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At least 19 recordsLinked to original sources

PubMed2026

ntSynt-viz: Visualizing synteny patterns across multiple genomes.

With the explosion of chromosome-scale genome assemblies being generated in recent years, there is vast potential for comparative genomics analyses through detecting multi-genome synteny. While existing tools can detect synteny blocks between multiple genomes, their text-based outputs make it challenging to intuitively explore large-scale synteny patterns. Interpretable, information-rich and easy-to-use synteny visualization tools are imperative to enable important biological insights from the synteny block data output by the aforementioned utilities. Here, we present ntSynt-viz, a command-line tool for automated sorting, normalization and plotting of multi-genome synteny blocks. We show how ntSynt-viz provides clearer and more easily interpretable chromosome painting ribbon plots compared to the state-of-the-art tools NGenomeSyn and plotsr when evaluating synteny between 14 human genomes, and compared to NGenomeSyn when comparing 9 hoverfly genomes. As plotsr is limited to comparing genomes with equal chromosome numbers, it was not applicable to the hoverfly dataset. Furthermore, we demonstrate how ntSynt-viz can also be applied to visualize syntenic patterns encoded in pangenome graphs, using a Minigraph-Cactus graph built from 16 Drosophila genomes. We expect that ntSynt-viz will provide crucial insights into large-scale synteny patterns between divergent genomes, thereby advancing research into key evolutionary questions.

Synteny↗

PubMed1995

Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting.

By comparative gene mapping, extended conservation of synteny between different mammalian species has become apparent. Mapping in these species could be accelerated by exact visualization of the chromosomal segments that exhibit conserved synteny. We have hybridized human chromosome-specific DNA libraries onto porcine metaphase spreads to examine the extent of conservation of synteny between the two species. The hybridization signals on pig chromosomes are of variable quality, but the analysis allowed us to assign for all human autosomes homologous chromosomal segments in the pig karyotype. Extended conservation of synteny was observed, often comprising whole chromosomes. In our analysis 47 segments of conserved synteny common to the human and pig karyotype were identified. Intrachromosomal rearrangements by inversion within and between these segments are described. These rearrangements are common events during evolution. Our analysis shows that conservation of synteny between human and pig is three times more than between humans and mice and, consequently, is characterized by fewer, but larger conserved segments.

Animals↗

PubMed1995

Synteny-mapping horse microsatellite markers using a heterohybridoma panel.

A panel of horse-mouse heterohybridoma cells was tested for genetic markers using biochemical and polymerase chain reaction-(PCR-) based tests. Biochemical markers included phosphoglucomutase (PGM), glucose phosphate isomerase (GPI) and 6-phosphogluconate dehydrogenase (PGD). Markers detected using PCR-based tests included microsatellite markers HTG2-15, HMS 1-3, 5-8, VHL20, ECA2 and genes for equine major histocompatibility gene ELA-DRA, tumour necrosis factor alpha (TNFA) and transferrin. The results were analysed for correlation and concordance. Based on the results, five synteny groups were identified, specifically between ELA-DRA, TNFA, HMS5 and HTG5; between HTG3 and HTG13; between HTG4, HTG8 and HMS3; between HTG6 and HMS1; and between HTG7, HTG9 and HMS6. Evidence was also found for synteny between HTG12, HMS7 and ECA2, however, confirmation requires further testing. Cytogenetic evaluation of the cell lines making up the panel indicated that large metacentric chromosomes were preferentially lost or tended to break at the centromere. Consequently, the results from this analysis can be used to identify synteny, but not to exclude synteny.

Animals↗

PubMed1994

Assignment of bovine synteny groups U27 and U8 to R-banded chromosome 12 and 27, respectively.

Two microsatellite-containing cosmids, clOBT361 and clOBT355 were localized to bovine R-banded chromosome 12 and 27, respectively, by fluorescence in situ hybridization. The two microsatellites were subcloned from the cosmids and named INRA209 and INRA206, respectively. Primers were designed from the sequence information and used for PCR amplification with a panel of 36 previously characterized hamster/bovine somatic cell hybrids. This allowed the assignment of the two microsatellites to bovine synteny groups U27 and U8, respectively. The result permits the conclusion that bovine synteny U27 corresponds to BTA12 and that bovine synteny group U8 corresponds to BTA27, reducing to five the number of unassigned bovine synteny groups. Furthermore, as a high level of polymorphism was revealed by the two microsatellites, they have all the required characteristics for good genetic map markers.

