The backbone of our genome assembly was largely based on pyrosequencing reads. First, we assembled quality-filtered reads to build contigs using the default settings of Newbler (version 2.5.3). Second, we mapped the SOLiD mate-pair tags using BioScope (version 1.3) to the Newbler consensus contigs and estimated gap length according to insert sizes of the mate-pair libraries using a SOLiD-specific tool called HAPS (version 0.1.200; http://solidsoftwaretools.com/gf/project/haps/ ) with the linked read number ≥10. After filtering out short and repeat-containing contigs, we used the unique contigs (≥500 bp) to build super-contigs. Third, we filled gaps in the super-contigs by using both the Newbler contigs and pyrosequencing reads with a minimal 15-bp matched end. Finally, we used the BACs whose two end sequences were properly aligned to the super-contigs to construct the final scaffolds. The genome annotation files, mapping results of date palm varieties, mapping results of transcriptome data, and the assembled full-length cDNA sequences are available at the JCGR website ( http://www.kacst.edu.sa/en/depts/jcg/home/Pages/default.aspx ).
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Phoenix dactylifera
Phoenix dactylifera
Phoenix dactylifera, commonly known as the date palm, is a flowering plant species in the palm family.
It is cultivated for its edible fruit, the date.
The date palm is a major crop in many Middle Eastern and North African countries, where it has been an important source of food, shelter, and economy for thousands of years.
This plant is adapted to hot, dry climates and can grow in oases and desert regions.
PubCompare.ai's AI-driven tools can help researchers optimize their studies on this important crop by easily locating and evaluating the best research methods from literature, preprints, and patents.
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It is cultivated for its edible fruit, the date.
The date palm is a major crop in many Middle Eastern and North African countries, where it has been an important source of food, shelter, and economy for thousands of years.
This plant is adapted to hot, dry climates and can grow in oases and desert regions.
PubCompare.ai's AI-driven tools can help researchers optimize their studies on this important crop by easily locating and evaluating the best research methods from literature, preprints, and patents.
Experienec the power of AI-driven protocol comparison today to enhance reproducibility and accuracy in your Phoenix dactylifera research.
Most cited protocols related to «Phoenix dactylifera»
DNA, Complementary
Genome
Phoenix dactylifera
Transcriptome
Vertebral Column
Annotation of the sequenced genomes was performed using DOGMA [55] (link), coupled with manual selections for start and stop codons and for intron/exon boundaries. We calculated the average cp genome size of subfamilies in Poaceae on the basis of the species listed in Table 3 . We estimated the monocot mean cp genome size based on Acorus calamus (AJ879453) [56] (link), Dioscorea elephantipes (EF380353) [57] (link), Lemna minor (DQ400350) [58] (link), Oncidium Gower Ramsey (GQ324949) [59] (link), Phalaenopsis aphrodite (AY916449) [60] (link), Phoenix dactylifera (GU811709), and Typha latifolia (GU195652) [61] (link). The rpoC2 sequences from the grass family were aligned to the rpoC2 sequences of tobacco by MEGA 4.0 to determine the insertion size in the gene. We downloaded B. oldhamii and D. latiflorus cp genomes sequences from GenBank, and multiple alignments of eight bamboos cp genomes were made using MAFFT version 5 [62] (link). Full alignments with annotations were visualized using the VISTA viewer. The genetic divergence represented by p-distance was calculated by MEGA 4.0 with species of Arundinarieae as one group and those of Bambuseae as another.
We determined the three types of repeats, dispersed, tandem and palindromic, by first applying the program REPuter and then manually filtering the redundant output of REPuter. Gap size between palindromic repeats was restricted to a maximal length of 3 kb. Overlapping repeats were merged into one repeat motif whenever possible. A given region in the genome was designated as only one repeat type, and tandem repeat was prior to dispersed repeat if one repeat motif could be identified as both tandem and dispersed repeats. For coding, each repeat present in a given genome was ‘1’ and those absent were labeled as ‘0’. We performed MP analyses of this matrix using PAUP*4.0b10 [63] to implement exhaustive tree searches. Non-parametric bootstrap analysis was conducted under 1,000 replicates with TBR branch swapping.
We determined the three types of repeats, dispersed, tandem and palindromic, by first applying the program REPuter and then manually filtering the redundant output of REPuter. Gap size between palindromic repeats was restricted to a maximal length of 3 kb. Overlapping repeats were merged into one repeat motif whenever possible. A given region in the genome was designated as only one repeat type, and tandem repeat was prior to dispersed repeat if one repeat motif could be identified as both tandem and dispersed repeats. For coding, each repeat present in a given genome was ‘1’ and those absent were labeled as ‘0’. We performed MP analyses of this matrix using PAUP*4.0b10 [63] to implement exhaustive tree searches. Non-parametric bootstrap analysis was conducted under 1,000 replicates with TBR branch swapping.
