Plants repetitive sequences nucleic acid. Medical search. Frequent questions

Within species, genomes vary in both gene content (e.g., tandem duplicated genes, CNVs dispersed throughout the genome, and PAVs of genes) and repetitive portions of the genome (e.g., transposable elements, knob repeats, centromere repeats). (biomedcentral.com)
The above-mentioned ab, of repetitive sequences in plant genomes (up to 99%), makes difﬁcult the application of this technique for, mapping individual plant genes [40]. (centrocardiobogota.com)
Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. (biomedcentral.com)
Sequences shared by a subset of genomes are referred as dispensable and they represent variable features. (biomedcentral.com)
Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
DLGP: A database for lineage-conserved and lineage-specific gene pairs in animal and plant genomes. (openwetware.org)
Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. (biomedcentral.com)
Here we retrieved 26,092 putative complete LTR-RTs from 10 lineages found in 10 fully sequenced angiosperm genomes and found putative vl-att sites that are a conserved structural landmark across these genomes. (biomedcentral.com)
TEs comprise approximately 45 % of the human genome and form the vast majority of the total DNA content of most plant genomes, in some cases reaching close to 80 % [ 4 - 6 ]. (biomedcentral.com)
The predominant TE found in plant genomes is the long terminal repeat retrotransposons (LTR-RTs). (biomedcentral.com)
Loss of photosynthesis has occurred independently in several plant and algal lineages, and represents a major metabolic shift with potential consequences for the content and structure of plastid genomes. (biomedcentral.com)
Unfortunately, the number of fully-sequenced non-photosynthetic plastid genomes is small, limited to Epifagus virginiana (a holoparasitic angiosperm), Euglena longa (a heterotrophic euglenid), and several apicomplexan parasites bearing secondary plastids of red algal origin called apicoplasts ( Plasmodium falciparum , Theileria parva , Eimeria tenella and Toxoplasma gondii ). (biomedcentral.com)
Retrotransposons (RNA mediated Class I TEs) are the most widespread class of eukaryotic TE, particularly relevant in shaping plant genomes ( [10] , [44] ). (sisef.it)
The observed differences in genome size in plants are accompanied by variations in the content of LTR retrotransposons, demonstrating that such elements might be important players in the evolution of plant genomes, along with polyploidy ( [11] ). (sisef.it)
His innovative biotechnologies and computational tools to study the sequence and function of genomes are advancing the understanding of the structure, evolution, and function of genomes for medicine - particularly autism spectrum disorders, cancer, and other human diseases - and agriculture. (agbt.org)
Transposable elements in plant genomes. (genomecoffea.org)
Because of their mobility mechanisms, transposons account for the vast majority of transgenic elements present in plant genomes. (genomecoffea.org)
Several methods have been developed to identify and annotate transposable elements in sequenced genomes. (genomecoffea.org)
Our aim is to study transposable elements in plant genomes, and more specifically in coffee genomes. (genomecoffea.org)

To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases ( APLs ). (biomedcentral.com)
Increased antioxidant enzyme activities (SOD, APX, and CAT) and upregulation of ROS pathway genes (CAT, APX, GR, and DHAR) were observed in PGPR inoculated okra plants under salinity stress. (hindawi.com)
Core genes are often under strong evolutionary selection, thus their sequences are transmitted almost without any alteration. (biomedcentral.com)
The amount of variations affecting dispensable genes varies and the similarity between homologous sequences tends to decrease according to their phylogenetic distance. (biomedcentral.com)
Identification of immune-relevant genes by expressed sequence tag analysis of head kidney from grass carp (Ctenopharyngodon idella). (openwetware.org)
A complex interaction between the cleavage and polyadenylation molecular complex and cis -elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. (frontiersin.org)
The euchromatin contained more genes that were simpler to sequence with the tools available at the time. (drishtiias.com)
Miniature Inverted TEs (MITEs) are defective, non autonomous forms of DNA transposons and are the predominant TE type in or near plant genes ( [10] ). (sisef.it)
Taking a single DNA sample from an individual's blood, researchers can pass the nucleic acids through a protein nanopore , using changes in electrical current arising from the molecular interactions to decode in real time the sequences from 40 genes known to be connected to 25 tandem repeat diseases. (sciencealert.com)

