Syntenic cross species chromosome. Medical search. Frequent questions

All beta-defensin genes are densely clustered in four to five syntenic chromosomal regions. (wikipedia.org)
The beta-defensin genes mapped closely on rat chromosome 16 and were closely linked to the alpha-defensins genes, suggesting that they are part of a gene cluster, similar to the organization reported for humans. (lookformedical.com)
Homologene links require common annotation across species allowing the genes to be identified as homologues. (animalgenome.org)
Supplementary Table 7: Gene categories enriched for duplications on each branch of the D. dunni species phylogeny, relative to unduplicated genes. (figshare.com)
A cross-species comparison of genomic sequences can help in predicting genes in the given query sequence. (biomedcentral.com)
The application of directed introgressive hybridization allows for agronomically important crops to integrate genes from closely related species and serves as an important method for the introduction of beneficial traits from one species of crop cultivar to another [ 1 ]. (biomedcentral.com)
Distribution and expression of the genes on chromosome 1. (nature.com)
Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and Brachypodium discovered 4,035 OrthoMCL groups as preliminary candidates of Wsm2 orthologs. (peerj.com)
The wild tomato species, Solanum pennellii , is reported to harbor broad resistance to Fol and was the source of two known Fol3 resistance genes. (ashs.org)
The genes which determine the character of an individual are carried by the chromosomes. (brainkart.com)
The genes for different characters may be present either in the same chromosome or in different chromosomes. (brainkart.com)
When the genes are present in different chromosomes, they assort independently according to Mendel's Law of Independent Assortment. (brainkart.com)
So they concluded that genes for purple colour and long pollen grain and the genes for red colour and round pollen grain were found close together in the same homologous pair of chromosomes. (brainkart.com)
But the two genes that are sufficiently far apart on the same chromosome are called unlinked genes or syntenic genes (Figure 3.3). (brainkart.com)
The linked genes are located very close together on the same chromosome such genes do not exhibit crossing over. (brainkart.com)
The groups of linearly arranged linked genes on a chromosome are called Linkage groups . (brainkart.com)
These findings suggest a scenario where collisions between DNA replication and transcription are frequent, leading to increased genetic variability, as seen by the increase SNP levels at chromosome subtelomeres and in DGF-1 genes containing putative origins. (biomedcentral.com)
Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. (biomedcentral.com)
Synteny in classical terms refers to the genes present on the same chromosome, like beads on the same string. (jove.com)
These genes are said to be syntenic in species X. (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)
In addition, the genes present in common chromosomal regions in two or more species, like the genes A, B and C, represent a conserved syntenic segment or conserved syntenic blocks. (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)
The elegant and original use of a probabilistic model of segregating alleles (implemented in the SEX-DETector method) allowed to identify both the sex and self-incompatibility loci [4], while this tool was initially developed for detecting sex-linked genes in species with strictly separated sexes (dioecy) [5]. (peercommunityin.org)

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)

In the absence of a finished quality genome sequence, insights into wheat genome structure and function have been accumulating through survey sequencing of individual chromosomes or chromosome-specific Bacterial Artificial Chromosome (BAC) libraries. (biomedcentral.com)
The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. (biomedcentral.com)

However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. (bvsalud.org)
Orthologous markers transferable between distantly related legume species allow for the rapid generation of genetic maps in species where there is little pre-existing genomic or EST information. (edu.au)
Background: The development of genetic markers is complex and costly in species with little pre-existing genomic information. (edu.au)
Some extrinsic methods use genomic sequences from other species. (biomedcentral.com)
Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. (biomedcentral.com)
Wsm2 is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. (peerj.com)
Recent progress in genome assembly of the sex chromosomes and the availability of population genomic datasets have now made it possible to study divergence and diversity processes of this important region in detail. (biomedcentral.com)

In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. (biomedcentral.com)

Sequence evolution of the pseudoautosomal region after the split between the avian and mammalian lineages, and leading up to extant mammalian species, involved the formation of several evolutionary strata mediated by recombination suppression between the sex chromosomes [ 18 , 19 , 20 ]. (biomedcentral.com)
In addition, orphan receptors similar to mammalian costimulatory receptors such as CD28 upon the T cell have been reported in fish species ( 6 , 7 ). (aai.org)
This indicates that an ancestral mammalian chromosome evolved into chromosome 16 in the tree shrew, and also the long arm of chromosome 10 in humans. (jove.com)

