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Background The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. Results To better understand the origins of date palm cultivation we sequenced and analyzed over 200 mitochondrial and chloroplast genomes from a geographically diverse set of date palms. Here we show that, based on mitochondrial and chloroplast genome-wide genotyping data, the most common cultivated date palms contain 4 haplotypes that appear associated with geographical region of cultivar origin. Conclusions These data suggest at least 3 and possibly 4 original maternal contributions to the current date palm population and doubles the original number. One new haplotype was found mainly in Tunisia, Algeria and Egypt and the second in Iraq, Iran and Oman. We propose that earliest date palm cultivation occurred independently in at least 3 distinct locations. This discovery will further inform understanding of the history and origins of cultivated date palm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5834-7) contains supplementary material, which is available to authorized users.

Understanding the genetic diversity in a crop population is key to its targeted breeding for desired traits, such as higher yields, better fruit quality and resistance to disease and changing climates. Date fruits represent a major crop in the Middle East and are key to achieving future food independence in arid countries like Qatar. We previously determined the genome of the date palm Phoenix dactylifera and showed that date palm trees world-wide divide into two distinct subpopulations of Eastern and Western origins. Here we applied a resource of SNPs from 179 commercially available date fruits to assess the genetic diversity of date palm trees grown in the State of Qatar. We found that palm trees in Qatar are mainly of Eastern origin, and that their genetic diversity doesn’t associate with regions of the State. Together with targeted genetic assays, our resource can be used in the future for date palm cultivar identification, to aid selecting suitable cultivars for targeted breeding, to improve a country’s date palm genetic diversity, and to certify the origin of date fruits and trees.

The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately tied to the history of human civilization. There are hundreds of commercial cultivars with distinct fruit shapes, colors, and sizes growing mainly in arid lands from the west of North Africa to India. The origin of date palm domestication is still uncertain, and few studies have attempted to document genetic diversity across multiple regions. We conducted genotyping-by-sequencing on 70 female cultivar samples from across the date palm–growing regions, including four Phoenix species as the outgroup. Here, for the first time, we generate genome-wide genotyping data for 13,000–65,000 SNPs in a diverse set of date palm fruit and leaf samples. Our analysis provides the first genome-wide evidence confirming recent findings that the date palm cultivars segregate into two main regions of shared genetic background from North Africa and the Arabian Gulf. We identify genomic regions with high densities of geographically segregating SNPs and also observe higher levels of allele fixation on the recently described X-chromosome than on the autosomes. Our results fit a model with two centers of earliest cultivation including date palms autochthonous to North Africa. These results adjust our understanding of human agriculture history and will provide the foundation for more directed functional studies and a better understanding of genetic diversity in date palm.

Objective: Information that is present in our DNA is transferred to RNA, which is in turn transcribed into proteins. This is a central principle of molecular biology. Over the years, there have been many attempts to document the thousands of places where transcribed RNA does not match the DNA template it was created from. This behavior is called RNA Editing, and is generally thought to be mainly an A->I change, that is, adenosine to inosine (read as guanine by DNA sequencers), with occasional cytosine to uracil changes as well. Cancer, with its volatility due to DNA base changes, gets more complex with the occurrences of RNA editing. To ensure a fair ground to study RNA editing, we have considered exome and RNASeq library pairs from the cancer-affected ovarian, lymph node and peritoneum tissues in three individual. This data set will help identify RNA editing locations in these tissues, and the role it plays in metastasis. Methods: The exome libraries were prepared using Illumina Paired End Sample Preparation kit and Agilent SureSelect Target Enrichment System kit. RNASeq libraries were prepared using Illumina paired-end protocol. Both the libraries were sequenced using the Illumina NextGen Sequencing platform. Exome libraries were aligned using bowtie2 and RNASeq using tophat2. SNPs were called using samtools. The RNAEditing database from Ensemble was used to filter out known editing sites. With the remaining editing locations, a blat was run against the surrounding sequence to check for similarity to other parts of the genome, to rule out editing sites being called as a result of incorrect alignment scoring. Results: From our preliminary analysis, we see that a majority of the RNA Editing positions represent A->I changes, with a few C->U changes as well. Some of these positional changes are seen across all tissues in an individual. There are few RNA edited sites that are mainly seen only in the metastatic locations, and not seen in the primary. Conclusions: By analyzing the initial results, we can identify the mutations and RNA edited sites that originate from the primary tumor tissue, and those that are acquired in the metastatic tissues.

Background: The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified.Results: Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome.Conclusions: Based on a modified gentoyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.