24,412 results match your criteria duplication genomic

Paroxysmal Kinesigenic Dyskinesia in Twins With Chromosome 16p11.2 Duplication Syndrome.

Neurol Genet 2021 Feb 11;7(1):e549. Epub 2021 Jan 11.

Department of Neurology (K.U., T.S.P.), and Division Genetics and Genomic Medicine (M.S.), Department of Pediatrics, Washington University School of Medicine, St. Louis, MO.

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February 2021

Bioinformatics and Expression Analysis of IDA-Like Genes Reveal Their Potential Functions in Flower Abscission and Stress Response in Tobacco ( L.).

Front Genet 2021 27;12:670794. Epub 2021 Apr 27.

Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.

The inflorescence deficient in abscission-like () genes have been shown to play critical roles in floral organ abscission, lateral root formation and various stress responses in . The gene family has been characterized in a number of plant species, while limited information is available about genes of tobacco. In the current study, 15 NtIDL members were identified in the tobacco genome, and were classified into six groups together with IDL members from other species. Read More

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A Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon.

Front Genet 2021 27;12:656334. Epub 2021 Apr 27.

Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway.

Atlantic salmon () is a major species produced in world aquaculture and an important vertebrate model organism for studying the process of rediploidization following whole genome duplication events (Ss4R, 80 mya). The current transcriptome is largely generated from genome sequence based predictions supported by ESTs and short-read sequencing data. However, recent progress in long-read sequencing technologies now allows for full-length transcript sequencing from single RNA-molecules. Read More

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Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe.

Proc Natl Acad Sci U S A 2021 May;118(20)

Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;

Whole-genome duplication (WGD) plays important roles in plant evolution and function, yet little is known about how WGD underlies metabolic diversification of natural products that bear significant medicinal properties, especially in nonmodel trees. Here, we reveal how WGD laid the foundation for co-option and differentiation of medicinally important ursane triterpene pathway duplicates, generating distinct chemotypes between species and between developmental stages in the apple tribe. After generating chromosome-level assemblies of a widely cultivated loquat variety and we define differentially evolved, duplicated gene pathways and date the WGD in the apple tribe at 13. Read More

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De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits.

BMC Genomics 2021 May 13;22(1):347. Epub 2021 May 13.

Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Background: Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar to snowdrop (Galanthus nivalis) agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. Read More

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Identification of microduplications at Xp21.2 and Xq13.1 in neurodevelopmental disorders.

Mol Genet Genomic Med 2021 May 12:e1703. Epub 2021 May 12.

Center for Statistical Genetics, Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York, NY, USA.

Background: Microduplications are a rare cause of disease in X-linked neurodevelopmental disorders but likely have been under reported due challenges in detection and interpretation.

Methods: We performed exome sequencing and subsequent microarray analysis in two families with a neurodevelopmental disorder.

Results: Here, we report on two families each with unique inherited microduplications at Xp21. Read More

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Epimutation of MMACHC compound to a genetic mutation in cblC cases.

Mol Genet Genomic Med 2021 May 12:e1625. Epub 2021 May 12.

Department of Pediatric Endocrinology and Genetic Metabolism, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.

Background: Methylmalonic aciduria (MMA) combined with homocystinuria, cobalamin(cbl)C deficiency type (OMIM 277400), is the most common autosomal recessive inherited disorder of intracellular cobalamin metabolism caused by mutations in the MMACHC gene (OMIM 609831), of which more than 100 mutations have been identified to date. In this study, we only identified a coding mutation in one allele at the MMACHC gene locus, and no large fragments deletion or duplication were found. Up to now, only three epimutation cblC cases were reported. Read More

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Striatal dopaminergic alterations in individuals with copy number variants at the 22q11.2 genetic locus and their implications for psychosis risk: a [18F]-DOPA PET study.

Mol Psychiatry 2021 May 12. Epub 2021 May 12.

Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College, London, UK.

Dopaminergic dysregulation is one of the leading hypotheses for the pathoetiology underlying psychotic disorders such as schizophrenia. Molecular imaging studies have shown increased striatal dopamine synthesis capacity (DSC) in schizophrenia and people in the prodrome of psychosis. However, it is unclear if genetic risk for psychosis is associated with altered DSC. Read More

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Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes.

Clin Epigenetics 2021 May 12;13(1):107. Epub 2021 May 12.

Department of Research, Cancer Registry of Norway, Oslo, Norway.

Background: Long-term stored serum is considered challenging for epigenomic analyses: as there are no cells, circulating DNA is scarce, and amplification removes epigenetic signals. Additionally, pre-analytical treatments and storage might introduce biases and fragmentation to the DNA. In particular, starting with low-input DNA can result in low-diversity libraries. Read More

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Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae).

