Search

The sense of smell helps us navigate the environment, but its molecular architecture and underlying logic remain unknown. The spatial location of odorant receptor genes (Olfrs) in the nose is widely thought to be independent of the structural diversity of the odorants they detect. Using spatial transcriptomics, we created a genome-wide 3D atlas of the mouse olfactory mucosa (OM). Topographic maps of genes differentially expressed in space reveal that bothOlfrsand non-Olfrsare distributed in a continuous and overlapping fashion over five broad zones in the OM. The spatial locations ofOlfrscorrelate with the mucus solubility of the odorants they recognize, providing direct evidence for the chromatographic theory of olfaction. This resource resolved the molecular architecture of the mouse OM, and will inform future studies on mechanisms underlyingOlfrgene choice, axonal pathfinding, patterning of the nervous system, and basic logic for the peripheral representation of smell.

Objective Fasting regimens can promote health, mitigate chronic immunological disorders, and improve age-related pathophysiological parameters in animals and humans. Several ongoing clinical trials are using fasting as a potential therapy for various conditions. Fasting alters metabolism by acting as a reset for energy homeostasis, but the molecular mechanisms underlying the beneficial effects of short-term fasting (STF) are not well understood, particularly at the systems or multiorgan level. Methods We performed RNA-sequencing in nine organs from mice fed ad libitum (0 h) or subjected to fasting five times (2–22 h). We applied a combination of multivariate analysis, differential expression analysis, gene ontology, and network analysis for an in-depth understanding of the multiorgan transcriptome. We used literature mining solutions, LitLab™ and Gene Retriever™, to identify the biological and biochemical terms significantly associated with our experimental gene set, which provided additional support and meaning to the experimentally derived gene and inferred protein data. Results We cataloged the transcriptional dynamics within and between organs during STF and discovered differential temporal effects of STF among organs. Using gene ontology enrichment analysis, we identified an organ network sharing 37 common biological pathways perturbed by STF. This network incorporates the brain, liver, interscapular brown adipose tissue, and posterior-subcutaneous white adipose tissue; hence, we named it the brain-liver-fats organ network. Using Reactome pathways analysis, we identified the immune system, dominated by T cell regulation processes, as a central and prominent target of systemic modulations during STF in this organ network. The changes we identified in specific immune components point to the priming of adaptive immunity and parallel the fine-tuning of innate immune signaling. Conclusions Our study provides a comprehensive multiorgan transcriptomic profiling of mice subjected to multiple periods of STF and provides new insights into the molecular modulators involved in the systemic immunotranscriptomic changes that occur during short-term energy loss., Highlights • A multi-organ transcriptomic atlas of short-term fasting (STF) in mice. • Data-driven grouping and gene functional clustering enhanced analytical depth. • The shared biological processes in mice forms a brain-liver-fats network. • STF orchestrates major changes in immune-related processes across many organs.

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.

The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content we analyzed date fruit metabolomics for association with genotype data from 121 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta-fructofuranosidase (invertase) gene in the reference Khalas genome, a low sucrose fruit. High sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains the all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end-point sucrose content in date fruit may be used in selective breeding in the future.

This article provides detailed information on the phenotypes and the metabolic profiles of 196 date fruits from 123 unique date fruit varieties. These date fruits are extensively diverse in their country of origin, variety and post harvesting conditions. We used a non-targeted mass-spectrometry based metabolomics approach to metabolically characterize date fruits, and measured 427 metabolites from a wide range of metabolic pathways. The metabolomics data for all the date fruit samples are available at the NIH Common Fund's Data Repository and Coordinating Center (supported by NIH grant, U01-DK097430) website, http://www.metabolomicsworkbench.org ), under Metabolomics Workbench StudyID: ST000867. The data are directly accessible at http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=ST000867&StudyType=MS&ResultType=1 .

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.