sequence) of the whole genome or its separate parts. (centrocardiobogota.com)
We performed whole-genome (WG) de novo sequencing and complete assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk in Korea. (biomedcentral.com)
The goal of our research was to produce molecular resources using whole-genome and transcriptome sequencing techniques. (biomedcentral.com)
The whole-genome sequencing has shown common or crystalline ice plants ( Mesembryanthemum crystallinum ) to switch from Calvin- Benson Cycle (C3) to CAM photosynthesis under a salt stress [ 15 ]. (biomedcentral.com)
From 2011 to 2017, we collected 32 strains of C gattii from 18 hospitals across China, of which 27 [84·4%] strains molecular traits were profiled by whole-genome sequencing (WGS) and multi-locus sequence typing (MLST) and compared with strains previously described in China from 2006 to 2020. (researchsquare.com)

All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. (biomedcentral.com)
Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri . (biomedcentral.com)
In addition to the annotation of gene space, a detailed annotation of repeated sequences and transposable elements (TEs) ( e.g. presence/absence, types, and location) is critical for understanding the biology of a genome, as well as an important tool for the improvement of high-quality genome assemblies. (biomedcentral.com)
The use of repeat libraries of one species to detect repeats from a related species (that diverged e.g. 10 million years ago) is highly problematic as it is known that intergenic space is rapidly evolving for the high turnover rates of transposable elements and repetitive sequence. (biomedcentral.com)
Illumina): highly repetitive sequences and transposable elements pose significant problems to assembly algorithms. (biomedcentral.com)
Among these repetitive sequences are the transposable elements (TEs), which are mobile genetic sequences present in plants and in all eukaryotes. (biomedcentral.com)
Transposable elements (TEs) are ancient (retro)-virus insertions inside a host genome and are peculiar mobile genetic elements accounting for a large proportion of repetitive DNA regions ( [29] ). (sisef.it)

Experimental methods of multi-dimensional NMR spectroscopy, dynamics and theoretical description of spin system evolution, multiple resonance NMR technique for structural studies of proteins and nucleic acids by NMR spectroscopy, contemporary methods of structural biology, studies of complex biomolecular systems. (muni.cz)
Nucleic acids and proteins: modern linguistics for the genomics and bioinformatics era / Bradley C. Hyman -- Structure and function of cell organelles / Jon Holy -- Cell signaling / Daniel A. Rappolee -- B. Transcription and translatio. (ewubd.edu)
In proteins, primary structure consists of specific chemical composition, and all units are arranged in sequence. (byjus.com)
Students know most macromolecules (polysaccharides, nucleic acids, proteins, lipids) in cells and organisms are synthesized from a small collection of simple precursors. (mysciencebox.org)
Students know large molecules (polymers), such as proteins, nucleic acids, and starch, are formed by repetitive combinations of simple subunits. (mysciencebox.org)
Students know amino acids are the building blocks of proteins. (mysciencebox.org)

Illumina single nucleotide polymorphism (SNP) chips, kompetitive allele-specific PCR (KASP) assays, genotyping-by-sequencing (GBS)) and sequencing (e.g. (biomedcentral.com)
We also report SNV numbers for three additional O. australiensis genotypes based on Illumina re-sequencing. (nature.com)
The complete genome of the Peepal tree was sequenced using two next-generation sequencers Illumina HiSeq1000 and MGISEQ-2000. (biomedcentral.com)

By comparing genomic sequences produced by various sequencing techniques, we reveal the significant gain of assembly continuity by using long-read-based techniques over short-read-based methods. (pacb.com)

Up to the present time, there is no, real success in obtaining pure fractions of individual, plant chromosomes by ﬂow sorting. (centrocardiobogota.com)
results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genome chromosomes and for, To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S-28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barleyHordeum vulgareL. (centrocardiobogota.com)
The new reference genome, called T2T-CHM13 , includes highly repetitive DNA sequences found in and around the telomeres (structures at the ends of chromosomes) and the centromeres (at the middle section of each chromosome). (drishtiias.com)
2023. Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. (genomecoffea.org)

