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Sökning: WFRF:(El Kassaby Yousry A.)

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1.
  • Cheng, Shi-Ping, et al. (författare)
  • Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
  • 2021
  • Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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2.
  • Funda, Tomas, et al. (författare)
  • Determination of paternal and maternal parentage in lodgepole pine seed : full versus partial pedigree reconstruction
  • 2014
  • Ingår i: Canadian Journal of Forest Research. - : Canadian science publishing. - 0045-5067 .- 1208-6037. ; 44:9, s. 1122-1127
  • Tidskriftsartikel (refereegranskat)abstract
    • Estimating seed orchards' maternal and paternal gametic contributions is of importance in assessing the genetic quality of seed crops. The advantage of full over partial pedigree reconstruction in investigating the mating dynamics in a lodgepole pine (Pinus contorta Dougl. ex. Loud. ssp. latifolia Engelm.) seed orchard population (N = 74) was demonstrated using nuclear and chloroplast microsatellite markers. We analyzed offspring of equivalent sample sizes representing full (bulk seed with unknown maternal and paternal parentage (n = 635)) and partial (11 maternal family arrays (n = 619)) pedigree reconstruction methods. Small differences in selfing rate, gene flow, and male reproductive success were observed between the two methods; however, the full pedigree reconstruction enabled simultaneous estimation of female-related fertility parameters (female reproductive success and effective number of maternal parents) that partial pedigree reconstruction could not provide. The use of bulk random sample of seed from orchards' crops is recommended when male and female fertility parameters, as well as selfing and contamination rates, are needed for seed orchards' seed crops genetic rating.
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3.
  • Hu, Xian-Ge, et al. (författare)
  • De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis
  • 2016
  • Ingår i: PLOS ONE. - 1932-6203. ; 11:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.
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4.
  • Hu, Xian-Ge, et al. (författare)
  • Global transcriptome analysis of Sabina chinensis (Cupressaceae), a valuable reforestation conifer
  • 2016
  • Ingår i: Molecular breeding. - 1380-3743 .- 1572-9788. ; 36:7
  • Tidskriftsartikel (refereegranskat)abstract
    • Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species' unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (similar to 9.0 bp) were obtained, and 116,814 unigenes (>= 200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.
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5.
  • Ismail, Mohamed, et al. (författare)
  • Comparative Nucleotide Diversity Across North American and European Populus Species
  • 2012
  • Ingår i: Journal of Molecular Evolution. - 0022-2844 .- 1432-1432. ; 74:5-6, s. 257-272
  • Tidskriftsartikel (refereegranskat)abstract
    • Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for P. tremula (theta (w) = 0.005, pi (T) = 0.007) as compared to P. balsamifera (theta (w) = 0.004, pi (T) = 0.005) or P. trichocarpa (theta (w) = 0.002, pi (T) = 0.003). Across species, the defense and the stress response loci accounted for the majority of the observed level of nucleotide diversity. In general, the studied loci did not deviate from neutral expectation either at the individual locus (non-significant normalized Fay and Wu's H) or at the multi-locus level (non-significant HKA test). Using molecular clock analysis, section Tacamahaca probably shared a common ancestor with section Populus approximately 4.5 million year ago. Divergence between the two closely related balsam poplars was about 0.8 million years ago, a pattern consistent with an isolation-with-migration (IM) model. As expected, P. tremula showed a five-fold higher substitution rate (2 x 10(-8) substitution/site/year) compared to the North American species (0.4 x 10(-8) substitution/site/year), probably reflecting its complex demographic history. Linkage disequilibrium (LD) varied among species with a more rapid decay in the North American species (< 400 bp) in comparison to P. tremula (a parts per thousand << 400 bp). The similarities in nucleotide diversity pattern and LD decay of the two balsam poplar species likely reflects the recent time of their divergence.
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6.
  • Jia, Kai-Hua, et al. (författare)
  • Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
  • 2021
  • Ingår i: Horticulture Research. - 2052-7276. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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7.
  • Jia, Kai-Hua, et al. (författare)
  • Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae)
  • 2020
  • Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571 .- 1752-4571. ; 13:4, s. 665-676
  • Tidskriftsartikel (refereegranskat)abstract
    • Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.
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8.
  • Jin, Yuqing, et al. (författare)
  • Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae)
  • 2019
  • Ingår i: G3. - : The Genetics Society of America. - 2160-1836 .- 2160-1836. ; 9:11, s. 3663-3672
  • Tidskriftsartikel (refereegranskat)abstract
    • Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species' genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species' 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.
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9.
  • Porth, Ilga, et al. (författare)
  • Evolutionary Quantitative Genomics of Populus trichocarpa
  • 2015
  • Ingår i: PLOS ONE. - 1932-6203. ; 10:11
  • Tidskriftsartikel (refereegranskat)abstract
    • Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing Q(ST)-F-ST) using clustering of individuals by climate of origin (temperature and precipitation). 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages) across the P. trichocarpa sampling range as population groupings. Narrow-sense QST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant QST). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show relationship to climate of origin. We consider our approach the most comprehensive, as it uncovers the molecular mechanisms of adaptation using multiple methods and tests. We also provide a detailed outline of the required analyses for studying adaptation to the environment in a population genomics context to better understand the species' potential adaptive capacity to future climatic scenarios.
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