We report a child with inherited, complete IRF9 deficiency who suffered from life-threatening influenza pneumonitis. IRF9 deficiency disrupts the activation of ISGF3 and impairs but does not abolish cellular responses to type I IFNs, as some ISGs are induced., Life-threatening pulmonary influenza can be caused by inborn errors of type I and III IFN immunity. We report a 5-yr-old child with severe pulmonary influenza at 2 yr. She is homozygous for a loss-of-function IRF9 allele. Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. The transcriptome induced by IFN-α2b in the patient’s cells is much narrower than that of control cells; however, induction of a subset of IFN-stimulated gene transcripts remains detectable. In vitro, the patient’s cells do not control three respiratory viruses, influenza A virus (IAV), parainfluenza virus (PIV), and respiratory syncytial virus (RSV). These phenotypes are rescued by wild-type IRF9, whereas silencing IRF9 expression in control cells increases viral replication. However, the child has controlled various common viruses in vivo, including respiratory viruses other than IAV. Our findings show that human IRF9- and ISGF3-dependent type I and III IFN responsive pathways are essential for controlling IAV.

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.

The date palm tree is a commercially important member of the genus Phoenix whose 14 species are dioecious with separate male and female individuals. To identify sex determining genes we sequenced the genomes of 15 female and 13 male Phoenix trees representing all 14 species. We identified male-specific sequences and extended them using phased single-molecule sequencing or BAC clones. We observed that only four genes contained sequences conserved in all analyzed Phoenix males. Most of these sequences showed similarity to a single genomic locus in the closely related monoecious oil palm. CYP703 and GPAT3, two single copy genes present in males and critical for male flower development in other monocots, were absent in females. A LOG-like gene appears translocated into the Y-linked region and is suggested to play a role in suppressing female flowers. Our data are consistent with a two-mutation model for the evolution of dioecy in Phoenix., The origin and evolution of separate sexes in plants are long-standing questions. Here, the authors use genus-wide sequencing to identify sex determining candidate genes in the genus Phoenix and demonstrate the consistence with the previously proposed two-mutation model.

Date palm (Phoenix dactylifera) is one of the most important crops in many arid land cultures. The date fruits are rich in essential nutrients, minerals, vitamins and fiber, making them a critical food source linked to the history of the Arab world. The most frequent method of propagation is by offshoots, which guarantees that the characteristics and quality of the fruit are maintained; however, it significantly reduces the genetic variability of the date palm plantations, making them extremely vulnerable to pests and diseases. During the past few years, advances on date palm research have provided some information about the molecular markers associated with different desirable agronomical traits, including gender and fruit color.We recently showed that P. dactylifera employs and XY sex-chromosome system, and generated a genetic map that localized this gender determination locus to the lower arm of linkage group 12. Based on this initial information, we designed markers to screen a Bacterial Artificial Chromosome (BAC) library of a male P. dactylifera to sequence the X and Y alleles in date palm. A combination of approaches that include next-generation (Illumina) and Single Molecule, Real-Time (SMRT) Sequencing (PacBio) of more than one hundred BAC clones, have allowed us to map eighty markers to eleven larger DNA contigs, containing the corresponding female and male specific regions, spanning approximately 4Mb. However, multiple sequence gaps still exist within and between the sequenced region, and further analysis have indicated that the borders of most assembled contigs correspond to repetitive elements, which likely constitute a big portion of the unassembled DNA sequences. Non-recombining regions of sex chromosomes, particularly the Y chromosome, are highly repetitive due to degeneration, making it more challenging to design markers and extend the assembled sequences by chromosome walking.These observations, led us to propose a parallel approach to complement and advance on the initial sequencing strategy. Date palm, and all other thirteen members of the genus Phoenix, are dioecious, with roughly half of the individuals planted from seed expected to be fruit-bearing female trees. The conservation of dioecy in this entire clade in the Palm family (Arecaceae) suggests that in the genus Phoenix, dioecy evolved before speciation. Therefore, we recently started using comparative genomics to analyze male and female individuals from the remaining thirteen Phoenix species, which has allowed us to narrow down the Y-specific region to a very small portion of the genome, containing only a few genes. Our latest findings are providing a new insight into the evolution of plant sex chromosomes and sex determination in date palm. Standardization and validation of new methodologies that allow for large-scale sequencing and analysis of polymorphisms in date palm, will provide valuable tools for the development of marker-assisted selection programs, for the improvement of date palm production. This will allow Qatar to diversify the varieties of dates it grows, and in the near future will allow us to test for the most desirable agricultural traits, which will significantly improve the quality of the fruit, making Qatar a more competitive date producer in the region.

