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Transcriptomic analysis of developing embryos of apricot (Prunus armeniaca L.)

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Abstract

Apricot (Prunus armeniaca L.) is an important, nutritionally valuable agricultural crop. A scarcity of transcriptomic and genomic data hinders progress toward understanding the molecular events of apricot embryogenesis, which is the primary determinant of fruit yield and kernel quality. In this study, three cDNA libraries were sequenced using an Illumina/Solexa platform. We obtained 35,928,496, 40,656,940, and 35,970,214 clean reads from endosperm formation (LT-A), embryo development (LT-B), and mature embryo (LT-C) cDNA libraries, respectively. De novo assembly of cDNA sequence data generated 35,614 unigenes with an average length of 973 bp. A total of 29,971 unigenes were matched in Nr, Nt, Swiss-Prot, KEGG, GO, and COG databases. The top matching species in the Nr database was P. persica (88.3% of matched Nr database accessions). A total of 8,327 differentially expressed genes (DEGs) were detected between LT-A and LT-B, of which 3,663 were upregulated and 4,664 were downregulated. Between LT-B and LT-C, 12,673 DEGs were detected, while 13,892 DEGs were uncovered between LT-A and LT-C. This work is the first reported application of next-generation sequencing techniques for transcriptome analysis of apricot embryo development. Besides providing valuable information on apricot embryo development, the comprehensive set of transcript sequences generated in this study may serve as additional molecular resources for the development of apricot functional genomics.

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Literature Cited

  • Abd El-Aal MH, Khalil MKM, Rahma EH (1986) Apricot kernel oil: Characterization, chemical composition and utilization in some baked products. Food Chem 19:287–298

    Article  Google Scholar 

  • Alpaslan M, Hayta M (2006) Apricot kernel: Physical and chemical properties. J Am Oil Chem Soc 83:469–471

    Article  CAS  Google Scholar 

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 13:3389–3402

    Article  Google Scholar 

  • Audic S, Claverie JM (1997) The significance of digital gene expression-profiles. Genome Res 7:986–995

    CAS  PubMed  Google Scholar 

  • Cheng Y, Dai X, Zhao Y (2006) Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in arabidopsis. Genes Dev 20:1790–1799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Decroocq V, Fave MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922

    CAS  PubMed  Google Scholar 

  • Dong JG, Fernández-Maculet JC, Yang SF (1992) Purification and characterization of 1-aminocyclopropane-l-carboxylate oxidase from apple fruit. Pro Natl Acad Sci USA 89:9789–9793

    Article  CAS  Google Scholar 

  • Femenia A, Rosello C, Mulet A, Canellas J (1995) Chemical composition of bitter and sweet apricot kernels. J Agric Food Chem 43:356–361

    Article  CAS  Google Scholar 

  • Fernández-Otero CI, de la Torre F, Lglesias R, Rodríguez-Gacio MC, Matilla AJ ( 2007) Stage-and tissue-expression of genes involved in the byosynthesis and signalling of ethylene in reproductive organs of damson plum. Plant Physiol Biochem 45:199–208

    Article  PubMed  Google Scholar 

  • Finkelstein R, Reeves W, Ariizumi T, Steber C (2008) Molecular aspects of seed dormancy. Annu Rev Plant Biol 59:387–415

    Article  CAS  PubMed  Google Scholar 

  • Friml J, Vieten A, Sauer M, Weijers D, Schwarz H, Hamann T, Offringa R (2003) Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis. Nature 426:147–153

    Article  CAS  PubMed  Google Scholar 

  • Galinha C, Hofhuis H, Luijten M, Willemsen V, Blilou I, Heidstra R, Scheres B (2007) Plethora proteins as dose-dependent master regulators of arabidopsis root development. Nature 449:1053–1057

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Viguera C, Bridle P, Ferreres F, Francisco A, Barberan T (1994) Influence of variety, maturity and processing on phenolic compounds of apricot juices and jams. Z Lebensm Unters Forsch 199:433–436

    Article  CAS  Google Scholar 

  • Geuna F, Banfi R, Bassi D (2005) Identification and characterization of transcripts differentially expressed during development of apricot (Prunus armeniaca L.) fruit. Tree Genet Genomes 1:69–78

    Article  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X (2011) Full-length transcriptome assembly from rna-seq data without a reference genome. Nat Biotechnol 29: 644–654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grigg SP, Galinha C, Kornet N, Canales C, Scheres B, Tsiantis M (2009) Repression of apical homeobox genes is required for embryonic root development in Arabidopsis. Curr Biol 19:1485–1490