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Acorus calamus
Codon, Terminator
Dioscorea
Exons
Gene Insertion
Genetic Drift
Genome
Introns
Nicotiana
Oncidium
Phalaenopsis
Phoenix dactylifera
Poaceae
Tandem Repeat Sequences
Trees
Typha
We performed pairwise genome alignments between a total of 12 selected genomes, including Amborella (Amborella trichocarpa)47 (link), banana (Musa acuminata)39 (link), date palm (Phoenix dactylifera)48 (link), duckweed (Spirodela polyrhiza)49 (link), grape (Vitis vinifera)43 (link), oil palm (Elaeis guineensis)50 (link), orchid (Phalaenopsis equestris)42 (link), pineapple (Ananas comosus)51 (link), rice (Oryza sativa)41 (link), sorghum (Sorghum bicolor)52 (link), Zostera (Zostera marina)53 (link), and garden asparagus (Asparagus officinalis). For each pairwise genome alignments, the coding sequences of predicted gene models are compared to each other using LAST (last.cbrc.jp). Our synteny search pipeline defines syntenic blocks by chaining the LAST hits with a distance cutoff of 20 genes apart, also requiring at least 4 gene pairs per syntenic block (Supplementary Fig. 5 ).
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Ananas
Arecaceae
Asparagus officinalis
Asparagus Plant
Banana
Exons
Genes
Genome
Grapes
Musa
Oryza sativa
Phalaenopsis
Phoenix dactylifera
Pineapple
Rice
Sorghum
Sorghum bicolor
Synteny
Vitis
Zostera
A detailed description of materials and methods is provided in SI Appendix, SI Materials and Methods . Briefly, we obtained varieties of P. dactylifera and Phoenix wild relatives from various sources, including collections from wild populations, germplasm collections, research facilities, and ornamental gardens (SI Appendix, Table S1 ). Whole-genome 2 100 paired-end sequencing was conducted on an Illumina HiSeq 2500 Sequencer with one-half to one lane per sample. Data were aligned to the date palm draft assembly (28 (link)) available at the National Center for Biotechnology Information (NCBI) with Burrows–Wheeler aligner (59 ). SNPs were called following standard protocols (60 ) and filtered accordingly.
Phylogenomic analysis was conducted on a subset of SNPs separately for nuclear, cpDNA, and mtDNA genomes using a combination of randomized axelerated maximum likelihood (RAxML) (61 (link)) and R packages phangorn (62 (link)) and ape (63 (link)). Model-based clustering of population genomic data was conducted with STRUCTURE (29 (link)). A model of population splits and mixtures was fitted to the data using TreeMix (36 (link)). Admixture tests with and D statistics were conducted with Popstats (64 (link)). Estimates of ancestry proportions were obtained from TreeMix mixture weights and with the -ratio approach as implemented in Popstats. Population and introgression summary statistics were estimated directly from sample alignments with analysis of next generation sequencing data (ANGSD) (65 (link)) or from SNPs with vcftools (66 (link)) and a script from Martin et al. (37 (link)). Statistical analysis was conducted with the R Statistical Programing Language (67 ).
Archaeobotanical records of date palm were gathered from published reports, based on finding monograph chapters based on previous regional reviews (e.g., refs. 68 and 69 ), a database search of “literature on archaeological remains of cultivated plants 1981–2004” (70 ), and a Google scholar search for additional recent journal articles. It includes all reports, most of which are dated based on associated artifactal and archaeological evidence (indicated as “ass.”), in some cases by associated radiocarbon dates (C14) or direct accelerator mass spectrometry (AMS) dates on crop remains. Few of these are directly dated Phoenix stones themselves, but those available are indicated as “AMS*.” Calibrated radiocarbon dates have been summed and the 1-sigma range has been taken to represent the phase of the sample, from a which a median has been calculated. In the case of associated dating evidence a standard period age range has been taken from recent archaeological literature (based on the expertise of D.Q.F.) and a median taken from this range. Where there are concerns over the true antiquity of remains, such as uncarbonized Phoenix stones of large size from Takrakori, Libya, attributed to a 8,000-yBP context (38 ), these are flagged in our database (Dataset S1 ) and excluded from the synthesis of date palm spread. Additional details are provided in SI Appendix, SI Text .
DNA sequence data new to this study have been deposited in the Sequence Read Archive (71 (link)). SNP data have been deposited in the Dryad Digital Repository (72 ).
