• [19]Bourgis F, Kilaru A, Cao X, Ngando-Ebongue G-F, 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, 108:12527-32.
• [20]Fan HK, Xiao Y, Yang YD, Xia W, Mason AS, Xia ZH, et al.: RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches. PLoS ONE 2013, 8:e59997.
• [21]Dong SB, Liu YL, Niu J, Ning Y, Lin SZ, Zhang ZX: De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing. Gene 2014, 544:220-7.
• [22]Wang R, Hanna MA, Zhou WW, Bhadury PS, Chen Q, Song BA, et al.: Production and selected fuel properties of biodiesel from promising non-edible oils: Euphorbia lathyris L., Sapium sebiferum L. and Jatropha curcas L. Bioresour Technol 2011, 102:1194-9.
• [23]Lai ZX, Lin YL: Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing. BMC Genomics 2013, 14:561. BioMed Central Full Text
• [24]Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, et al.: Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics 2010, 11:663. BioMed Central Full Text
• [25]Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al.: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29:644-52.
• [26]Sangwan RS, Tripathi S, Singh J, Narnoliya LK, Sangwan NS: De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism. Gene 2013, 525:58-76.
• [27]Liu YL, Huang ZD, Ao Y, Li W, Zhang ZX: Transcriptome analysis of Yellow Horn (Xanthoceras sorbifolia Bunge.): a potential oil-rich seed tree for biodiesel in China. PLoS ONE 2013, 8:e74441.
• [28]Consortium GO: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32:D258-61.
• [29]Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al.: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41. BioMed Central Full Text
• [30]Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
• [31]Anders S, Huber W: Differential expression of RNA-Seq data at the gene level–the DESeq package. European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; 2012.
• [32]Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-8.
• [33]Rawsthorne S: Carbon flux and fatty acid synthesis in plants. Prog Lipid Res 2002, 41:182-96.
• [34]Andriotis VM, Kruger NJ, Pike MJ, Smith AM: Plastidial glycolysis in developing Arabidopsis embryos. New Phytol 2010, 185:649-62.
• [35]Plaxton WC: The organization and regulation of plant glycolysis. Annu Rev Plant Biol 1996, 47:185-214.
• [36]Weber AP, Schwacke R, Flügge U-I: Solute transporters of the plastid envelope membrane. Annu Rev Plant Biol 2005, 56:133-64.
• [37]Knappe S, Löttgert T, Schneider A, Voll L, Flügge UI, Fischer K: Characterization of two functional phosphoenolpyruvate/phosphate translocator (PPT) genes in Arabidopsis-AtPPT1 may be involved in the provision of signals for correct mesophyll development. Plant J 2003, 36:411-20.
• [38]Fatland BL, Ke J, Anderson MD, Mentzen WI, Cui LW, Allred CC, et al.: Molecular characterization of a heteromeric ATP-citrate lyase that generates cytosolic acetyl-coenzyme A in Arabidopsis. Plant Physiol 2002, 130:740-56.
• [39]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, 123:497-508.
• [40]Randall DD, Miernyk JA, Fang TK, Budde RJ, Schuller KA: Regulation of the pyruvate dehydrogenase complexes in plants. Ann N Y Acad Sci 1989, 573:192-205.
• [41]Nikolau BJ, Ohlrogge JB, Wurtele ES: Plant biotin-containing carboxylases. Arch Biochem Biophys 2003, 414:211-22.
• [42]Bourrellier ABF, Valot B, Guillot A, Ambard-Bretteville F, Vidal J, Hodges M: Chloroplast acetyl-CoA carboxylase activity is 2-oxoglutarate-regulated by interaction of PII with the biotin carboxyl carrier subunit. Proc Natl Acad Sci U S A 2010, 107:502-7.
• [43]Andre C, Haslam RP, Shanklin J: Feedback regulation of plastidic acetyl-CoA carboxylase by 18: 1-acyl carrier protein in Brassica napus. Proc Natl Acad Sci U S A 2012, 109:10107-12.
• [44]Bates PD, Stymne S, Ohlrogge J: Biochemical pathways in seed oil synthesis. Curr Opin Plant Biol 2013, 16:358-64.
• [45]Cahoon EB, Clemente TE, Damude HG, Kinney AJ: Oil Crops Handbook of Plant Breeding (Modifying Vegetable Oils for Food and Non-Food Purposes). Volume 4. Springer, New York; 2010.
• [46]Voelker TA, Hayes TR, Cranmer AM, Turner JC, Davies HM: Genetic engineering of a quantitative trait: metabolic and genetic parameters influencing the accumulation of laurate in rapeseed. Plant J 1996, 9:229-41.
• [47]Knutzon DS, Thompson GA, Radke SE, Johnson WB, Knauf VC, Kridl JC: Modification of Brassica seed oil by antisense expression of a stearoyl-acyl carrier protein desaturase gene. Proc Natl Acad Sci U S A 1992, 89:2624-8.