Animals↗

PubMed1994

Assignment of bovine synteny group U2 to chromosome 9.

One cosmid containing a microsatellite (INRA144, D9S14) was assigned to bovine synteny group U2 by somatic cell genetics and localized to bovine chromosome 9q25 by fluorescent in situ hybridization. These results permitted the assignment of one more synteny group to a bovine chromosome. There are now 22 out of 31 bovine synteny groups which are related to a chromosome. The mapping data have been entered in the BovMap database, Jouy-en-Josas, France.

Animals↗

PubMed2025

Synteny plot quality control with SyntenyQC.

SUMMARY: SyntenyQC is a data pre-processing tool for the construction of synteny plots. It supports genomic data collection, annotation and dereplication to facilitate (and in some cases fundamentally enable) the construction of informative synteny plots. AVAILABILITY AND IMPLEMENTATION: SyntenyQC is a command line app developed using Python version 3.10 and tested using pytest. SyntenyQC is available on PyPI (https://pypi.org/project/SyntenyQC) under the MIT License, along with a detailed user tutorial. Package tests can be viewed at https://github.com/Tim-Kirkwood/SyntenyQC.

Synteny↗

PubMed1994

A set of 99 cattle microsatellites: characterization, synteny mapping, and polymorphism.

Cattle microsatellite clones (136) were isolated from cosmid (10) and plasmid (126) libraries and sequenced. The dinucleotide repeats were studied in each of these sequences and compared with dinucleotide repeats found in other vertebrate species where information was available. The distribution in cattle was similar to that described for other mammals, such as rat, mouse, pig, or human. A major difference resides in the number of sequences present in the bovine genome, which seemed at best one-third as large as in other species. Oligonucleotide primers (117 pairs) were synthesized, and a PCR product of expected size was obtained for 88 microsatellite sequences (75%). Synteny or chromosome assignment was searched for each locus with PCR amplification on a panel of 36 hamster/bovine somatic cell hybrids. Of our bovine microsatellites, eighty-six could be assigned to synteny groups of chromosomes. In addition, 10 other microsatellites--HEL 5, 6, 9, 11, 12, 13 (Kaukinen and Varvio 1993), HEL 4, 7, 14, 15--as well as the microsatellite found in the kappa-casein gene (Fries et al. 1990) were mapped on the hybrids. Microsatellite polymorphism was checked on at least 30 unrelated animals of different breeds. Almost all the autosomal and X Chr microsatellites displayed polymorphism, with the number of alleles varying between two and 44. We assume that these microsatellites could be very helpful in the construction of a primary public linkage map of the bovine genome, with an aim of finding markers for Economic Trait Loci (ETL) in cattle.

Animals↗

PubMed1994

Cloning by synteny: identifying C. briggsae homologues of C. elegans genes.

Phylogenetic comparisons of gene and protein sequences between related species are often used to identify evolutionarily conserved elements that are important for gene expression, function, or regulation. However, homologoues may sometimes be difficult to identify by conventional low stringency hybridisation techniques, if they have undergone substantial sequence divergence. A new approach, cloning by synteny, is described that was used to identify the C. briggsae homologue of the C. elegans sex-determining gene tra-2. We show that four genes tra-2, ppp-1, art-1, and sod-1 are organised in a syntenic cluster and suggest that extensive conservation of gene linkage may exist between C. briggsae and C. elegans. We have also constructed a C. briggsae cDNA library to facilitate characterisation of these genes. Given the rapid progress in the physical mapping and sequencing of the C. elegans genome, cloning by synteny may provide the fastest method for identifying C. briggsae gene homologues, especially for genes encoding novel proteins.

Amino Acid Sequence↗

PubMed1995

Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region.

In order to facilitate the map-based cloning of the barley stem rust resistance gene Rpg1, we have demonstrated a high degree of synteny at a micro level between the telomeric region of barley chromosome 1P and rice chromosome 6. We have also developed and applied a simple and efficient method for selecting useful probes from large insert genomic YAC and cosmid clones. The gene order within the most terminal 6.5 cM of barley chromosome 1P was compared with the most terminal 2.7 cM of rice chromosome 6. Nine rice probes, previously mapped in rice or isolated from YAC or cosmid clones from this region, were mapped in barley. All, except one, were in synteny with the rice gene order. The exception, probe Y617R, was duplicated in barley. One copy was located on a different chromosome and the other in a non-syntenic position on barley chromosome 1P. The barley probes from this region could not be mapped to rice, but two of them were inferred to be in a syntenic location based on their position on a rice YAC. This work demonstrates the utility of applying the results of genetic and physical mapping of the small genome cereal rice to map-based cloning of interesting genes from large genome relatives.

