3,099 results match your criteria duplication event

Novel antimicrobial anionic cecropins from the spruce budworm feature a poly-L-aspartic acid C-terminus.

Proteins 2021 May 11. Epub 2021 May 11.

Institut de biologie intégrative et des systèmes (IBIS) and Faculté de médecine, Université Laval, Quebec City, Canada.

Cecropins form a family of amphipathic α-helical cationic peptides with broad-spectrum antibacterial properties and potent anticancer activity. The emergence of bacteria and cancer cells showing resistance to cationic antimicrobial peptides (CAMPs) has fostered a search for new, more selective and more effective alternatives to CAMPs. With this goal in mind, we looked for cecropin homologs in the genome and transcriptome of the spruce budworm, Choristoneura fumiferana. Read More

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Pests, diseases, and aridity have shaped the genome of Corymbia citriodora.

Commun Biol 2021 May 10;4(1):537. Epub 2021 May 10.

University of Queensland/QAAFI, Brisbane, QLD, Australia.

Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes. Read More

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Mutations Are Independent Poor Prognostic Factors in Pediatric Acute Myeloid Leukemia.

Front Oncol 2021 21;11:632094. Epub 2021 Apr 21.

Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.

The prognostic impact of () mutations remains controversial for patients with acute myeloid leukemia (AML). Here, we aimed to determine the clinical implication of mutations in a large cohort of pediatric AML. The clinical data of 870 pediatric patients with AML were downloaded from the therapeutically applicable research to generate effective treatment (TARGET) dataset. Read More

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Analysis of recently duplicated TYRP1 genes and their effect on the formation of black patches in Oujiang-color common carp (Cyprinus carpio var. color).

Anim Genet 2021 May 3. Epub 2021 May 3.

Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.

Tyrp1 gene, as a member of the tyrosinase family, has undergone a recent duplication event during fourth-round whole genome duplication in common carp. In this research, three Tyrp1 genes were identified in Oujiang-color common carp (Cyprinus carpio var. color). Read More

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Sequence Read Depth Analysis of a Monophyletic Cluster of Y Chromosomes Characterized by Structural Rearrangements in the AZFc Region Resulting in DYS448 Deletion and DYF387S1 Duplication.

Front Genet 2021 16;12:669405. Epub 2021 Apr 16.

Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.

The azoospermia factor c region (AZFc), located in the long arm of the human Y chromosome, is frequently involved in chromosome rearrangements, mainly due to non-allelic homologous recombination events that occur between the nearly identical sequences (amplicon) that comprises it. These rearrangements may have major phenotypic effects like spermatogenic failure or other pathologies linked to male infertility. Moreover, they may also be relevant in forensic genetics, since some of the Y chromosome short tandem repeats (Y-STRs) commonly used in forensic analysis are located in amplicons or in inter-amplicon sequences of the AZFc. Read More

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Chromosome-scale assembly of the Kandelia obovata genome.

Hortic Res 2020 May 2;7(1):75. Epub 2020 May 2.

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. Read More

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Comprehensive analysis of structural, functional, and evolutionary dynamics of Leucine Rich Repeats-RLKs in Thinopyrum elongatum.

Int J Biol Macromol 2021 Apr 30;183:513-527. Epub 2021 Apr 30.

Mid-Florida Research and Education Center, University of Florida, Apopka, FL 32703, United States. Electronic address:

Leucine Rich Repeats-receptor-like protein kinases (LRR-RLKs) regulate several critical biological processes ranging from growth and development to stress response. Thinopyrum elongatum harbours many desirable traits such as biotic and abiotic stress resistance and therefore commonly used by wheat breeders. In the present investigation, in-silico analysis of LRR-RLKs yielded 589 genes of which 431 were membrane surface RLKs and 158 were receptor like cytoplasmic kinases. Read More

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The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant.

Hortic Res 2020 May 1;7(1):63. Epub 2020 May 1.

Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008, China.

Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits. Although two draft genomes of tea plant (Camellia sinensis) have been published recently, the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement. Here, we performed a genome-wide chromosome conformation capture technique (Hi-C) to obtain a chromosome-scale assembly based on the draft genome of C. Read More

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In silico analysis of Naegleria fowleri cathepsin B paralogs: important drug targets.