• [48]Pidkowich MS, Nguyen HT, Heilmann I, Ischebeck T, Shanklin J: Modulating seed β-ketoacyl-acyl carrier protein synthase II level converts the composition of a temperate seed oil to that of a palm-like tropical oil. Proc Natl Acad Sci U S A 2007, 104:4742-7.
• [49]Koo AJ, Ohlrogge JB, Pollard M: On the export of fatty acids from the chloroplast. J Biol Chem 2004, 279:16101-10.
• [50]Zhao LF, Katavic V, Li FL, 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, 64:1048-58.
• [51]Behrouzian B, Buist PH: Fatty acid desaturation: variations on an oxidative theme. Curr Opin Chem Biol 2002, 6:577-82.
• [52]Kim S, Yamaoka Y, Ono H, Kim H, Shim D, Maeshima M, et al.: AtABCA9 transporter supplies fatty acids for lipid synthesis to the endoplasmic reticulum. Proc Natl Acad Sci U S A 2013, 110:773-8.
• [53]Barron EJ, Stumpf P: Fat metabolism in higher plants XIX. The biosynthesis of triglycerides by avocado-mesocarp enzymes. Biochim Biophys Acta 1962, 60:329-37.
• [54]Yang W, Simpson JP, Li-Beisson Y, Beisson F, Pollard M, Ohlrogge JB: A land-plant-specific glycerol-3-phosphate acyltransferase family in Arabidopsis: substrate specificity, sn-2 preference, and evolution. Plant Physiol 2012, 160:638-52.
• [55]Gidda SK, Shockey JM, Rothstein SJ, Dyer JM, Mullen RT: Arabidopsis thaliana GPAT8 and GPAT9 are localized to the ER and possess distinct ER retrieval signals: Functional divergence of the dilysine ER retrieval motif in plant cells. Plant Physiol Biochem 2009, 47:867-79.
• [56]Maisonneuve S, Bessoule J-J, Lessire R, Delseny M, Roscoe TJ: Expression of rapeseed microsomal lysophosphatidic acid acyltransferase isozymes enhances seed oil content in Arabidopsis. Plant Physiol 2010, 152:670-84.
• [57]Eastmond PJ, Quettier A-L, Kroon JT, Craddock C, Adams N, Slabas AR: PHOSPHATIDIC ACID PHOSPHOHYDROLASE1 and 2 regulate phospholipid synthesis at the endoplasmic reticulum in Arabidopsis. Plant Cell 2010, 22:2796-811.
• [58]Kim HU, Li Y, Huang AH: Ubiquitous and endoplasmic reticulum-located lysophosphatidyl acyltransferase, LPAT2, is essential for female but not male gametophyte development in Arabidopsis. Plant Cell 2005, 17:1073-89.
• [59]Lu C, Xin Z, Ren Z, Miquel M: An enzyme regulating triacylglycerol composition is encoded by the ROD1 gene of Arabidopsis. Proc Natl Acad Sci U S A 2009, 106:18837-42.
• [60]Saha S, Enugutti B, Rajakumari S, Rajasekharan R: Cytosolic triacylglycerol biosynthetic pathway in oilseeds. Molecular cloning and expression of peanut cytosolic diacylglycerol acyltransferase. Plant Physiol 2006, 141:1533-43.
• [61]Shockey JM, Gidda SK, Chapital DC, Kuan J-C, Dhanoa PK, Bland JM, et al.: Tung tree DGAT1 and DGAT2 have nonredundant functions in triacylglycerol biosynthesis and are localized to different subdomains of the endoplasmic reticulum. Plant Cell 2006, 18:2294-313.
• [62]Zhang M, Fan J, Taylor DC, Ohlrogge JB: DGAT1 and PDAT1 acyltransferases have overlapping functions in Arabidopsis triacylglycerol biosynthesis and are essential for normal pollen and seed development. Plant Cell 2009, 21:3885-901.
• [63]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, 43:413-7.
• [64]Jolivet P, Roux E, d’Andrea S, Davanture M, Negroni L, Zivy M, et al.: Protein composition of oil bodies in Arabidopsis thaliana ecotype WS. Plant Physiol Biochem 2004, 42:501-9.
• [65]Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E: AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol 2006, 140:818-29.
• [66]Baud S, Lepiniec L: Physiological and developmental regulation of seed oil production. Prog Lipid Res 2010, 49:235-49.
• [67]Xu Q, Zhao WM, Chen Y, Tong YY, Rong GH, Huang ZY, et al.: Transcriptome profiling of the goose (Anser cygnoides) ovaries identify laying and broodiness phenotypes. PLoS ONE 2013, 8:e55496.
• [68]Løvdal T, Saha A: Reference gene selection in Carnobacterium maltaromaticum, Lactobacillus curvatus and Listeria innocua subjected to temperature and salt stress. Mol Biotechnol 2014, 56:210-22.
• [69]Niu J, Zhu BQ, Cai J, Li PX, Wang LB, Dai HT, et al.: Selection of reference genes for gene expression studies in Siberian Apricot (Prunus sibirica L.) germplasm using Quantitative Real-Time PCR. PLoS ONE 2014, 9:e103900.