Genetics and genetic engineering has placed an important role in improvement of plant production. (centrocardiobogota.com)
Meet the Editor-in-Chief APPS's Editor-in-Chief, Dr. Theresa Culley (University of Cincinnati), studies the evolution of plant breeding systems and invasive species biology, using ecological and population genetic methods. (centrocardiobogota.com)
Genetic engineering is an attractive approach that can generate plants resistant to salt stress [ 18 ]. (hindawi.com)
Genome sequencing on C gattii in recent years has become a powerful tool to reveal novel lineages as well as genetic variations that were associated with phenotypes and virulence in different lineages and/or subtypes within the same lineage. (researchsquare.com)
Every organism's genetic code is contained in its Deoxyribose Nucleic Acid (DNA) , the building blocks of life. (drishtiias.com)
The findings have revealed a large number of genetic variations , and these variations appear in large part within these repeated sequences. (drishtiias.com)
Genome sequencing can be used to identify genetic markers for disease resistance and drought tolerance in various crop plants. (drishtiias.com)
Retrotransposable elements are important and peculiar genetic components derived from ancient retrovirus insertion inside plants genome. (sisef.it)

The ﬁrst section introduces sequence-basedanalyses,includinggeneﬁnd-ing, gene family and phylogenetic analy-ses, and comparative genomics approaches. (centrocardiobogota.com)

The fastest and most common way to annotate the repetitive fraction of a genome assembly is to create repeat libraries derived from a set of previously identified representative repetitive sequences and screen the target genome using homology-based searches. (biomedcentral.com)

8 provided an update to the OryzaGenome database which includes short-read sequencing data for several non-AA genome Oryza species. (nature.com)
False negatives arise due to repeat/TE sequence diversification across taxa which can hamper the identification of distinctive repeat features ( i.e. lineage specific sequences) of the species. (biomedcentral.com)
In spite of the abundance of research on the roles of TE on the genome biology in humans, model organisms (e.g., mice and Drosophila ), and plants (especially crop species), few studies on TE have been conducted in livestock and poultry. (biomedcentral.com)
Next-generation sequencing (NGS) technologies have accelerated the generation of draft genome sequences of Moraceae plant species. (biomedcentral.com)
The genome sequencing of non-model plant species F. religiosa was first mentioned in The Neem Genome book chapter [ 3 ]. (biomedcentral.com)
The study described by comparing both species with and without the C4 trait and different tissues within a C4 plant using RNA-seq suggests ways of integration into the underlying C3 metabolism [ 16 ]. (biomedcentral.com)
Any cytogenetic investigation regarding NOR variability, telomere sequence and genome size in the Indian species becomes the most promising field to decipher chromosome evolution against the background of species diversity and evolution, especially in the Indian subcontinent. (pensoft.net)
The analysis of next-generation sequencing data revealed four viral groups with seven species, of which up to five were simultaneously detected in a single trypanosomatid isolate. (bvsalud.org)
Phylogenetic analysis of 16S rRNA, gpd and recA gene sequences showed that the eight novel strains could not be assigned to any recognized species. (microbiologyresearch.org)
Analysis of these elements faces major obstacles and challenges, including their repetitive nature, structural polymorphism, species specificity and, conversely, conservation across genera and families, as well as their high rate of divergence, even between closely related species. (genomecoffea.org)

To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. (biomedcentral.com)
Biopolymers provide an alternative to oil based plastics, as they are made from plants, usually polymers of starch or polylactic acid (PLA). (cichlidresearch.com)

The completely sequenced S. fibuligera genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of S. fibuligera in the degradation of fermentation mash. (biomedcentral.com)
Epigenetic mechanisms regulating gene expression / John R. McCarrey -- Gene families and evolution / Ben F. Koop -- Repetitive DNA: detection, annotation, and analysis / Jerzy Jurka -- Molecular genetics of disease and the human genome project / Paromita Deb-Rinker and Stephen W. Scherer -- B. Clinical human genetics. (ewubd.edu)
Rapid identification and reliable annotation of transgenic elements is an important issue in genomic sequence analysis. (genomecoffea.org)

Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. (biomedcentral.com)
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. (frontiersin.org)
Pattern discovery: methods and software / Brona Brejova, Tomas Vinar, and Ming Li -- The role of transcription factor binding sites in promoters and their In Silico detection / Thomas Werner -- An introduction to multiple sequence alignment and analysis / Steven M. Thompson -- 3D molecular visualization with protein explorer / Eric Martz -- Multiple sequence alignment and analysis: the Seqlab interface: a practical guide / Steven M. Thompson -- D. Analysis of gene expression: microarrays and other tools. (ewubd.edu)