Eur Rev Med Pharmacol Sci 2021 Apr;25(8):3162-3172

Jamil ur Rehman Center for Genome Research, Dr. Punjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.

Naegleria fowleri is a deadly human pathogen that causes primary amoebic meningoencephalitis (PAM). In this study, in silico investigations of two important N. fowleri cathepsin B paralogs, i. Read More

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The evolution of opsin genes in five species of mirid bugs: duplication of long-wavelength opsins and loss of blue-sensitive opsins.

BMC Ecol Evol 2021 Apr 26;21(1):66. Epub 2021 Apr 26.

State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (IPP-CAAS), Beijing, 100193, People's Republic of China.

Background: Color vision and phototactic behavior based on opsins are important for the fitness of insects because of their roles in foraging and mate choice. Related topics, including the duplication and loss of opsin genes, have been well investigated in insect orders such as Coleoptera, Lepidoptera, Hymenoptera, Odonata and Orthoptera, and the findings have been used to develop pest management strategies involving light trapping. Mirid bugs of Hemiptera, which are pests that cause heavy economic losses, show capacity for color discrimination and phototaxis. Read More

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Interrogating the 5'UTR tandem repeats of retrotransposon roo of Drosophila about horizontal transfer.

Ana Domínguez

Genetica 2021 Apr 26. Epub 2021 Apr 26.

Departamento de Biología Funcional, Área de Genética, Universidad de Oviedo, 33071, Oviedo, Spain.

Horizontal transfer in Drosophila has been inferred for several families of transposable elements. Specifically, the retroelement roo has been suggested to have been horizontally transferred between the species D. melanogaster, D. Read More

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A genomic amplification affecting a carboxylesterase gene cluster confers organophosphate resistance in the mosquito : From genomic characterization to high-throughput field detection.

Evol Appl 2021 Apr 16;14(4):1009-1022. Epub 2021 Feb 16.

Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS - Université Grenoble-Alpes Grenoble France.

By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterize a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito and to develop a molecular assay to monitor the associated resistance alleles in the field. Read More

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Genetic rearrangement during site specific integration event facilitates cell line development of a bispecific molecule.

Biotechnol Prog 2021 Apr 23:e3158. Epub 2021 Apr 23.

Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA.

Site specific integration (SSI) expression systems offer robust means of generating highly productive and stable cell lines for traditional monoclonal antibodies. As complex modalities such as antibody-like molecules comprised of greater than two peptides become more prevalent, greater emphasis needs to be placed on the ability to produce appreciable quantities of the correct product of interest (POI). The ability to screen several transcript stoichiometries could play a large role in ensuring high amounts of the correct POI. Read More

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Chromosomal-scale genome assembly of Eleutherococcus senticosus provides insights into chromosome evolution in Araliaceae.

Mol Ecol Resour 2021 Apr 23. Epub 2021 Apr 23.

State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.

Siberian ginseng (Eleutherococcus senticosus, also known as ciwujia) belongs to the Araliaceae family, which contains more than 1,500 species in 41 genera with diverse chromosome numbers and genome sizes. General consensus posits that ancient whole-genome duplication events and rapid evolutionary radiation are the driving forces for this variation in genome properties. In an attempt to generate more genomic information for the Araliaceae family, we report here a 1. Read More

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CD200R1L is a functional evolutionary conserved activating receptor in human neutrophils.

J Leukoc Biol 2021 Apr 22. Epub 2021 Apr 22.

Center for Translational Immunology, Dept. Immunology, University Medical Center Utrecht, Utrecht University, Oncode Institute, Utrecht, The Netherlands.

Inhibitory and activating immune receptors play a key role in modulating the amplitude and duration of immune responses during infection and in maintaining immune balance in homeostatic conditions. The CD200 Receptor (CD200R) gene family in humans encodes one inhibitory receptor, CD200R1, and one putative activating member, CD200R1 Like (CD200R1L). It is demonstrated that CD200R1L is endogenously expressed by human neutrophils and activates cellular functions such as reactive oxygen species (ROS) production via Syk, PI3Kβ, PI3Kδ, and Rac GTPase signaling. Read More

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Genome-wide analysis of SET-domain group histone methyltransferases in apple reveals their role in development and stress responses.

