Abstract
The date palm (Phoenix dactylifera L.), famed for its sugar-rich fruits (dates) and cultivated by humans since 4,000 B.C., is an economically important crop in the Middle East, Northern Africa, and increasingly other places where climates are suitable. Despite a long history of human cultivation, the understanding of P. dactylifera genetics and molecular biology are rather limited, hindered by lack of basic data in high quality from genomics and transcriptomics. Here we report a large-scale effort in generating gene models (assembled expressed sequence tags or ESTs and mapped to a genome assembly) for P. dactylifera, using the long-read pyrosequencing platform (Roche/454 GS FLX Titanium) in high coverage. We built fourteen cDNA libraries from different P. dactylifera tissues (cultivar Khalas) and acquired 15,778,993 raw sequencing reads—about one million sequencing reads per library—and the pooled sequences were assembled into 67,651 non-redundant contigs and 301,978 singletons. We annotated 52,725 contigs based on the plant databases and 45 contigs based on functional domains referencing to the Pfam database. From the annotated contigs, we assigned GO (Gene Ontology) terms to 36,086 contigs and KEGG pathways to 7,032 contigs. Our comparative analysis showed that 70.6 % (47,930), 69.4 % (47,089), 68.4 % (46,441), and 69.3 % (47,048) of the P. dactylifera gene models are shared with rice, sorghum, Arabidopsis, and grapevine, respectively. We also assigned our gene models into house-keeping and tissue-specific genes based on their tissue specificity.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-012-9924-z) contains supplementary material, which is available to authorized users.
Highlights
Date palm, Phoenix dactylifera L., gains a considerable fame for its fruits, which have an excellent capability to enrich sugar in mesocarp up to 50 % of the total weight (Bourgis et al 2011)
Armed with the next-gen sequencing tools, we are in a unique position to significantly improve our understanding of P. dactylifera genomics and biology
There have been only two significant reports on P. dactylifera genomic data based on the next-gen sequencing technologies; one concerns a draft genome sequence assembly (Al-Dous et al 2011) and the other is a comparative analysis between the fruits of oil palm and P. dactylifera, where mechanisms of carbon partition were explored in depth (Bourgis et al 2011)
Summary
Phoenix dactylifera L., gains a considerable fame for its fruits (dates), which have an excellent capability to enrich sugar in mesocarp up to 50 % of the total weight (Bourgis et al 2011). Illumina HiSeq2000 and Life Technologies SOLiD systems are able to generate huge numbers of reads per machine run but shorter read lengths. Both platforms, are powerful for detecting low-abundant transcripts and validating homoploymeric nucleotide tracts that are less abundant but remain ambiguous in the Roche/454 data. There have been only two significant reports on P. dactylifera genomic data based on the next-gen sequencing technologies; one concerns a draft genome sequence assembly (Al-Dous et al 2011) and the other is a comparative analysis between the fruits of oil palm and P. dactylifera, where mechanisms of carbon partition were explored in depth (Bourgis et al 2011). We generated 30,854 of annotated gene models that are treated as putative full-length cDNAs and compared them to the latest data from other plant species, including rice (49,066; RGAP7, October 31, 2011) and Arabidopsis thaliana (37,761; TAIR9); the amount of gene models is comparable for an initial annotation of plant genomes
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
