Highlights include: a predicted genome size of ~550Mbp, a scaffold N50 of 4250bp with most ordered gaps being extremely short, ~45,000 scaffolds greater than 2kb, 850,000 novel high quality SNPs between parental alleles, 37% GC in the nuclear genome, 302Mb of assembled sequence with 18.5Mb of ordered gaps, ~292Mb of sequence unique at the 24mer level, and draft Chloroplast gene sequences.
The scientific name is Phoenix dactylifera L., while the variety name is 'Khalas'. Combining the two we get 'PdactyK' for short.
It is our hope that the results provided here will be a starting point for researchers doing genetic studies of date palm. The assembly is a draft assembly using next generation sequencing reads and as such requires caution in it usage. While short range contiguity is of high quality, longer range contiguity (spanning gaps) is less certain. Manual inspection of contigs based on mate pair validity showed contigs/scaffolds up to 12kb were consistently assembled correctly. The quality of these scaffolds is roughly equivalent to other plant draft sequences such as rice and papaya. Larger scaffolds are more likely to have errors. As such researchers should be careful in operations such as PCR primer design when spanning gaps in the assembly (denoted by N's in the sequence).
DNA for this project was obtained from leaves kinldy provided by the Qatar Plant Tissue Culture Lab in the Dept of Agriculture and Water Research (Qatar Ministry of Municipal Affairs and Agriculture).
Click here to download Date Palm Research Data
Last modified on
Tuesday, 06-Oct-2009 11:35:15 SAUST