It allowed mapping of the ASGR locus and apospory phenotype to linkage group 3, in a region syntenic with chromosome 3 of Urochloa ruziziensis and chromosome 1 of Setaria italica. (bvsalud.org)
In any species the number of linkage groups corresponds to the number haploid set of chromosomes. (brainkart.com)

If dominant or recessive alleles are present on two different, but homologous chromosomes they inherit apart into different gamete are called repulsion or trans configuration (Figure: 3. (brainkart.com)
However, these maps will now be anchored to a new, different backbone and therefore, different homologous regions from different chromosomes may be loaded as well. (animalgenome.org)

Although a direct and simple syntenic relationship was observed between M. truncatula and Lens culinaris genomes, there is evidence of moderate chromosomal rearrangement. (edu.au)
The blue bars at the bottom indicate the regions syntenic with A. fumigatus ( AF ) and A. nidulans ( AN ) genomes (see Methods). (nature.com)
This is due to the complexity of their small (~1.5Mb) but fragmented genomes that typically consist of a linear chromosome and both linear and circular plasmids. (cdc.gov)
Consequently, our goal was to generate complete, plasmid-resolved genomes for a comparative analysis of sTBRF species of the Western Hemisphere. (cdc.gov)
the Genomes FTP repository , containing genome and genome annotation data files (including FASTA, GFF and GTF files) for D. melanogaster and other Drosophila species, organized by genome/FlyBase release number. (flybase.org)
Unfortunately, since we don't quite know how to construct viable genomes of extinct species, much less grow the creatures themselves, we don't know whether the depiction of the science is right. (genomevisualization.com)

These sequence-based comparisons from UCSC define the anchors to allow cross-species comparisons across physical maps. (animalgenome.org)
Genome sequence comparisons across species using bioinformatics revealed three members of the RCAN gene family, RCAN1 , RCAN2 , and RCAN3 , present in most jawed vertebrates, with one member observed in most invertebrates and fungi. (molcells.org)
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)
This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. (biomedcentral.com)
Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. (biomedcentral.com)
The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. (biomedcentral.com)

Chromosome 8p23 contains at least two copies of the duplicated beta-defensin cluster. (wikipedia.org)

For example, users can view synteny/homologue blocks and homology lines across species for specific regions while hiding other, less interesting portions of the chromosome. (animalgenome.org)
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)
Yet, several regions of chromosomes in both mice and humans have maintained common gene order or synteny. (jove.com)

To investigate the variation and evolution of the E genome, we developed a complete set of E genome-specific painting probes for identification of the individual chromosomes 1E to 7E based on the genome sequences of Th. (bvsalud.org)
CONCLUSIONS: To truly understand the biological differences observed between species of TBRF spirochetes, complete chromosome and plasmid sequences are needed. (cdc.gov)

VCMap can be used for many tasks such as: comparing QTL across species, viewing evolutionary rearrangements across species, comparing genome builds within species, comparing different map types within species, and so on. (animalgenome.org)
The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. (biomedcentral.com)
PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species. (biomedcentral.com)
Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular cultivated species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. (biomedcentral.com)
What is lacking, however, is a robust phylogenetic framework that encompasses species and generic diversity across the family in order to maximise the potential of these new data sources in a wider evolutionary context. (biomedcentral.com)

Supplementary Figure 1: Phylogeny of the dunni group relative to other Drosophila species. (figshare.com)
. C.B Bridges (1919) discovered that crossing over is completely absent in some species of male Drosophila . (brainkart.com)

Syntenic regions on the same chromosome (shown as Muller elements, A-F) are labelled with grey ribbons, while syntenic regions between difference chromosomes are labelled in red. (figshare.com)
When other comparative maps are loaded on top of that backbone, they will load all chromosomes that have syntenic regions that fall on the single chromosome of the backbone map, usually from more than one chromosome. (animalgenome.org)
The species with common ancestry tend to show conserved syntenic regions. (jove.com)

Expression levels of RCAN homologs are responsive to external stressors such as reactive oxygen species, Ca 2+ , amyloid β, and hormonal changes and upregulated in pathological conditions, including Alzheimer's disease, cardiac hypertrophy, diabetes, and degenerative neuropathy. (molcells.org)
Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. (biomedcentral.com)