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. (uchicago.edu)

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. (biomedcentral.com)
The invention of new methods of DNA sequencing and computational analysis helped complete the reading of the remaining 8% of the genome. (drishtiias.com)

The newly developed assessment is based on nanopore technology, which can analyze long DNA or RNA fragments in known repetitive regions of the human genome. (sciencealert.com)
Current gene sequencing tests require machines as large as fridges, whereas the nanopore technology is no bigger than a stapler. (sciencealert.com)

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. (uchicago.edu)

Similarities in amino acid sequences between various organisms also suggest common descent, and the fossil record also shows cases in which one plant or animal type evolved into different types over time. (rationalwiki.org)
Regardless of the slight differences, all organisms use the same coding mechanism for translating the code into amino acid sequences. (rationalwiki.org)

The database allows sequence browsing, downloading, and similarity searches. (biomedcentral.com)
When closely related organisms are analyzed, reasonable thresholds on sequences similarity are applied to recognize gene families. (biomedcentral.com)
Sequence similarity and database searching / David S. Wishart -- GCG database searching / David J. Heard -- C. Identifying functional and structural sequence elements. (ewubd.edu)

Assembling a plant genome is challenging due to the abundance of repetitive sequences, yet no standard is available to evaluate the assembly of repeat space. (pacb.com)

Furthermore, we reveal that each plant genome has a distinguishable LTR-RT lineage amplification pattern that could be related to the vl-att sites diversity. (biomedcentral.com)
The cloning and sequencing of amplification products and a Cleaved Amplified Polymorphisms (CAPs) approach on the identified retrotransposons, showed a high level of diversity among the multiple copies of both elements. (sisef.it)

The universal distribution of vl-att sites represents a new structural feature common to plant LTR-RTs and retroviruses. (biomedcentral.com)
It has been shown by coding sequence and structural similarities that LTR-RTs are related to retroviruses [ 15 ], it has been suggested that retroviruses evolved from the Gypsy superfamily after acquisition of the envelope gene [ 16 ]. (biomedcentral.com)
We questioned whether vl-att sites are specific to the Del lineage or are conserved structural landmarks across plant LTR-RTs and, therefore, a new structural feature common to plant LTR-RTs and retroviruses. (biomedcentral.com)
The first two precepts of Cell Theory were enunciated near the middle of the 19th century, after many observations of plant and animal cells revealed common structural features (e.g., a nucleus, a wall or boundary, a common organization of cells into groups to form multicellular structures of plants and animals and even lower life forms). (eduhyme.com)

We speculate that the sequence diversity of vl-att sites could be important for the life cycle of retrotransposons, as it was shown for retroviruses. (biomedcentral.com)

The structures and functions of all living organisms are encoded in the same basic nucleic molecules, DNA and RNA . (rationalwiki.org)

Conversely, de novo methods such as Piler [ 3 ] and RepeatModeler ( http://www.repeatmasker.org/RepeatModeler.html ) have been developed to identify repeats in genome assemblies based on the number of times a sequence motif appears in an input file. (biomedcentral.com)

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. (uchicago.edu)

Basic techniques for the analysis of nucleic acids. (unipv.it)
Sequencing and analysis of Neanderthal genomic DNA. (uchicago.edu)
Installing bioinformatics software in a server-based computing environment / Brian Fristensky -- Management of a server-based bioinformatics resource / Brian Fristensky -- C. Command line sequence analysis. (ewubd.edu)
Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. (microbiologyresearch.org)

See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
The T2T consortium used the now-complete genome sequence as a reference to discover more than 2 million additional variants in the human genome. (drishtiias.com)

Polymers, including biopolymers, are made of repetitive units called monomers.Biopolymers inherently have a well defined structure: The exact chemical composition and the sequence in which these units are arranged is called the primary structure. (cichlidresearch.com)
The growing need for lubricious coatings and surfaces in medical … Biopolymers in nature are produced by a range of microorganisms and plants. (cichlidresearch.com)