Viruses, Bacteria and Fungal pathogens have been responsible for destruction and degradation of plants worldwide. Most often, these pathogens live a symbiotic relationship with the plant, enhancing plant growth and at times as predators, causing a wide variety of diseases. Date palms are cultivated widely in the Middle Eastern region due to their multi-faceted uses and are valued most for their nutritious fruit – the date. The trees flourish in deep sandy loam soils and can also grow in salty and alkaline soils. An old Arab folk saying “Its feet in water and its head in file” aptly describe Date Palm trees. Therefore, the importance of Date Palm trees to Qatar and in broad to the region (Arabian Peninsula) cannot be undermined.Date palm cultivation is hindered by several constraints; especially it's vulnerability to a wide range of bacterial, viral and fungi pathogens present in the environment. Outbreaks of diseases like Bayoud disease caused by Fusarium oxysporum was reported in Morocco and spread to neighboring countries Algeria and Tunisia, resulting in destruction of millions of trees since its outbreak a century ago. This outbreak impacted socio economic conditions of farmers as poor quality but disease resistant cultivars started dominating the landscape at the expense of commercial cultivars. In Qatar, localized incidences of disease in Date Palm trees have been reported. In 2003, Department of Agricultural Development reported a first instance of Neck bending disease on Date Palm trees growing alongside the road of Majlis AL-Taawin located in Doha, Qatar. Neck Bending was previously reported in Iraq. Therefore, continuous efforts are needed to scan for opportunistic environmental pathogens, which in future can lead to disease outbreaks. In this work, we present our findings of environmental pathogens detected with our new Date-Pathogen pipeline (DPP) using geographical sampling of Date Palm Trees covering all municipalities in the State of Qatar.A total of 96 leaf samples were sequenced on HiSeq2500 using libraries prepared by Genotyping-by-Sequencing methodology. We identified 4 different variants of the virus Enterobacteria spp in 31 samples. They belonged to two municipalities, Al Wakrah and Al Rayyan region. We uncovered two different bacteria namely Propionibacterium acnes and Staphylococcus epidermidis in a total of 52 samples growing in the Al Rayyan Municipality region in Qatar. Eight different variants of Propionibacterium was found in all the samples except one. The above bacterial pathogens are causative agents to cause acnes in human skin and known to have no effects on plants. A recent study in 2014 has reported an example of inter kingdom bacterial host transfer involving human pathogen Propionibacterium acnes Zappae and grapevine plants. This could suggest that the strain of Propionobacterium acnes identified in our samples might be in future case of interkingdom transfer from human to date palm trees. Two fungal pathogens – Saccharomyces cerevisiae and Fusarium graminearium were also found in 42 samples. It has been shown that Saccharomyces cerevisiae produces plant hormone indole-3-acetic acid (IAA), which in sufficient quantity triggers fungal cells to be more infectious in host organism. This infection was found in trees from Al Wakrah and Al Raayan municipalities. Fusarium graminearium are known to cause fusarium head blight in wheat, barley and oat. Previously, other Fusarium species oxysporum have been found to cause Bayoud disease in date palm trees which have resulted in degradation of date palm trees in Morocco and Algeria. However, Fusarium graminearium is reported in Qatar for the first time in date palm trees growing at Doha, Al Khor, Al Daayen, Al Shamal and Umm Salal municipalities. The above results are preliminary analysis and will be explored further in the next few months.

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.

