Sequence synteny. Medical search. Frequent questions

In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
The Encyclopædia Britannica gives the following description of synteny, using the modern definition: Genomic sequencing and mapping have enabled comparison of the general structures of genomes of many different species. (wikipedia.org)
Shared synteny is one of the most reliable criteria for establishing the orthology of genomic regions in different species. (wikipedia.org)
Shared order between genomic sequences provide a great deal of information. (bioconductor.org)
The accessibility of almost complete genome sequences of uncultivable microbial species from metagenomes necessitates computational methods predicting microbial phenotypes solely based on genomic data. (biomedcentral.com)
All comparitive maps are based on the UCSC synteny for genomic maps. (animalgenome.org)
And in Nature Plants , an international research team publishes a new high-quality genome sequence of the rose , highlighting the utility of genomic and epigenomic approaches in studying key traits in ornamentals and other plants. (genomeweb.com)
The advent of high-throughput next-generation sequencing technologies and assembly algorithm improvements have occurred thick accumulation of genomic data in the public domain. (symapdb.org)
Therefore comparative genomic analysis of T . equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T . equi relative to sequenced apicomplexan parasites. (biomedcentral.com)
Comparative genomic analysis of T . equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp . (biomedcentral.com)
To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
Genomic sequencing of A. fulgidus suggests that three [Ni-Fe]-CODHs are present, a "bacterial" monomeric CooS and two archaeal CdhAB-type CODHs [ 9 - 11 ]. (hindawi.com)
During the past decade, two major developments-the emergence of massively parallel, ultra-cheap DNA sequencing technologies and the use of these technologies as digital readouts for functional genomic assays-have led to a profusion of data describing various features of genomes, epigenomes, and transcriptomes 1 , 2 . (biorxiv.org)
Collectively, our results will be conducive to understanding the genera demarcation within the Iridoviridae family based on genomic synteny and component (codon usage preference) and contribute to the existing taxonomy methods for the Iridoviridae family. (figshare.com)
This comparative genomic analysis highlights high chromosomal synteny across the species yet diverse plasmid composition. (cdc.gov)

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. (nature.com)
Synteny is widely used in studying complex genomes, as comparative genomics allows the presence and possibly function of genes in a simpler, model organism to infer those in a more complex one. (wikipedia.org)
2009): Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes. (boku.ac.at)
1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. (jcvi.org)
JAX Synteny Browser software can be used for any two genomes where the genome coordinates for syntenic blocks and attributes defined biological features in one or both genomes available in the widely used standard bioinformatics file formats. (symapdb.org)
The level of conservation of gene order (synteny) and linkage between two genomes will depend on the relative contributions of inter- and intrachromosomal rearrangements. (biomedcentral.com)
So a genome-vs-genome alignment can lead to some artifacts due to the fact that the two genomes have been sequenced with different techniques. (biostars.org)
We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis . (asm.org)
Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. (darkenergybiosphere.org)
A majority of sTBRF spirochete genomes' plasmid sequences are either missing or are deposited as unassembled sequences. (cdc.gov)
RESULTS: Utilizing a Borrelia specific pipeline, genomes of sTBRF spirochetes from the Western Hemisphere were sequenced and assembled using a combination of short- and long-read sequencing technologies. (cdc.gov)
We sequenced the whole genomes of 176 P. aeruginosa isolates collected in 2013-2014 by the Antimicrobial Resistance Surveillance Program. (who.int)
The population of P. aeruginosa in the Philippines was diverse, with clonal expansions of XDR genomes belonging to multi-locus sequence types ST235, ST244, ST309, and ST773. (who.int)

Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)
Shared synteny (also known as conserved synteny) describes preserved co-localization of genes on chromosomes of different species. (wikipedia.org)
Stronger-than-expected shared synteny can reflect selection for functional relationships between syntenic genes, such as combinations of alleles that are advantageous when inherited together, or shared regulatory mechanisms. (wikipedia.org)
Additionally, exceptional conservation of synteny can reflect important functional relationships between genes. (wikipedia.org)
Primer sets for 21 genes yielded eight horse-specific markers, which were mapped with the UC Davis horse-mouse somatic cell hybrid panel into two synteny groups: UCD14 and UCD21. (etsu.edu)
1 In prokaryotes , genes encoding collaborative proteins are organized as a contiguous sequence called an operon. (reasons.org)
The work by the Berkeley investigators indicates that the precise sequencing of operon genes ensure not only that all the right proteins are made, but also that proteins are made at the right levels to support the cell's metabolic demands. (reasons.org)
More than 650 million base pairs (>25%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. (jcvi.org)
Synteny in classical terms refers to the genes present on the same chromosome, like beads on the same string. (jove.com)
In evolutionary perspective, synteny refers to the phenomenon of co-localization of genes on a chromosome of two or more different species. (jove.com)
Therefore, the genes A and A1, B and B1 and C and C1 represent a synteny between the two species, X and Y. (jove.com)
Even after millions of years of divergence, several genes present on the long arm of human chromosome 10 and the tree shrew's chromosome 16 show conserved synteny in some regions. (jove.com)
John H. Renwick first coined the term "synteny" in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. (jove.com)
They use their reference sequence to analyze loci controlling ornamental traits - including continuous flowering, double flower, self-incompatibility, and prickle density - and identify and characterize candidate genes for the traits. (genomeweb.com)
The sequence represents an important resource for studying polyploidization, meiosis, and developmental processes, and will help "accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them, and the exploitation of synteny across Rosaceae ," the researchers say. (genomeweb.com)
Our aim was to clone and sequence the cDNA of the BB diabetes prone (DP) and diabetes resistant (DR) alleles of all seven Gimap genes in the congenic DR. lyp rat line with 2 Mb of BB DP DNA introgressed onto the DR genetic background. (hindawi.com)
The fact that the Gimap genes are located together in a tight cluster on RNO4 (and in conserved synteny with many other species), combined with their sequence similarities, suggests the possibility that the proteins carry out similar function. (hindawi.com)
The male sterilizing factors are produced by recombination of the mitochondrial genome and consist of unusual genes or open reading frames (ORFs) that usually contain a portion of functional mitochondrial genes and sequences of unknown origin ( Hanson and Bentolila, 2004 ). (frontiersin.org)
Potential C. elegans orthologs for II of the 12 protein-coding genes predicted in the B. malayi sequence were identified. (biomedcentral.com)
Kent and Zahler [ 9 ] compared 8.1 megabases (Mb) of fragmentary C. briggsae sequence derived from sequenced cosmid clones to C. elegans and derived a mean syntenic fragment length of 8.6 klobases (kb), or approximately 1.8 genes (there is one gene per 5 kb in C. elegans ) [ 13 ]. (biomedcentral.com)
The genome sequence will allow scientists to locate and identify genes that can improve and strengthen crops and increase yield in order to help solve the Earth's looming food crisis by creating new strains of the cereal crops that make up 60% of humankind's diet. (bio5.org)
The phylogenetic tree based on the 23 re-annotated core genes (Maximum Likelihood, ML-Tree) and amino acid sequences (composition vector, CV-Tree) were found to be consistent with previous reports. (figshare.com)
This was further supported by long-read sequencing of one representative XDR isolate, which revealed the presence of an integron carrying multiple resistance genes, including bla VIM-2 , with differences in gene composition and synteny to other P. aeruginosa class 1 integrons described before. (who.int)

Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study. (biomedcentral.com)

Sequencing of the A. oryzae genome was accomplished using the whole-genome shotgun (WGS) approach. (nature.com)
Landscape of somatic mutations in 560 breast cancer whole-genome sequences. (nature.com)

To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. (sequentiabiotech.com)
In genetics, the term synteny refers to two related concepts: In classical genetics, synteny describes the physical co-localization of genetic loci on the same chromosome within an individual or species. (wikipedia.org)
This situation is called synteny, translated roughly as possessing common chromosome sequences. (wikipedia.org)
Similarly, in genomics, the genetic loci on a chromosome are syntenic regardless of whether this relationship can be established by experimental methods such as DNA sequencing/assembly, genome walking, physical localization or hap-mapping. (wikipedia.org)
Students of (classical) genetics employ the term synteny to describe the situation in which two genetic loci have been assigned to the same chromosome but still may be separated by a large enough distance in map units that genetic linkage has not been demonstrated. (wikipedia.org)
During evolution, rearrangements to the genome such as chromosome translocations may separate two loci, resulting in the loss of synteny between them. (wikipedia.org)
Comparative anchor tagged sequences (CATS) from human Chromosome 5 (HSA5) were used as PCR primers to produce molecular markers for synteny mapping in the horse. (etsu.edu)
These data, in conjunction with earlier human chromosome painting studies of the horse karyotype and synteny mapping of horse microsatellite markers physically mapped by FISH, confirm the assignment of UCD21 to ECA21 and suggest that UCD14 is located on ECA14. (etsu.edu)
CONCLUSIONS: To truly understand the biological differences observed between species of TBRF spirochetes, complete chromosome and plasmid sequences are needed. (cdc.gov)