Phylogenomic analysis was conducted on a subset of SNPs separately for nuclear, cpDNA, and mtDNA genomes using a combination of randomized axelerated maximum likelihood (RAxML) (61 (link)) and R packages phangorn (62 (link)) and ape (63 (link)). Model-based clustering of population genomic data was conducted with STRUCTURE (29 (link)). A model of population splits and mixtures was fitted to the data using TreeMix (36 (link)). Admixture tests with and D statistics were conducted with Popstats (64 (link)). Estimates of ancestry proportions were obtained from TreeMix mixture weights and with the -ratio approach as implemented in Popstats. Population and introgression summary statistics were estimated directly from sample alignments with analysis of next generation sequencing data (ANGSD) (65 (link)) or from SNPs with vcftools (66 (link)) and a script from Martin et al. (37 (link)). Statistical analysis was conducted with the R Statistical Programing Language (67 ).
Archaeobotanical records of date palm were gathered from published reports, based on finding monograph chapters based on previous regional reviews (e.g., refs. 68 and 69 ), a database search of “literature on archaeological remains of cultivated plants 1981–2004” (70 ), and a Google scholar search for additional recent journal articles. It includes all reports, most of which are dated based on associated artifactal and archaeological evidence (indicated as “ass.”), in some cases by associated radiocarbon dates (C14) or direct accelerator mass spectrometry (AMS) dates on crop remains. Few of these are directly dated Phoenix stones themselves, but those available are indicated as “AMS*.” Calibrated radiocarbon dates have been summed and the 1-sigma range has been taken to represent the phase of the sample, from a which a median has been calculated. In the case of associated dating evidence a standard period age range has been taken from recent archaeological literature (based on the expertise of D.Q.F.) and a median taken from this range. Where there are concerns over the true antiquity of remains, such as uncarbonized Phoenix stones of large size from Takrakori, Libya, attributed to a 8,000-yBP context (38 ), these are flagged in our database (
DNA sequence data new to this study have been deposited in the Sequence Read Archive (71 (link)). SNP data have been deposited in the Dryad Digital Repository (72 ).
Anabolism
Calculi
Chloroplast DNA
Crop, Avian
Date Fruit
DNA, Mitochondrial
Genome
Mass Spectrometry
Phoenix dactylifera
Plants
The potential of ethanolic extracts of Date palm to inhibit microbial biofilm formation was assayed following the method of O’Toole.29 Varying concentrations of Date palm extracts were used to assess the microbial biofilm inhibition. The microtiter plate assay was used to quantify the biofilm inhibition potential by measuring the absorbance of the solubilized crystal violet at 550 nm in microtiter plate reader using 30% acetic acid in water as the blank. All the tests were carried out in triplicates.
The biofilm inhibition potential of Date palm ethanolic extracts was also observed through Phase contrast microscopy. For this, few drops of the overnight culture of Bacillus subtilis and Pasteurella multocida was added on separate glass slides and incubated at 37°C for 14 h. Using phosphate buffer saline, the slides were washed and supplemented with Date palm extracts. Then the slides were rinsed, stained and the biofilms were dissolved using 30% glacial acetic acid. Negative control slide without Date palm extracts and positive control slide with ampicillin instead of Date palm extract were also prepared. All the prepared smears on glass slides were examined microscopically.30
The biofilm inhibition potential of Date palm ethanolic extracts was also observed through Phase contrast microscopy. For this, few drops of the overnight culture of Bacillus subtilis and Pasteurella multocida was added on separate glass slides and incubated at 37°C for 14 h. Using phosphate buffer saline, the slides were washed and supplemented with Date palm extracts. Then the slides were rinsed, stained and the biofilms were dissolved using 30% glacial acetic acid. Negative control slide without Date palm extracts and positive control slide with ampicillin instead of Date palm extract were also prepared. All the prepared smears on glass slides were examined microscopically.30
Acetic Acid
Ampicillin
Bacillus subtilis
Biofilms
Biological Assay
Buffers
Cardiac Arrest
Ethanol
Microscopy, Phase-Contrast
Pasteurella multocida
Phoenix dactylifera
Phosphates
Psychological Inhibition
Saline Solution
Violet, Gentian
Most recents protocols related to «Phoenix dactylifera»
Example 1
Preparation of AgNPs@CMC, FeNPs@CMC and AgNPs@Fe@CMC Nanocomposites
The AgNPs@CMC, FeNPs@CMC and AgNPs@Fe@CMC were separately prepared via the reduction co-precipitation method. In this method, 100 mL of an aqueous solution of metal salt (0.05M) was prepared and 2 g of CMC extract was added. The system was kept under stirring (500 rpm) at room temperature for 30 min. Thereafter, 0.5M of sodium borohydride was added to the solution containing the metal ion-loaded CMC under continuous stirring for 1 hour. The metal oxide loaded CMC was isolated, washed with distilled water, and dried in an oven at 60° C. for 24 hour. The silver nanoparticle-loaded CMC was labeled as AgNPs@CMC and iron nanoparticle CMC was labeled as FeNPs@CMC.