Dates constitute the primary exportable agricultural product in Qatar and current efforts are being made to improve its production. Varieties with desirable morphological traits are usually maintained using clonal propagation leading to the establishment of uniform palm plantations. This practice reduces the genetic diversity among palm orchards and makes them more vulnerable to pests and diseases. The biggest limitation in date palm propagation from seeds is that half of the planted offspring are expected to be male individuals with no agricultural value. Previous cytological studies indicated the presence of heteromorphic sex chromosomes in date palm, but enzymatic approaches intended to anticipate gender determination have been unsuccessful. Single nucleotide polymorphism (SNP) analysis of female and male individuals from the commercial varieties Khalas, Deglet Noor and Medjool, allowed the identification of a sex-linked region that segregates with gender, and extends to 24 scaffolds. This sex locus was genetically mapped to the lower arm of linkage group 12, and was estimated to extend up to 13 Mb, or 2% of the genome. Our objective was to physically map the male/female determination region in date palm using a bacterial artificial chromosome (BAC) library. This library represents 12x genome coverage and clones have an average insert size of 125 kb. A first round of PCR screening of this library was developed using the sequence information from the 24 SNP-enriched scaffolds to generate PCR-based primers around gender segregating markers. Plasmid DNA from multiple BACs was barcoded, pooled and sequenced using Illumina MiSeq and 150 paired-end reads were then assembled and compared to the existing date palm reference genomes from Qatar and Saudi Arabia. Next generation sequencing of eighty-two BACs has allowed the mapping of nineteen markers to six large assembled contigs with an estimated average size of 496.4 kb spanning approximately 2.9 Mb. Preliminary analysis of the assembled sequences indicated that we have positively identified a genomic region highly enriched in gender-linked SNPs, with male and female alleles segregating in a 1:1 ratio. This is what we would have expected from an XY sex chromosome system. Multiple sequence gaps still exist within and between the sequenced region, and further analysis has indicated that many BAC end sequences correspond to repetitive elements that likely constitute a big portion of the unassembled DNA sequences. During the second phase of this study, we have designed and tested twenty-one new PCR markers that we expect will help to close the gaps, determine the minimum tilling path and obtain a complete sequence and physical map of the sex-determination region. Our ultimate goal is to detect the critical mutation that gave rise to male and female separation. This is the first time such level of detail in a dioecious plant will be achieved. Furthermore, standardization of a reliable sequencing and screening procedure will allow us to characterize other genomic regions associated with desirable commercial properties in date fruits. This in turn will provide a valuable tool for the development of marker-assisted selection programs and ultimately for the improvement of date palm production.

Introduction and Background: The date palm is a critical tree to Arabian Gulf agriculture, history and culture. Dates are a major source of nutrition in the region, and the tree itself plays an important role in the development of sustainable agriculture in many drought and saline-affected regions of the world. Date palm development presents a challenge, however, as the tree is a dioecious species, that is, individual plants are either male or female and are indistinguishable during the first 5-8 years, until flowering begins. We recently identified a region of the date palm genome linked to gender, which showed that the date palm employs an XY system of gender inheritance similar to that of humans. Methods and Technology: As part of a development plan we recently released a draft sequence of the date palm genome (Khalas female). In our findings, we identified sequence variations on four contigs that were strongly linked to gender and validated them in a large pedigree. We identified an additional 20 contigs with some evidence of linkage to gender. Validation of new gender-linked contigs will help in the fine-mapping of a possible single mutation, which results in gender determination in date palm. To validate linkage we have amplified the DNA of 7 male and 7 female date palm samples using 20 specifically designed primers. The PCR products obtained are sequenced by Sanger's sequencing. The sequenced regions from these contigs are from a diverse set of male and female date palms. We are studying these sequences and regions to identify a possible specific mutation or other gene content difference that determines plant gender. Result: We have confirmed linkage in many of the contigs, and these provide a set of genes within the "degraded" male sequence which may offer clues to how gender is determined biochemically and developmentally in date palm. Conclusion: There may be many more additional contigs which we are investigating to aid in the mapping of more variations and mutations, which correspond to different traits and features in the date palm, particularly dealing with gender.

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.