Here, we develop a specialized target‐capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. (researchgate.net)
Shared synteny (or disruption, called breakpoints) can be used as phylogenetic signals to sort out species relationship. (biostars.org)
Furthermore, the information provided by synteny analysis and codon usage preference (relative synonymous codon usage, correspondence analysis, ENC-plot and Neutrality plot) also supports the phylogenetic relationship. (figshare.com)

Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae -specific blocks (lacking synteny with A. nidulans and A. fumigatus ) in a mosaic manner throughout the genome of A. oryzae . (nature.com)
An examination of the content and distribution of repetitive DNA sequences to identify the location of such sequences within specific chromosomes and their conservation across species of the Pinaceae family. (le.ac.uk)
Determine level of synteny or conservation of gene order between species within the Pinaceae family. (le.ac.uk)
The establishment of synteny maps will provide a powerful tool to investigate the quantitative conservation of map location of trait loci across species and environments. (le.ac.uk)
Based on synteny analysis and high resolution DNA data from all known modern primates, scientists have proposed a karyotype for the common ancestor of all of these species. (jove.com)
Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species. (jove.com)
Furthermore, other near-human species such as Zeltron, Chiss , and Sullustan share the human ortholog of this locus, which supports the inference that the ancestral sequence was noncoding, and that the GLABR has de novo origins in the Wookiee. (ubc.ca)
To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi . (biomedcentral.com)

Several new genomics technologies have become available that offer long-read sequencing or long-range mapping with higher throughput and higher resolution analysis than ever before. (nature.com)
The analysis of synteny in the gene order sense has several applications in genomics. (wikipedia.org)
Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. (biomedcentral.com)
The JAX Synteny Browser for mouse-human comparative genomics. (symapdb.org)
His recent research interests include genome editing to engineer immunity against viral infection and using the next generation sequencing to explore viral population genomics and genetic diversity and to discover new viruses and novel viral strains. (bio5.org)
Rod Wing, PhD, and his lab, The Arizona Genomics Institute, specialize in building what geneticists call a physical map of a genome- a crucial foundation of any genome sequencing effort. (bio5.org)

GOblet: annotation of anonymous sequence data with Gene Ontology and pathway terms. (mpg.de)

Equine Synteny Mapping of Comparative Anchor Tagged Sequences (CATS) F" by Alexandre R. Caetano, Leslie A. Lyons et al. (etsu.edu)
The dog genome: survey sequencing and comparative analysis. (jcvi.org)
Comparative expressed sequence tag analysis. (mpg.de)
A backbone map is the primary map that will serve as the anchor off of which all comparative maps loaded will locate their sequence. (animalgenome.org)

Most models of genome evolution concern either genetic sequences, gene content or gene order. (biomedcentral.com)

Conversely, translocations can also join two previously separate pieces of chromosomes together, resulting in a gain of synteny between loci. (wikipedia.org)
The new "spider‐specific" probes were used to sequence UCE loci in 51 specimens. (researchgate.net)

Single pass sequencing of cDNA clones provides a rapid route to gene discovery and production of EST's (2). (le.ac.uk)
Systematic sequencing of cDNA clones derived from xylem and leaf tissue will produce a new generation of research tools for conifer biology. (le.ac.uk)
Consider one thing: the human genome has been generated with BAC clones sequencing, while the chicken genome is probably done by shotgun sequencing. (biostars.org)

Synteny between the genome assemblies of four Eutypa lata isolates represented as circos plots. (figshare.com)
C) Genome synteny between isolates TAS7, B003, MA101 and 511-17. (figshare.com)
The multi-locus sequence type, presence of antimicrobial resistance (AMR) determinants, and relatedness between the isolates were derived from the sequence data. (who.int)

The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)

Resolving the complexity of the human genome using single-molecule sequencing. (nature.com)

Fluorescent in situ hybridisation (FISH) on metaphase chromosomes and on extended chromatin will be used to physically locate repetitive as well as single copy DNA sequences on conifer chromosomes and to integrate physical and genetic maps. (le.ac.uk)

When compared to the complete genome of C. elegans , evidence for conservation of long-range synteny and microsynteny was found. (biomedcentral.com)

If, on the other hand, A. nidulans and A. fumigatus are assumed to have lost 7-9 Mb of sequence after branching off from their A. oryzae -like ancestor, a greater proportion of syntenic blocks would be conserved between each of them and A. oryzae than between the two. (nature.com)

There is quite a good Wikipedia page on sequence alignment , if you need a simple guide or clarification. (biostars.org)

BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)

Synteny construction and visualization requires computational and bioinformatics skills to prepare input files for synteny analysis pipeline. (symapdb.org)
Evolutionary turnover may cause inconsistencies between sequence orthology and functional homology that substantially limit this type of analysis. (biorxiv.org)

