Abstract
Expressed sequence tags (EST) were generated from a normalized cDNA library of the date palm Sukkari cv. to understand the high-quality and better field performance of this well-known commercial cultivar. A total of 6943 high-quality ESTs were generated, out of them 6671 are submitted to the GenBank dbEST (LIBEST_028537). The generated ESTs were assembled into 6362 unigenes, consisting of 494 (14.4%) contigs and 5868 (84.53%) singletons. The functional annotation shows that the majority of the ESTs are associated with binding (44%), catalytic (40%), transporter (5%), and structural molecular (5%) activities. The blastx results show that 73% of unigenes are significantly similar to known plant genes and 27% are novel. The latter could be of particular interest in date palm genetic studies. Further analysis shows that some ESTs are categorized as stress/defense- and fruit development-related genes. These newly generated ESTs could significantly enhance date palm EST databases in the public domain and are available to scientists and researchers across the globe. This knowledge will facilitate the discovery of candidate genes that govern important developmental and agronomical traits in date palm. It will provide important resources for developing genetic tools, comparative genomics, and genome evolution among date palm cultivars.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Wrigley G (1995) Date palm, Phoenix dactylifera. In: Smartt J, Simmonds NW (eds) Evolution of crop plants, 2nd edn. Longman, London, pp 399–403
Al-Mssallem IS (1996) Date palm. Arab Global Encyclopedia 7:182–187
Malek JA (2010) Next generation DNA sequencing applied to the date palm tree (Phoenix dactylifera). Acta Hort 882:249–252
Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM et al (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29:521–527
Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W, Tan J et al (2013) Genome sequence of the date palm Phoenix dactylifera L. Nat Commun 4:2274
Yang M, Zhang X, Liu G et al (2010) The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.) PLoS One 5(9):e12762
Fang Y, Wu H, Zhang T, Yang M, Yin Y, Pan L et al (2012) A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS One 7(5):e37164
Yin YX, Zhang XW, Fang YJ, Pan LL, Sun GY, Xin CQ et al (2012) High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.) Plant Mol Biol 78:617–626
Zhang G, Pan L, Yin Y, Liu W, Huang D, Zhang T et al (2012) Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.) Plant Mol Biol 79:521–536
Mathew LS, Spannag M, Al-Malki A, George B, Torres M, Al-Dous EK et al (2014) A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms. BMC Genomics 15:285
Jain SM, Al-Khayri JM, Johnson DV (eds) (2011) Date palm biotechnology. Springer, Dordrecht, p 743
Radwan O, Arro J, Keller C, Korban S (2015) RNA-Seq transcriptome analysis in date palm suggests multi-dimensional responses to salinity stress. Trop Plant Biol 8:74–86
Pertea G, Huang X, Liang F, Antonescu V, Sultana R et al (2003) TIGR gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652
Altschul SF, Gish W, Miller W, Myers EW (1990) Lipman DJ: Basic local alignment search tool. J Mol Biol 215:403–410
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ et al (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanchisa M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27:29–34
Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB et al (2004) Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res 32:e37
Zhulidov PA, Bogdanova EA, Shcheglov AS, Shagina IA, Wagner LL, Khazpekov GL et al (2005) A method for the preparation of normalized cDNA libraries enriched with full-length sequences. Rus J Bioorg Chem 31:170–177
Young BD, Anderson MLM (1985) Quantitative analysis of solution hybridisation. In: Hames BD, Higgins SJ (eds) Nucleic acid hybridisation. IRL Press, Washington, DC, pp 47–71
Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA et al (2002) A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res 12:1935–1942
Acknowledgment
The authors are grateful to the National Plan for Science and Technology (NPST) program project number 08-BIO-164-2 and to the Deanship of the Scientific Research/Agricultural Research Center at King Saud University for financial support.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Al-Faifi, S.A. et al. (2017). Analysis of Expressed Sequence Tags (EST) in Date Palm. In: Al-Khayri, J., Jain, S., Johnson, D. (eds) Date Palm Biotechnology Protocols Volume II. Methods in Molecular Biology, vol 1638. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7159-6_23
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7159-6_23
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7158-9
Online ISBN: 978-1-4939-7159-6
eBook Packages: Springer Protocols