Chromosome Mapping↗

PubMed1983

Genetics and linkage relationships of the C3 polymorphism: discovery of C3-Se linkage and assignment of LES-C3-DM-Se-PEPD-Lu synteny to chromosome 19.

The C3 complement system was examined in our Danish material of normal families, which had earlier been examined for 59 marker systems, and in a myotonic dystrophy family material. A total of 8 alleles were recognized, with allele frequencies as follows: C3*S = 0.7902, C3*F = 0.2018, C3*S rare (3 lumped together) = 0.0036, C3*F rare (2 lumped together) = 0.0024; a silent allele was recognized in three families and its frequency estimated to C3*QO = 0.002. The distribution of unrelated individuals did not deviate significantly from the Hardy-Weinberg expectation, it was not significantly different between the sexes, and for none of the mating types was there any significant deviation from the expected ratios of children. As to linkage relationships of C3 with marker systems and with myotonic dystrophy, there was evidence (most of it first presented at the 6th International Congress of Human Genetics, Jerusalem 1981) for synteny with ABH secretion (Se): C3-Se (males) z = 4.35, theta = 0.12 and with Lewis secretion (LES): C3-LES (males z = 3.63, theta = 0.04). There were indicative or suggestive lod scores for Se-PEPD (males & females z = 2.41, theta = 0.00), C3-Lu (z = 1.88, theta = 0.15), C3-DM (z = 1.69, theta = 0.06) and PEPD-C3 (male z = 0.95, theta = 0.17). The most likely sequence of these 6 systems would appear to be LES-C3-DM-(Se-PEPD)-Lu and the synteny would reside on chromosome 19.

ABO Blood-Group System↗

PubMed1992

Synteny mapping of the bovine IGHG2, CRC and IGF1 genes.

A panel of bovine-murine hybrid cell lines was analysed for 10 loci, including three (IGF1, IGHG2 and the calcium release channel gene [CRC]) that have previously been mapped in man, but not in cattle. The IGF and CRC genes were indirectly mapped to chromosomes 5 and 18 respectively and the syntenies of the HOX2 and GH genes and of the NP and FOS genes were confirmed. The results also show that the IGHG2 locus, which is linked to NP and FOS on human chromosome 14, is separated from these genes in cattle. By showing synteny of the IGHG2 and MPI loci, the IGHG2 locus has been indirectly mapped to chromosome 21.

Animals↗

PubMed1992

[Homology and evolution of gene orders: combinatorial measure of synteny group similarity and simulation of the evolution process].

Combinatorial measure of synteny group similarity allowing quantitative comparison of evolutional divergence of genomes with the known distribution of homologous genes along the chromosomes is proposed. Computer simulation of chromosome evolution process resulting in gene localization changes was performed. It is sufficient to fix about 50 large rearrangements, like chromosome breakages, fusions and translocations for disappearance of significant similarity between the daughter and parental genomes, in respect of gene distribution in synteny groups.

Biological Evolution↗

PubMed1995

Genomic reorganization and disrupted chromosomal synteny in the siamang (Hylobates syndactylus) revealed by fluorescence in situ hybridization.

We employed in situ hybridization ("chromosome painting") of chromosome-specific DNA libraries of all human chromosomes to establish homologies between the human and siamang karyotypes (Hylobates syndactylus, 2n = 50). Numerous intra- and interchromosomal rearrangements have led to a massive reorganization of the siamang karyotype. There have been a minimum of 33 translocations. The 24 siamang autosomes are composed of 60 recognizable segments that show DNA homology to regions of the 22 human autosomes. Only two autosomes have not been involved in translocations. The siamang presents a case, in a primate closely related to humans, in which chromosome morphology and synteny are highly disturbed in a manner similar to that encountered among rodents.

Animals↗

PubMed1994

Characterization of the goat lactoferrin cDNA: assignment of the relevant locus to bovine U12 synteny group.