BMC Genomics 2021 Apr 19;22(1):283. Epub 2021 Apr 19.

State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: Histone lysine methylation plays an important role in plant development and stress responses by activating or repressing gene expression. Histone lysine methylation is catalyzed by a class of SET-domain group proteins (SDGs). Although an increasing number of studies have shown that SDGs play important regulatory roles in development and stress responses, the functions of SDGs in apple remain unclear. Read More

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Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication.

G3 (Bethesda) 2021 Apr 19. Epub 2021 Apr 19.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.

Baker's yeast contains a large number of duplicated genes; some function redundantly, whereas others have more specialized roles. We used the MLH family of DNA mismatch repair proteins as a model to better understand the steps that lead to gene specialization following a gene duplication event. We focused on two highly conserved yeast MLH proteins, Pms1 and Mlh3, with Pms1 having a major role in the repair of misincorporation events during DNA replication and Mlh3 acting to resolve recombination intermediates in meiosis to form crossovers. Read More

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Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA.

PLoS One 2021 15;16(4):e0249735. Epub 2021 Apr 15.

Department of Biology, Tokyo Gakugei University, Tokyo, Japan.

Multidomain proteins can have a complex evolutionary history that may involve de novo domain evolution, recruitment and / or recombination of existing domains and domain losses. Here, the domain evolution of the plant-specific Ca2+-permeable mechanosensitive channel protein, MID1-COMPLEMENTING ACTIVITY (MCA), was investigated. MCA, a multidomain protein, possesses a Ca2+-influx-MCAfunc domain and a PLAC8 domain. Read More

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The dystrophia myotonica WD repeat-containing protein DMWD and WDR20 differentially regulate USP12 deubiquitinase.

FEBS J 2021 Apr 12. Epub 2021 Apr 12.

Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.

Despite its potential clinical relevance, the product of the DMWD (dystrophia myotonica, WD repeat containing) gene is a largely uncharacterized protein. The DMWD amino acid sequence is similar to that of WDR20, a known regulator of the USP12 and USP46 deubiquitinases (DUBs). Here, we apply a combination of in silico and experimental methods to investigate several aspects of DMWD biology. Read More

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Technical note: multi-alleles at the DYS385ab locus with high frequency in a Han Chinese population from southwestern China.

Int J Legal Med 2021 Apr 12. Epub 2021 Apr 12.

Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.

Y-chromosome short tandem repeat (Y-STR) markers have been widely used in forensic applications and usually show monoallelic or diallelic genotypic patterns at certain double-copied loci. In this study, we have found 13 samples among 703 males with multi-alleles at the DYS385ab locus, including one with five mutant alleles, nine with four, and three with three. The frequency of abnormal DYS385ab genotypes was 1. Read More

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The chromosome-level Hemerocallis citrina Borani genome provides new insights into the rutin biosynthesis and the lack of colchicine.

Hortic Res 2021 Apr 7;8(1):89. Epub 2021 Apr 7.

Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, 410128, China.

Hemerocallis citrina Borani (huang hua cai in Chinese) is an important horticultural crop whose flower buds are widely consumed as a delicious vegetable in Asia. Here we assembled a high-quality reference genome of H. citrina using single-molecule sequencing and Hi-C technologies. Read More

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Data silos are undermining drug development and failing rare disease patients.

Orphanet J Rare Dis 2021 Apr 7;16(1):161. Epub 2021 Apr 7.

Department of Medicine, Orphan Disease Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Data silos are proliferating while research and development activity explode following genetic and immunological advances for many clinically described disorders with previously unknown etiologies. The latter event has inspired optimism in the patient, clinical, and research communities that disease-specific treatments are on the way. However, we fear the tendency of various stakeholders to balkanize databases in proprietary formats, driven by current economic and academic incentives, will inevitably fragment the expanding knowledge base and undermine current and future research efforts to develop much-needed treatments. Read More

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Ten years of collaborative progress in the Quest for Orthologs.

