NEW YORK (GenomeWeb News) – A Qatar research team announced this week that they have mapped the draft genome of date palm, Phoenix dactylifera, using second generation sequencing.
Researchers from Weill Cornell Medical College in Qatar used whole genome shotgun sequencing to sequence the draft genome of a P. dactylifera variety called Khalas. Those involved say the proof-of-concept study demonstrates the WCMC-Q core lab's ability to do large scale genomics projects. In addition, the team hopes the draft genome will contribute to a more complete understanding of date palm genetics as well as insights into improving yield, quality, and disease resistance.
The project, which was launched last year, relied on whole genome shotgun second generation sequencing to sequence the genome of date palm, an important agricultural plant in the Middle East, northern Africa, and Pakistan.
"We were able to develop a relatively unbiased view of the gene space of the entire date palm plant at a fraction of the cost and in a much shorter period of time," WCMC-Q Genomics Laboratory Director Joel Malek said in a statement. "Using this approach, which takes advantage of lower repetitive DNA in the date palm gene regions, we have increased the publicly available knowledge of the date palm gene by about 1,000 fold."
The researchers used Illumina's Genome Analyzer II with paired-end reads. Malek told GenomeWeb Daily News in a follow-up e-mail after this article was initially published that the group has approximately 20X coverage of the genome so far.
Malek reportedly established the genomics lab at WCMC-Q in 2008. The lab is part of a biomedical research program, also launched last year and supported by the Qatar Foundation for Education, Science, and Community Development. The program was established in an effort to make Qatar a Middle East research hub.
Researchers obtained DNA for the sequencing effort from date palm leaves supplied by the Qatar Department of Agricultural and Water Research's Plant Tissue Culture Lab. Based on their results, the researchers estimate that the date palm genome is roughly 550 million base pairs. According to the WCMC-Q website, they also identified 850,000 new SNPs via comparisons between parental alleles.
Evidence from manual contig inspection suggests the assembly is consistently correct for scaffolds that are 12,000 bases or less. Overall, researchers noted, the quality appears to be comparable to that of draft versions of the rice and papaya genomes, though researchers are continuing to improve genome assembly and annotation.
"The assembly is a draft assembly using next-generation sequencing reads and as such requires caution in its usage," according to WCMC-Q's date palm draft sequence web site. "While short range contiguity is of high quality, longer range contiguity (spanning gaps) is less certain."
The WCMC-Q team plans to publish the final, annotated version of the date palm genome, including data analysis and interpretation. In the meantime, the date palm draft genome is being made freely available online as a resource for others interested in date palm genetics.