Syst Biol 2021 May 12. Epub 2021 May 12.

Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA.

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. Read More

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Highly variable chloroplast genome from two endangered Papaveraceae lithophytes and .

Ecol Evol 2021 May 19;11(9):4158-4171. Epub 2021 Mar 19.

Institute of Medicinal Plant Development Chinese Academy of Medical Sciences & Peking Union Medical College Key Lab of Chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of the People's Republic of China Beijing China.

The increasingly wide application of chloroplast (cp) genome super-barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus . Read More

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Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus.

Sci Rep 2021 May 11;11(1):9987. Epub 2021 May 11.

National Center for Biotechnology,, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia.

The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Read More

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Characterization and expression analysis of tandemly duplicated nicotinic acetylcholine receptors in pearl oysters after stimulation of pathogen-related molecular patterns.

Comp Biochem Physiol B Biochem Mol Biol 2021 May 8:110615. Epub 2021 May 8.

Fishery College, Guangdong Ocean University, Zhanjiang 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China. Electronic address:

Nicotinic acetylcholine receptors (nAChRs) are a class of ligand-gated ion channels that participate in signal transduction and are reported to play an important role in the immunomodulation of vertebrates and invertebrates. Previous studies have shown that the nAChRs in mollusks have undergone large-scale expansion after tandem repeats and retrotransposition, with the most expansion observed in bivalves. This study characterized the sequence of a tandem repeat nAChR unique to several bivalve mollusks and investigated its functions in Pinctada fucata martensii. Read More

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Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties.

Mol Biol Evol 2021 May 11. Epub 2021 May 11.

Univ Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France.

Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions of their environment. In spite of wide fundamental interest, however, studies providing insights into this adaptation are scarce, because of practical difficulties inherent to the purification and characterization of halophilic enzymes. In this work, we describe the evolutionary history of malate dehydrogenases (MalDH) within Halobacteria (a class of the Euryarchaeota phylum). Read More

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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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The transposable element environment of human genes differs according to their duplication status and essentiality.

Genome Biol Evol 2021 Apr 15. Epub 2021 Apr 15.

Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Evry Val d'Essonne, ENSIIE, Paris, UMR CNRS 8071, France USC INRA, 23 bvd de France 91037 Evry CEDEX.

Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an evolutionary mechanism that also provides new genetic material and opportunities to acquire new functions. 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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Tracking the recruitment and evolution of snake toxins using the evolutionary context provided by the genome.

Proc Natl Acad Sci U S A 2021 May;118(20)

Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo 05503-900, Brazil;

Venom is a key adaptive innovation in snakes, and how nonvenom genes were co-opted to become part of the toxin arsenal is a significant evolutionary question. While this process has been investigated through the phylogenetic reconstruction of toxin sequences, evidence provided by the genomic context of toxin genes remains less explored. To investigate the process of toxin recruitment, we sequenced the genome of , a clinically relevant pitviper. Read More

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Characterization of KPC-82, a KPC-2 variant conferring resistance to ceftazidime-avibactam in a carbapenem non-susceptible, clinical isolate of .

Antimicrob Agents Chemother 2021 May 10. Epub 2021 May 10.

Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA

KPC-82 is a KPC-2 variant, identified in a carbapenem non-susceptible that confers high-level resistance to ceftazidime-avibactam. Genomic analysis revealed that is carried by a chromosomally integrated Tn transposon (disrupting porin gene ) and evolved by a 6-nucleotide tandem-repeat duplication causing a two-amino-acid insertion (Ser-Asp) within the Ala-Ser loop. Similar to related KPC variants, KPC-82 showed decreased carbapenemase activity when expressed in a heterologous background and remained susceptible to carbapenem/β-lactamase inhibitor combinations. Read More

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Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development.

BMC Plant Biol 2021 May 10;21(1):210. Epub 2021 May 10.

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

Background: Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear. Read More

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Characterization of the complete chloroplast genome of a hybrid species × .

Mitochondrial DNA B Resour 2021 Apr 23;6(4):1492-1493. Epub 2021 Apr 23.

College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China.

'' ×  '' is a hybrid species with important ornamental In the research, Illumina high-throughput sequencing technologies was used to sequence the chloroplastic genome of '' ×  ''. The genome features of '' ×  '' and the phylogenetic relationships were reported and established. The total length of the complete chloroplast genome is 154,741 bp, consisting of a pair of inverse duplication regions 26,968 bp, a large single-copy region 84,410 bp and a small single-copy region 16,395 bp. Read More

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Making Choices: DNA Replication Fork Recovery Mechanisms.