Mol Biol Evol 2021 Apr 2. Epub 2021 Apr 2.

Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan.

Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology - evolutionary relatedness - is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Read More

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The evolutionary fate of rpl32 and rps16 losses in the Euphorbia schimperi (Euphorbiaceae) plastome.

Sci Rep 2021 Apr 2;11(1):7466. Epub 2021 Apr 2.

Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.

Gene transfers from mitochondria and plastids to the nucleus are an important process in the evolution of the eukaryotic cell. Plastid (pt) gene losses have been documented in multiple angiosperm lineages and are often associated with functional transfers to the nucleus or substitutions by duplicated nuclear genes targeted to both the plastid and mitochondrion. The plastid genome sequence of Euphorbia schimperi was assembled and three major genomic changes were detected, the complete loss of rpl32 and pseudogenization of rps16 and infA. Read More

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Whole-Genome Sequencing in Diagnostics of Selected Slovenian Undiagnosed Patients with Rare Disorders.

Life (Basel) 2021 Mar 5;11(3). Epub 2021 Mar 5.

Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia.

Several patients with rare genetic disorders remain undiagnosed following comprehensive diagnostic testing using whole-exome sequencing (WES). In these patients, pathogenic genetic variants may reside in intronic or regulatory regions or they may emerge through mutational mechanisms not detected by WES. For this reason, we implemented whole-genome sequencing (WGS) in routine clinical diagnostics of patients with undiagnosed genetic disorders and report on the outcome in 30 patients. Read More

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Genome-Wide Analysis of Tubulin Gene Family in Cassava and Expression of Family Member during Various Stress.

Plants (Basel) 2021 Mar 31;10(4). Epub 2021 Mar 31.

Department of Biosciences, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China.

Filamentous temperature-sensitive protein Z (Tubulin/FtsZ) family is a group of conserved GTP-binding (guanine nucleotide-binding) proteins, which are closely related to plant tissue development and organ formation as the major component of the cytoskeleton. According to the published genome sequence information of cassava (), 23 genes () were identified, which were divided into four main groups based on their type and phylogenetic characteristics. The same grouping generally has the same or similar motif composition and exon-intron structure. Read More

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Impact of the Whole Genome Duplication Event on PYK Activity and Effects of a PYK1 Mutation on Metabolism in .

Front Mol Biosci 2021 16;8:656461. Epub 2021 Mar 16.

Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States.

Evolution of aerobic fermentation (crabtree effect) in yeast is associated with the whole genome duplication (WGD) event, suggesting that duplication of certain genes may have altered yeast metabolism. The pyruvate kinase (PYK) gene is associated with alterations in cell metabolism, and duplicated during the WGD, generating PYK1 and PYK2. Thus, the impact of WGD on PYK activity and role of PYK in yeast metabolism were explored. Read More

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Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily.

Plant Physiol 2021 Apr;185(3):857-875

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.

The emergence of type III polyketide synthases (PKSs) was a prerequisite for the conquest of land by the green lineage. Within the PKS superfamily, chalcone synthases (CHSs) provide the entry point reaction to the flavonoid pathway, while LESS ADHESIVE POLLEN 5 and 6 (LAP5/6) provide constituents of the outer exine pollen wall. To study the deep evolutionary history of this key family, we conducted phylogenomic synteny network and phylogenetic analyses of whole-genome data from 126 species spanning the green lineage including Arabidopsis thaliana, tomato (Solanum lycopersicum), and maize (Zea mays). Read More

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A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae).

Hortic Res 2020 Apr 1;7(1):46. Epub 2020 Apr 1.

Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, China.

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. Read More

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Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins.

Sci Adv 2021 Mar 31;7(14). Epub 2021 Mar 31.

Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain.

Of five known adenovirus genera, high-resolution structures are available only for mammalian-infecting mastadenoviruses. We present the first high-resolution structure of an adenovirus with nonmammalian host: lizard atadenovirus LAdV-2. We find a large conformational difference in the internal vertex protein IIIa between mast- and atadenoviruses, induced by the presence of an extended polypeptide. Read More

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