    Article  CAS  PubMed  Google Scholar 

  • Grimplet J, Romieu C, Audergon JM, Marty I, Albagnac G, Lambert P, Bouchet JP (2005) Transcriptomic study of apricot fruit (Prunus armeniaca) ripening among 13006 expressed sequence tags. Physiol Plant 125:281–292

    Article  Google Scholar 

  • Haciseferogullari H, Gezer I, Özcan MM, Murat Asma B (2007) Post-harvest chemical and physical mechanical properties of some apricot varieties cultivated in Turkey. J Food Eng 79:364–373

    Article  CAS  Google Scholar 

  • Hayama H, Shimada T, Fujii H, Ito A, Kashimura Y (2006) Ethylene-regulation of fruit softening and softening-related genes in peach. J Exp Bot 57:4071–4077

    Article  CAS  PubMed  Google Scholar 

  • Hundertmark M, Hincha DK (2008) LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 9:118

    Article  PubMed  PubMed Central  Google Scholar 

  • Indira Iyer R, Nagar PK, Sircar PK (1984) Cytokinin Changes in embryo and endosperm of cassia fistula during fruit growth. J Plant Physiol 117:87–92

    Article  CAS  PubMed  Google Scholar 

  • Jiang YQ, Ma RC (2003) Generation and analysis of expressed sequence tags from almond (Prunus dulcis Mill.) pistils. Sex Plant Reprod 16:197–207

    Article  CAS  Google Scholar 

  • Jung S, Jiwan D, Cho I, Lee T, Abbott A, Sosinskin B, Main D (2009) Synteny of Prunus and other model plant species. BMC Genomics 10:76

    Article  PubMed  PubMed Central  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kurakawa T, Ueda N, Maekawa M, Kobayashi K, Kojima M, Nagato Y, Sakakibara H (2007) Direct control of shoot meristem activity by a cytokinin-activating enzyme. Nature 445:652–655

    Article  CAS  PubMed  Google Scholar 

  • Lau S, Slane D, Herud O, Kong J, Jürgens G (2012) Early embryogenesis in flowering plants: setting up the basic body pattern. Annu Rev Plant Biol 63:483–506

    Article  CAS  PubMed  Google Scholar 

  • Lu P, Porat R, Nadeau JA, O'Neill SD (1996) Identification of a meristem L1 layer-specific gene in Arabidopsis that is expressed during embryonic pattern formation and defines a new class of homeobox genes. Plant Cell 8:2155–2168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Manganaris GA, Rasori A, Bassi D, Geuna F, Ramina A, Tonutti P (2011) Comparative transcript profiling of apricot (Prunus armeniaca L.) fruit development and on-tree ripening. Tree Genet Genomes 7:609–616

    Article  Google Scholar 

  • Martínez-Gómez P, Crisosto CH, Bonqhi C, Rubio M (2011) New approaches to Prunus transcriptome analysis. Genetica 139:755–769

    Article  PubMed  Google Scholar 

  • Milazzo S, Ernst E, Lejeune S, Boehm K, Horneber M (2011) Laetrile treatment for cancer. Cochrane Database Syst Rev. 9:CD005476

    Google Scholar 

  • Mok DW, MC M (2001) Cytokinin metabolism and action. Ann Rev Plant Physiol Plant Mol Biol 52:89–118

    Article  CAS  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  CAS  PubMed  Google Scholar 

  • Mothes K, Engelbrecht L (1961) Kinetin induced directed transport of substances in excised leaves in the dark. Phytochemistry. 1:58–62

    Article  CAS  Google Scholar 

  • Murphy DJ (1997) Cellular and molecular biology of plant seed development. New Phytol 142:1–3

    Article  Google Scholar 

  • Ogundiwin EA, Marti C, Forment J, Pons C, Granell A, Gradziel TM, Peace CP (2008) Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruits. Plant Mol Biol 68:379–397

    Article  CAS  PubMed  Google Scholar 

  • Pedersen CB, Kyle J, Jenkinson AM, Gardner PT, McPhail DB, Duthie GG (2000) Effects of blueberry and cranberry juice consumption on the plasma antioxidant capacity of healthy female volunteers. Eur J Clin Nutr 54: 405–408

    Article  CAS  PubMed  Google Scholar 

  • Plimmer JR (1977) Pesticide Chemistry in the 20th Century. United States: American Chemical Society

    Book  Google Scholar 

  • Pouchkina-Stantcheva NN, Mcgee BM, Boschetti C, Tolleter D, Chakrabortee S, Popova AV, Meersman F (2007) Functional divergence of former alleles in anancient asexual invertebrate. Science 318:268–271