Many computational methods for gaining functional insights from sequence data are based on the simple, but powerful, observation that functionally important nucleotides tend to remain unchanged over evolutionary time, because mutations at these sites generally reduce fitness and are therefore eliminated by natural selection 7 - 15 . (biorxiv.org)

In light of the more recent shift in the meaning of synteny, this conservation of gene content and linkage without preservation of order has also been termed mesosynteny. (wikipedia.org)
Whereas shared ancestry and functional constraints will increase conservation of linkage and synteny between taxa, rearrangement events will tend to randomize gene order over time. (biomedcentral.com)

Synteny blocks are coloured based on the reference sequence and query assembly is represented in grey. (figshare.com)

Illumina single nucleotide polymorphism (SNP) chips, kompetitive allele-specific PCR (KASP) assays, genotyping-by-sequencing (GBS)) and sequencing (e.g. (biomedcentral.com)

It is not trivial to build genome alignments accurately, and often require two core steps - generating anchors and chain anchors to form large unambiguous synteny blocks. (biostars.org)
So think of genome alignments as BLAST (find similar sequences) + CLUSTALW (align). (biostars.org)

The predicted structures of the Gimap proteins show common sequences and motifs, such as GTP-binding domains in the N-terminal half, but with differing C-terminal ends [ 2 , 3 ]. (hindawi.com)

Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. (nature.com)
This paper presents new structural and algorithmic results around the scaffolding problem, which occurs prominently in next generation sequencing. (biomedcentral.com)
This hands on course will give you additional experience in analyzing next generation sequencing data. (lu.se)
Detection of Tick-borne Bacteria from Whole Blood Using 16S Ribosomal RNA Gene PCR Followed by Next-Generation Sequencing. (cdc.gov)
To address these shortcomings, we developed a 16S ribosomal RNA (rRNA) gene PCR with next-generation sequencing approach to detect tick-borne bacteria in whole blood. (cdc.gov)

In current biology, synteny more commonly refers to colinearity, i.e. conservation of blocks of order within two sets of chromosomes that are being compared with each other. (wikipedia.org)
Yet, several regions of chromosomes in both mice and humans have maintained common gene order or synteny. (jove.com)

Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. (bioconductor.org)
In this work, we present a novel technique that builds on the straightforward observation that gene order conservation ('synteny') decreases in time as a result of gene mobility. (blogspot.com)

In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. (mdpi.com)

Study of synteny can show how the genome is cut and pasted in the course of evolution. (wikipedia.org)

Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)

Un-ambiguous orthologs were identified and synteny blocks anchored to these regions. (ubc.ca)

Contig IDs are labelled A) Genome synteny between E . lata isolate MA101 and isolate 511-17 and B) E . lata isolate MA101 and isolate TAS7. (figshare.com)

Fig. 5: Detecting methylated nucleotides using single-molecule sequencing. (nature.com)

A toolset for deciphering and managing biological sequences. (rdocumentation.org)

This suggests that the genome size differences are largely due to sequence acquisition in A. oryzae . (nature.com)

A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
Here, we present a web-based tool 'Evol2Circos' to give GUI- user-friendly and web-based tools for analyzing user-specific data for construction synteny and visualization, and to facilitate information browsing using different fish syntenic circos, bar, dual and dot plot. (symapdb.org)
We have generated fitCons scores for three human cell types based on public data from EN-CODE. (biorxiv.org)

Most pipeline also has built-in rules to make sure you are more likely to find orthologous sequences. (biostars.org)

Synteny was analysed as described in the Methods. (nature.com)

The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)

Fig. 2: Structural variant detection with long-read sequencing. (nature.com)
Fig. 4: Example of a novel isoforms discovered using long-read sequencing. (nature.com)

Anatomy4

Organisms16

Diseases2

Chemicals and Drugs3

Analytical, Diagnostic and Therapeutic Techniques and Equipment7

Phenomena and Processes30

Disciplines and Occupations2

Technology, Industry, Agriculture2

Information Science8

Genomic15

Genomes13

Genes24

Regions of conserved synteny1

Whole-genome2

Chromosome9

Phylogenetic3

Species8

Genomics6

Annotation1

Comparative4

Genome Evolution1

Loci2

Clones3

Isolates3

Transcriptome1

Human genome1

Genetic1

Microsynteny1

Syntenic blocks1

Alignment1

Primers1

Analysis2

Computational1

Linkage2

Assembly1

Polymorphism1

Alignments2

Proteins1

Next-generation5

Chromosomes2

Order2

Viral1

Evolution1

Contiguous1

Blocks1

Isolate1

Nucleotides1

Biological1

Largely1

Data3

Pipeline1

Methods1

Base pairs1

Long-read2