Semin Cell Dev Biol 2021 May 22;113:27-37. Epub 2020 Oct 22.

Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.

DNA replication is laden with obstacles that slow, stall, collapse, and break DNA replication forks. At each obstacle, there is a decision to be made whether to bypass the lesion, repair or restart the damaged fork, or to protect stalled forks from further demise. Each "decision" draws upon multitude of proteins participating in various mechanisms that allow repair and restart of replication forks. Read More

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Genome wide identification, classification and functional characterization of heat shock transcription factor in cultivated and ancestral cotton (Gossypium).

Int J Biol Macromol 2021 May 6. Epub 2021 May 6.

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China. Electronic address:

Heat shock transcription factors (HSF) have been demonstrated to play a significant transcriptional regulatory role in plants and considered as an integral part of signal transduction pathways against environmental stresses. 42, 39, 67, and 79 nonredundant HSF genes were identified from G. arboreum (A2), G. Read More

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Cotton DMP gene family: Characterization, evolution, and expression profiles during development and stress.

Int J Biol Macromol 2021 May 6. Epub 2021 May 6.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China. Electronic address:

Members of DOMAIN OF UNKNOWN FUNCTION 679 membrane protein (DMP) gene family, a type of plant-specific membrane proteins, have been proposed to function in various physiological processes such as reproductive development and senescence in plants. Here, a total of 174 DMP genes were identified and analyzed in 16 plant species (including 58 DMPs in four cotton species). Phylogenetic analysis showed that these DMPs could be clustered into five subfamilies (I-V). Read More

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Comments on the evolution of TRPV6.

Ann Anat 2021 May 6;238:151753. Epub 2021 May 6.

Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, 66421 Homburg, Saar, Germany. Electronic address:

It is well known that not all biological findings derived from animals can be directly applied to humans. The TRPV6 protein may serve as an example which highlights these inter-species differences as an example of parallel evolutionary pathways. TRPV6 (and TRPV5) belong to a family of ion channels from the transient receptor potential group but are selectively permeable for Ca, in contrast to other members of the family. Read More

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Genome-wide analysis of gibberellin-dioxygenases gene family and their responses to GA applications in maize.

PLoS One 2021 7;16(5):e0250349. Epub 2021 May 7.

College of Agronomy, Jilin Agricultural University, Changchun, China.

Gibberellin-dioxygenases genes plays important roles in the regulating plant development. However, Gibberellin-dioxygenases genes are rarely reported in maize, especially response to gibberellin (GA). In present study, 27 Gibberellin-dioxygenases genes were identified in the maize and they were classified into seven subfamilies (I-VII) based on phylogenetic analysis. Read More

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A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop.

Plant J 2021 May 7. Epub 2021 May 7.

Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.

Traditional crops historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over reliant on a small number of internationally-traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (especially where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient and biodiverse agriculture. Read More

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Confirmation of Xp22.11 Duplication as a Germline Susceptibility Alteration in a Wilms Tumor Arising in Horseshoe Kidney.

Fetal Pediatr Pathol 2021 May 7:1-6. Epub 2021 May 7.

The Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.

Background: There is strong evidence of a genetic contribution to Wilms tumor, such as gene variation or epigenetic changes at chromosome locus 11p15. A previous genome wide association study (GWAS) of Wilms tumor identified other significant association loci including Xp22. A 4-year-old girl developed a Wilms tumor of the left isthmus of a horseshoe kidney. Read More

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Genetic Variation and Its Implication for Vivax Malaria Treatment in Madagascar.

Front Pharmacol 2021 20;12:654054. Epub 2021 Apr 20.

Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States.

is one of the five human malaria parasite species, which has a wide geographical distribution and can cause severe disease and fatal outcomes. It has the ability to relapse from dormant liver stages (hypnozoites), weeks to months after clearance of the acute blood-stage infection. An 8-aminoquinoline drug primaquine (PQ) can clear the hypnozoites, and thus can be used as an anti-relapse therapeutic agent. Read More

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The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae.

Nat Plants 2021 May 6. Epub 2021 May 6.

State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China.

Miscanthus, a member of the Saccharinae subtribe that includes sorghum and sugarcane, has been widely studied as a feedstock for cellulosic biofuel production. Here, we report the sequencing and assembly of the Miscanthus floridulus genome by the integration of PacBio sequencing and Hi-C mapping, resulting in a chromosome-scale, high-quality reference genome of the genus Miscanthus. Comparisons among Saccharinae genomes suggest that Sorghum split first from the common ancestor of Saccharum and Miscanthus, which subsequently diverged from each other, with two successive whole-genome duplication events occurring independently in the Saccharum genus and one whole-genome duplication occurring in the Miscanthus genus. Read More

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