Lactoferrin (LTF), which is the major iron-binding protein in milk and physiological fluids, belongs to the transferrin family. We report here the sequence of a caprine LTF cDNA, 2411 bp in length, encoding the pre-protein (709 amino acid residues). Sequence comparisons reveal that structural features, including iron-binding sites, cysteine residues involved in disulphide bonds are remarkably conserved between LTF proteins from various species. Of the 5 potential glycosylation sites identified, only one site appears to be conserved between artiodactyls, rodents and humans. Using a somatic cell hybrid panel, the LTF locus was assigned to the bovine U12 syntenic group. This assignment and the localization of the LTF gene on bovine chromosome 22 (BTA 22) by Schwerin et al. (1) using fluorescent in situ hybridization achieves an additional analogy between a synteny group and a chromosome in cattle. Since serum transferrin (STF) had been previously mapped on BTA 1, in cattle LTF and STF loci are not localized on the same chromosome, conversely to the situation observed in humans (HSA 3) and mice (MMU 9).

Amino Acid Sequence↗

PubMed1994

Mapping of the gene for the tyrosine kinase Itk to a region of conserved synteny between mouse chromosome 11 and human chromosome 5q.

The protein-tyrosine kinase gene Itk is expressed preferentially in T lymphoid cells of the mouse and is induced by IL-2. A related gene, Btk, is expressed in the murine B lymphoid and myeloid lineages. Because mutations in Btk and the corresponding human gene are associated with X-linked immunodeficiency syndromes, it was of interest to map Itk and its human counterpart. By Southern blot analysis of DNA from the progeny of two multilocus crosses, murine Itk was mapped to Chromosome 11. By fluorescence in situ hybridization, human ITK was mapped to 5q32-q33. Murine Itk and its human homologue lie within regions of conserved synteny that include several growth factor and growth factor receptor genes. This region in humans is frequently deleted in the myelodysplastic syndrome, suggesting possible involvement of ITK in this disorder.

Agammaglobulinaemia Tyrosine Kinase↗

PubMed1989

Regional localization of the TIMP gene on the human X chromosome. Extension of a conserved synteny and linkage group on proximal Xp.

The gene encoding a tissue inhibitor of metallo-proteinases, TIMP, has previously been shown to be X-linked in both the human and mouse genomes. We have used a series of somatic cell hybrids segregating translocation and deletion X chromosomes to map the TIMP gene on the human X chromosome. In combination with previous data, the gene can be assigned to Xp11.23----Xp11.4. Genetic linkage analyses demonstrate that TIMP is linked to the more distal ornithine transcarbamylase (OTC) locus at a distance of about 22 centimorgans. The data are consistent with the conclusion that TIMP maps to a conserved synteny and linkage group on the proximal short arm of the human X chromosome and on the pericentric region of the mouse X chromosome, including loci for synapsin-1, a member of the raf oncogene family, OTC, and TIMP.

Animals↗

PubMed1994

Synteny conservation of the Huntington's disease gene and surrounding loci on mouse Chromosome 5.

The mouse homologs of the Huntington's disease (HD) gene and 17 other human Chromosome (Chr) 4 loci (including six previously unmapped) were localized by use of an interspecific cross. All loci mapped in a continuous linkage group on mouse Chr 5, distal to En2 and I16, whose human counterparts are located on Chr 7. The relative order of the loci on human Chr 4 and mouse Chr 5 was maintained, except for a break between D5H4S115E and Idua/rd, with relocation of the latter to the opposite end of the map. The mouse HD homolog (Hdh) mapped within a cluster of seven genes that were completely linked in our data set. In human these loci span a approximately 1.8 Mb stretch of human 4p16.3 that has been entirely cloned. To date, there is no phenotypic correspondence between human and mouse mutations mapping to this region of synteny conservation.

Animals↗

PubMed1975

Synteny between the pro+ marker and human glutamate oxaloacetate transaminase.

Chinese hamster ovary cells with a specific auxotrophy for proline were fused with human cells from a variety of sources and the resulting hybrids analyzed for human genetic markers. Of 63 hybrid clones examined, 27 possessed both proline and cytoplasmic glutamate oxaloacetate transaminase markers; 36 had neither; and no clones were found possessing one and not the other. These results constitute evidence that the proline and glutamate oxalocetate transaminase markers are syntenic. Evidence for absence of synteny between these and a variety of other human genes is presented. Biochemical tracer experiments established that the proline biosynthetic pathway through glutamate has been restored in the Pro+ hybrids.

Animals↗