All polymers are composed of monomers, the repetitive units. (byjus.com)
These polymers would create a viable industry as these plant materials are derived from non- food crops. (byjus.com)

Indeed, in several lineages of plants and algae photosynthesis has been lost altogether, but the plastid has been retained for these and other purposes [ 3 ]. (biomedcentral.com)
Well-known examples of this include holoparasitic plants, many lineages of heterotrophic algae and parasitic apicomplexans (such as the malaria parasite). (biomedcentral.com)

Basic knowledge of animal and plant cell biology, chemistry and mathematics. (unipv.it)

Since the advent of second generation sequencing (SGS) technologies, the scientific community has been inundated with hundreds of genome assemblies of varying quality. (biomedcentral.com)
Characterizing natural variation using next-generation sequencing technologies. (uchicago.edu)

Sequencing data showed that the tdnQ sequences of A, C, B were very closely related, while the tdnQ fragment of BN3.1 and P. putida were only about 83% identical to the other sequences. (sciepub.com)
The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. (biomedcentral.com)
The scope of studies ranges from those focused-on sequencing, mass spectrometry, bioimaging and other high-through-put techniques in data to medicine, pharmacology, and populational studies. (nih.gov)
He is also interested in the large-scale infrastructure required for modern bioinformatics including storage and access methods for high throughput sequencing data. (agbt.org)

The diversity has been examined of the plasmids and of the gene tdnQ, involved in oxidative deamination of aniline in three bacterial isolates that are able to metabolise both aniline and 3-chloroaniline (3-CA). Strains A and B were isolated in this study from a wastewater treatment plant and were identified as Comamonas testosterone and Delftia acidovorans, respectively. (sciepub.com)
Just in this one gene, however, there are a diversity of ways short DNA sequences can be repeated, which makes a blanket diagnostic test difficult. (sciencealert.com)

Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion. (openwetware.org)

Norwegian Kjell Kleppe came up with the idea of amplifying DNA using primers - markers for specific DNA sequences - as early as the 1970s. (analytik-jena.com)

has been identified as the 2nd most consensus (ERIC) sequences which · 60 environmental samples were tak- frequent organism causing ventilator- are common to Gram-negative enteric en throughout the ICU, including associated pneumonia, the 4th most bacteria [11,12]. (who.int)

Understanding mechanisms underlying human gene expression variation with RNA sequencing. (uchicago.edu)
Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. (frontiersin.org)
In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions. (frontiersin.org)

We present the nucleotide sequence of a 2,555-base-pair portion of this fragment containing an open reading frame (ORF) of 601 amino acids. (agri.gov.il)

Plasmid control of ptoluenesulfonic acid degradation in Comamonas testosteroni BS1310. (sciepub.com)

Our goal was to maximize the value of museum collections for pathogen-based research by using targeted sequence capture. (cdc.gov)
Probe-based, targeted sequencing has been used to enrich pathogens from complex host‒pathogen DNA mixtures ( 21 ). (cdc.gov)
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. (frontiersin.org)

In this study, we characterized plant growth-promoting rhizobacteria (PGPR) containing 1-aminocyclopropane-1-carboxylate (ACC) deaminase and examined their effect on salinity stress tolerance in okra through the induction of ROS-scavenging enzyme activity. (hindawi.com)

Two retrotransposons, belonging to the two major classes of LTR and non-LTR elements, were characterized trough a SCAR (Sequence Characterized Amplified Region) strategy. (sisef.it)
Structure of non-autonomous and autonomous LTR retrotransposons in plants (Orozco-Arias et al. (genomecoffea.org)

In plants, some researchers have successfully used TE to improve the economic properties and stress resistance of crops. (biomedcentral.com)

Two pairs of co-dominant polymorphisms were detected, and were converted into sequence-specific PCR markers desirable for routine marker implementation. (cropscience.org.au)

5. The anatomy and physiology of plants and animals illustrate the complementary nature of structure and function. (mysciencebox.org)
Students know plants and animals have levels of organization for structure and function, including cells, tissues, organs, organ systems, and the whole organism. (mysciencebox.org)

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Organisms24

Diseases4

Chemicals and Drugs68

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

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Technology, Industry, Agriculture8

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Genomes19

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Illumina3

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Annotation3

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Structural4

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