2012). Virtual Comparative Map (VCMap): A comparative genomics tool designed to facilitate cross-species annotation. (animalgenome.org)
The GUI is also designed to allow users to load their own private annotations and genomics data to facilitate information comparison across species to meet the ultimate researcher-driven goal of comparative genomics. (animalgenome.org)
VCMap was designed to fill a gap in the need for genomics viewers to compare QTL and annotations across species at a chromosomal level with multiple map types. (animalgenome.org)

PHAN HTT , ELLWOOD SR, FORD R, THOMAS S &OLIVER R (2006) Differences in syntenic complexity between Medicago truncatula with Lens culinaris and Lupinus albus. (edu.au)

With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 correctly. (biomedcentral.com)
We extracted whole-cell protein lysates from RF Borrelia cultures and synthesized six recombinant RF antigens (Borrelia immunogenic protein A (BipA) derived from four species of RF Borrelia, glycerophosphodiester phosphodiesterase (GlpQ), and Borrelia miyamotoi membrane antigen A (BmaA)) to detect reactivity in laboratory derived (Peromyscus sp. (cdc.gov)
Segregation among soft tick RF species (Borrelia hermsii, Borrelia parkeri and Borrelia turicatae) was inadequate (58%) owing to observed cross-reactivity among recombinant BipA protein targets. (cdc.gov)
Although not adequately specific to accurately categorize exposure to soft tick RF species, the recombinant BipA protein targets from soft and hard tick RF species show utility in accurately discriminating mouse exposures to LD or RF Borrelia, and accurately segregate hard tick from soft tick RF Borrelia exposure. (cdc.gov)

These ancestral chromosomes would have undergone several rounds of chromosome rearrangement, fusion or breakage, facilitating diversity and speciation into the primate species of today. (jove.com)
During the course of evolution, the ancestral chromosome underwent several rearrangements, breakage, and fusion events to evolve into the chromosomes of mice and humans. (jove.com)
For example, it took around 180 chromosomal breakage-and-rejoining events for the evolution of ancestral chromosomes into human and mice chromosomes. (jove.com)

Supplementary Table 3: Table showing average synonymous divergence between each species pair. (figshare.com)
Here we investigate molecular divergence times for Solanaceae using a densely-sampled species-level phylogeny. (biomedcentral.com)

These variable loops contribute significantly to corresponding gene expression variability across cells and species, possibly by refining sub-TAD-scale loop contacts responsible for cell-type-specific enhancer-promoter interactions. (nature.com)

Even though VCMap only loads a single chromosome at a time, in most cases, it is still impossible to display all of the available features for that chromosome at once. (animalgenome.org)

Supplementary Figure 6: Proportion of gene categories with enrichments of duplications in D. nigrodunni (D. nig), D. arawakana (D. ara) or both species. (figshare.com)

Here, we provide a chromosome-specific view into the organization and evolution of the D genome of bread wheat, in comparison to one of its ancestors, revealing recent genome rearrangements. (biomedcentral.com)

1) across the entire phylogeny and on each species branch, also the upper outliers for D. nigrodunni and D. arawakana relative to the other species. (figshare.com)
Our large time-calibrated phylogeny provides a significant step towards completing a fully sampled species-level phylogeny for Solanaceae, and provides age estimates for the whole family. (biomedcentral.com)

They have been isolated in several species, and in humans, two beta-defensins have been identified. (lookformedical.com)

The regulator of calcineurin (RCAN) was first reported as a novel gene called DSCR1, encoded in a region termed the Down syndrome critical region (DSCR) of human chromosome 21. (molcells.org)
The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. (biomedcentral.com)
Induction of apoptosis by cross-linking antibodies certain to human B-lymphoma cells: expression of Annexin V binding websites on the antibody cap. (ncbcs.org)

Included in the analysis were the two recently isolated species from Central and South America, Borrelia puertoricensis n. sp. (cdc.gov)

Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. (biomedcentral.com)
However, we observed an almost equal proportion of syntenic blocks in the three species. (nature.com)
During the course of evolution, species undergo random mutations, survive natural selection and evolve into several lineages all while mostly maintaining conserved syntenic blocks over many chromosomes. (jove.com)