    Article  CAS  PubMed  Google Scholar 

  • Sakai H, Honma T, Aoyama T, Sato S, Kato T, Tabata S, Oka A (2001) ARR1, a transcription factor for genes immediately responsive to cytokinins. Science 294:1519–1521

    Article  CAS  PubMed  Google Scholar 

  • Schlereth A, Möller B, Liu W, Kientz M, Flipse J, Rademacher EH, Schmid M (2010) Monopteros controls embryonic root initiation by regulating a mobile transcription factor. Nature 464:913–916

    Article  CAS  PubMed  Google Scholar 

  • Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC (2009) Short-read sequencing technologies for transcriptional analyses. Ann Rev Plant Biol 60:305–333

    Article  CAS  Google Scholar 

  • Trainotti L, Bonghi C, Ziliotto F, Zanin D, Rasori A, Casadoro G, Ramina A (2006) The use of microarray PEACH1.0 to investigate transcriptome changes during transition from preclimacteric to climacteric phase in peach fruit. Plant Sci 170:606–613

    Article  CAS  Google Scholar 

  • Trainotti L, Tadiello A, Casadoro G (2007) The involvement of auxin in the ripening of climacteric fruits comes of age: the hormone plays a role of its own and has an intense interplay with ethylene in ripening peaches. J Exp Bot 58:3299–3308

    Article  CAS  PubMed  Google Scholar 

  • Tunnacliffe A, Lapinski J, Mcgee B (2005) A putative LEA protein, but no trehalose, is present in anhydrobiotic bdelloid rotifers. Hydrobiologia 546:315–321

    Article  CAS  Google Scholar 

  • Verde I, Abbott AG, Scalabrin S, Junq S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weijers D, E Benkova, KE Jäger, A Schlereth, T Hamann, M Kientz, JC Wilmoth (2005) Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. EMBO J 24:1874–1885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • White CN, Rivin CJ (2000) Gibberellins and seed development in maize. II. Gibberellin synthesis inhibition enhances abscisic acid signaling in cultured embryos. Plant Physiol 122:1089–1098

    CAS  PubMed  Google Scholar 

  • Won C, Shen X, Mashiguchi K, Zheng Z, Dai X, Cheng Y, Kasahara H (2011) Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis. Proc Natl Acad Sci USA 108: 18518–18523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu H, Gao Y, Wang J (2012) Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique. PLoS One 7:e30646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamamoto T, Mochida K, Imai T, Shi YZ, Ogiwara I, Hayashi T (2002) Microsatellite markers in peach [Prunus persica (L.) Batsch] derived from an enriched genomic and cDNA libraries. Mol Ecol Notes 2:298–301

    Article  CAS  Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:293–297

    Article  Google Scholar 

  • Zhao P, Liu F, Ma M, Gong J, Wang Q, Jia P, Zheng G, Liu H (2011) Overexpression of AtLEA3-3 confers resistance to cold stress in Escherichia coli and provides enhanced osmotic stress tolerance and ABA sensitivity in Arabidopsis thaliana. Mol Biol Cell 45:785–796

    CAS  Google Scholar 

  • Zhao Y, Christensen SK, Fankhauser C, Cashman JR, Cohen JD, Weigel D, Chory J (2001) A role for flavin monooxygenase-like enzymes in auxin biosynthesis. Science 291:306–309

    Article  CAS  PubMed  Google Scholar 

  • Ziliotto F, Begheldo M, Rasori A, Bonghi C, Tonutti P (2008) Transcriptome profiling of ripening nectarine (Prunus persica L. Batsch) fruit treated with 1-MCP. J Exp Bot 59:2781–2791

    CAS  PubMed  Google Scholar 

  • Ziosi V, Bonghi C, Bregoli AM, Trainotti L, Biondi S, Sutthiwal S, Kondo S (2008) Jasmonate-induced transcriptional changes suggest a negative interference with the ripening syndrome in peach fruit. J Exp Bot 59:563–573

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, 830052, China

    Yujia Bai, Min Wang, Jing He, Yongxia Tao, Wei Huang & Zuoshan Feng

  2. Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection/Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huaian, 223300, China

    Weicheng Hu

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  1. Yujia Bai
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  2. Weicheng Hu
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  3. Min Wang
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Correspondence to Zuoshan Feng.

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Bai, Y., Hu, W., Wang, M. et al. Transcriptomic analysis of developing embryos of apricot (Prunus armeniaca L.). Hortic. Environ. Biotechnol. 57, 197–206 (2016). https://doi.org/10.1007/s13580-016-0002-3

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