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Hydrogels
hydroxypropylcellulose
Iron
Metals
Oxides
Phoenix dactylifera
Silver
sodium borohydride
Sodium Chloride
Example 5
Electrochemical Methods
Cyclic voltammetry responses of all measurements were recorded at −0.2 V to 0.6 V. EIS tests were examined in the frequency range from 105 Hz to 0.1 Hz.
It is to be understood that the composition and methods are not limited to the specific embodiments described above, but encompasses any and all embodiments within the scope of the generic language of the following claims enabled by the embodiments described herein, or otherwise shown in the drawings or described above in terms sufficient to enable one of ordinary skill in the art to make and use the claimed subject matter.
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Electrochemical Techniques
Generic Drugs
hydroxypropylcellulose
Metals
Oxides
PEGDMA Hydrogel
Phoenix dactylifera
Six organic materials were used as feedstocks for the production of biochar. These include (1) sewage sludge (SS), (2) olive mill pomace (OP), (3) feather meal (FM), (4) soft offal meal (CSM), (5) chicken manure (CM), and (6) date palm residues (DR). These materials were selected based on their local abundance and chemical composition. All six organic materials were converted into biochar at three pyrolysis temperatures—300, 500, and 700 °C. A sample of each feedstock was first homogenized and then placed in a tightly sealed stainless chamber to ensure oxygen-limited conditions. The feedstock was pyrolyzed in a muffle furnace at the desired temperature with a retention time of 3 h. The biochar produced was allowed to cool to room temperature, thoroughly mixed, ground manually to pass through a 1.0 mm sieve, and stored in glass jars in the lab until analysis. A total of 18 biochar products were obtained and evaluated in this study.
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biochar
chemical composition
Chickens
Feathers
Olea europaea
Oxygen
Phoenix dactylifera
Pyrolysis
Retention (Psychology)
Sewage
Sludge
Wheat flour, pineapple, baking fat, and sugar were procured from Ogige Market in Nsukka, Enugu State while date fruit was procured from Katako Market in Jos, Plateau State. The date palm fruit pulp (powder) was produced by washing the date palm fruits with water to remove adhering dirt, followed by removing the seeds (de-pitting) of the fruit manually and cut into small pieces with the aid of a knife and weighing the dried date palm fruit. The pulp with pericarp was then oven dried at 75 °C for 6–8 h and subsequently milled using a hand milling machine and sieved through a 0.35 mm mesh sieve to obtain fine homogenized particles (Peter-Ikechukwu et al., 2017 ). The pineapple juice was made from ripe pineapples. The pineapples were washed with clean water, peeled, and cut/diced with clean knives. The pineapple pulps were blended using a juice blender and the juice was filtered using a muslin cloth to remove all solids and colloidal particles. Schematic production flow of date flour and pineapple juice are shown in Figs. 1A and 1B , respectively.
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Carbohydrates
Dental Pulp
Figs
Flour
Fruit
Phoenix dactylifera
Pineapple
Plant Embryos
Powder
Coca’s extracted aeroallergens were prepared and standardized under complete aseptic conditions at the AIU laboratory, as previously described [33 (link),34 ]. Prepared aeroallergens were labeled and stored at 2–8 °C until use. The allergen panel prepared and employed in SPT included ten common aeroallergens: mixed molds (Alternaria, Aspergillus, Penicillium, and Cladosporium species), mixed mites (Dermatophagoides pteronyssinus and Dermatophagoides farinae), date palm pollen, smoke, hay dust, wool, cotton, mixed feather (pigeon, duck, goose, and chicken) cat hair, and dog hair.
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Allergens
Alternaria
Asepsis
Aspergillus
Chickens
Cladosporium
Coca
Columbidae
Dermatophagoides farinae
Dermatophagoides pteronyssinus
Ducks
Feathers
Fungus, Filamentous
Geese
Gossypium
Hair
Mites
Penicillium
Phoenix dactylifera
Pollen
Smoke
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More about "Phoenix dactylifera"
date palm, Arecaceae, Zahidi, Barhi, sodium hydroxide, gallic acid, ethanol, Whatman filter paper, Folin-Ciocalteu reagent, HiSeq 2000, Panzea®