KEY MESSAGE: Chromosome-specific painting probes were developed to identify the individual chromosomes from 1 to 7E in Thinopyrum species and detect alien genetic material of the E genome in a wheat background. (bvsalud.org)

Supplementary Figure 2: Proportion of females surviving each day, for each species used in each cross, compared to virgin female survival. (figshare.com)

Solanaceae are a particularly interesting angiosperm family, not only because they include many major crop species (e.g., potato - Solanum tuberosum , tomato - S. lycopersicum , eggplant - S. melongena , sweet and chili peppers - Capsicum spp. (biomedcentral.com)

PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. (biomedcentral.com)

SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research. (bvsalud.org)
To enable genetic improvement of the untapped, important species, we obtained a 7.85-Gb high-quality genome of L. chinensis with a particularly long contig N50 (318.49 Mb). (bvsalud.org)
This will enable the construction of comparative genetic maps, help to determine patterns of chromosomal evolution in the legume family, and characterise syntenic relationships between M. truncatula and cultivated legumes. (edu.au)
In addition to 126 M. truncatula cross-species markers from Department of Plant Pathology, University of California (USA), these markers were used to generate comparative genetic maps of lentil (Lens culinaris Medik. (edu.au)
A Syntenic Cross Species Aneuploidy Genetic Screen Links RCAN1 Expression to β-Cell Mitochondrial Dysfunction in Type 2 Diabetes. (lu.se)

Since vector abundance constitute one of the foremost factors in malaria transmission, we have created several habitat suitability models to describe this vector species' current distribution. (researchgate.net)
suitability models to describe this vector species' current distribution. (researchgate.net)

Trypanosoma cruzi , the etiological agent of Chagas disease, presents high variability in both chromosomes size and copy number among strains, though the underlying mechanisms are unknown. (biomedcentral.com)

In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice ( Oryza sativa ) and Brachypodium distachyon . (peerj.com)

Crosses following curing of the strain with Tetracycline-Hydrochloride. (figshare.com)

It has been built with multiple features that allow researchers to customize comparative views across species. (animalgenome.org)

To allow integration of annotation and QTL across species, a trait ontology (Vertebrate Trait Ontology, VTO) (3) is used to allow users to select related phenotype annotations to meet these goals. (animalgenome.org)

These observations suggest that fish species might have APCs and a costimulatory system. (aai.org)

Avian MHC organization is of particular interest because the chicken Gallus gallus , the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. (biomedcentral.com)

These findings led to the hypothesis that chromosome structure directly influences cellular phenotypes. (nature.com)

Chromatin looping is important for gene regulation, and studies of 3D chromatin structure across species and cell types have improved our understanding of the principles governing chromatin looping. (nature.com)

The increased resolution in the chronogram combined with the large increase in species sampling will provide much needed data for the examination of many biological questions using Solanaceae as a model system. (biomedcentral.com)

Size of other chromosome. (ucsc.edu)

The guided user interface (GUI) provides chromosomal level views optimized for quantitative trait locus (QTL) visualization and comparison of QTL across species. (animalgenome.org)
B. Comparison of TE content across species and if that content is shared between species or is unique to one species. (figshare.com)

Among the Papilionoideae, we compared ESTs from the phylogenetically distant species, M. truncatula, Lupinus albus and Glycine max, to produce 500 intron-targeted amplified polymorphic markers (ITAPs). (edu.au)

This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. (bvsalud.org)

For the backbone map, you must specify a single chromosome to be loaded at a time. (animalgenome.org)

Anatomy63

Organisms25

Diseases21

Chemicals and Drugs23

Analytical, Diagnostic and Therapeutic Techniques and Equipment25

Psychiatry and Psychology1

Phenomena and Processes165

Disciplines and Occupations3

Technology, Industry, Agriculture4

Information Science6

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Genes26

Presence of syntenic1

Bacterial Artificial2

Genomic7

Wheat chromosome1

Mammalian3

Linkage2

Homologous2

Genomes6

Sequence6

Beta-defensin1

Synteny4

Sequences2

Evolutionary5

Drosophila2

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Reactive oxygen2

Genomics3

Complexity1

Protein4

Ancestral3

Divergence2

Gene expression1

VCmap1

Duplications1

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Humans1

Human3

Analysis1

Blocks3

Individual1

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Solanum1

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Genetic5

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