Synteny and genome. Medical search. Frequent questions

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)
Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans 5 and Aspergillus fumigatus 6 . (nature.com)
The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (nature.com)
Using genome assemblies from across the Apicomplexa (which includes malaria and toxoplasmosis parasites) it was shown that genetic synteny (genes arranged in the same groupings in different genomes) was substantially less than expected from animal genomes, suggesting that the parasite genomes have undergone major rearrangements or that their most recent common ancestor is more ancient than previously thought. (wikipedia.org)
All genomes encode conserved genes. (biomedcentral.com)
In both studies, regions of 'double synteny' (DS) were identified in which single genes or groups of genes expressed homology relationships with alternating chromosomal regions of S. cerevisiae . (biomedcentral.com)
Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L. (biomedcentral.com)
Here, we use a computational approach to perform genome-wide identification and analysis of 611 orthologues of the Arabidopsis thaliana flowering genes. (springer.com)
Conservation of the genes belonging to the photoperiod, gibberellin and autonomous pathways was observed, while orthologues of the key genes found in the vernalisation pathway (FRI, FLC) were absent from the quinoa genome. (springer.com)
A portion of the rice genome has been examined in order to evaluate the feasibility of using rice as a surrogate genome for map-based cloning of maize genes. (biomedcentral.com)
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)
In this study, we first identified all the CAMTA homologous genes in the whole genome of maize. (frontiersin.org)
2007. Evolution of genes and genomes on the Drosophila phylogeny. . (umd.edu)
Using a 454 sequencing-based approach, SNPs have been identified in genes across the lentil genome. (usda.gov)
In this work, a genome-wide identification of the bHLH genes in Chinese white pear was performed, and we characterized the functional roles of these PbrbHLH genes in response to abiotic stresses. (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)
Then, we selected 48 genes that may encode uncharacterised effectors (e. g. no detectable amino acid identity to other proteins or with a particular putative biochemical activity) from the genome of C. trachomatis strain L2/434/Bu. (europa.eu)
In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. (who.int)

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. (mpg.de)
Our research in plant and animal genomes, at the whole genome and transcriptome levels, will impact successful genetic selections toward the goal of feeding the 9 billion people toward the year 2050. (bio5.org)

Synteny between the genome assemblies of four Eutypa lata isolates represented as circos plots. (figshare.com)
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)
Despite the wealth of genomic data generated in past years, chromosomal level genome assemblies currently exist for only two species, Heliconius melpomene and Heliconius erato, each a representative of one of the two major clades of the genus. (bvsalud.org)
Here, we use these reference genomes to improve the contiguity of previously published draft genome assemblies of 16 Heliconius species. (bvsalud.org)
The genome assemblies and functional annotations of scallop species are also available in the MolluscDB database ( http://mgbase.qnlm.ac/page/download/download ). (nature.com)
Are they 'redone' between different genome assemblies? (biostars.org)
Are they re-done as genome assemblies are revised? (biostars.org)

Synteny blocks are coloured based on the reference sequence and query assembly is represented in grey. (figshare.com)
However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. (biomedcentral.com)
Thus, the increase in genome size seems to be due to an A. oryzae lineage-specific acquisition of sequence, rather than loss of sequence in A. nidulans and A. fumigatus . (nature.com)
This suggests that the genome size differences are largely due to sequence acquisition in A. oryzae . (nature.com)
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)
Comparison of B. malayi BAC-end genome survey sequence to C. elegans also revealed a bias towards intrachromosome rearrangements. (biomedcentral.com)
2003 ). In 2017, the first chromosome-scale reference genome sequence of quinoa was published, and it has provided the much-needed resource for plant biologists to design molecular breeding and crop improvement programs for quinoa (Jarvis et al. (springer.com)
The genome sequence of quinoa serves as an entry point for deciphering the complex molecular pathways that contribute to floral evocation. (springer.com)
Although, the sequence of Chinese white pear genome (cv. (biomedcentral.com)

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)
Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study. (biomedcentral.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)
Two groups have attempted to assess genome rearrangement rates and modes in comparisons between these two species. (biomedcentral.com)
Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus. (bvsalud.org)
Genome sizes are somewhat variable among species (270-422 Mb) and in one small group of species (Heliconius hecale, Heliconius elevatus, and Heliconius pardalinus) expansions in genome size are driven mainly by repetitive sequences that map to four small regions in the H. melpomene reference genome . (bvsalud.org)
strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. (frontiersin.org)
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)
In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. (mdpi.com)
1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. (jcvi.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)
As Wookiees are a humanoid species, we postulate that when an all-against-all comparison is done with the Wookiee wookiee and Homo Sapien genomes, a portion of the Wookie genome will be distinct. (ubc.ca)
Otherwise, the absence of the phenotypic characteristics of plausible orthologs was attributed to the theorized inactivation within the genomes of other humanoid species. (ubc.ca)
Shared synteny (or disruption, called breakpoints) can be used as phylogenetic signals to sort out species relationship. (biostars.org)

We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae , (2) reconstruction of gene arrangements ancestral to A. gossypii , S. cerevisiae , and K. waltii , (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. (biomedcentral.com)
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. (mpg.de)
Most models of genome evolution concern either genetic sequences, gene content or gene order. (biomedcentral.com)
AGI has earned a reputation for providing extremely high-quality maps, as documented in previous sequencing efforts leading to the genome sequences of rice and corn. (bio5.org)
So think of genome alignments as BLAST (find similar sequences) + CLUSTALW (align). (biostars.org)

Comparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. (biomedcentral.com)
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)
We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization. (biomedcentral.com)
Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement. (mpg.de)
We study statistical estimators of the number of genomic events separating two genomes under a Double Cut-and Join (DCJ) rearrangement model, by a method of moment estimation. (biomedcentral.com)

The genome was confirmed to comprise eight chromosomes (chromosomes 1-8 in decreasing size), the assignment of which is different from a previous report 7 ( Supplementary Table S1 and schematic drawing in Supplementary Fig. S1 ). (nature.com)
Using a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto chromosomes , resulting in 95.7-99.9% of their genomes anchored to chromosomes . (bvsalud.org)
The existence of syntenic patterns between ancestral gene sets and A. gossypii , S. cerevisiae , and K. waltii , and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. (biomedcentral.com)
Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies. (nature.com)

The work should be of interest to colleagues in the fields of evolutionary biology, chromatin biology and genome biology. (elifesciences.org)
Genome Biology 8 (5), p. (mpg.de)
Part of Genome Biology , 2023. (uu.se)

The limitations of current methods are particularly evident in the vast noncoding regions of eukaryotic genomes, which, despite important recent progress 3 - 6 , remain poorly annotated and understood. (biorxiv.org)

Phylogenetic analysis of the three aspergilli using the whole-genome data showed that A. nidulans branched off earlier than A. oryzae and A. fumigatus 5 . (nature.com)
Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii . (biomedcentral.com)
The problem of reconstructing ancestral genomes in a given phylogenetic tree arises in many different comparative genomics fields. (biomedcentral.com)

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements. (jax.org)

When compared to the complete genome of C. elegans , evidence for conservation of long-range synteny and microsynteny was found. (biomedcentral.com)
Recently, a complete genome from a gray seal infected by a parapoxvirus was reported and constituted a putative novel virus in this genus ( 1 ). (cdc.gov)

In 2012 her lab helped develop a computational tool, MCScanX, to identify synteny across genomes, which has been cited >650 times. (wikipedia.org)
We describe a novel computational method for estimating the probability that a point mutation at each position in a genome will influence fitness. (biorxiv.org)

Here we report an update to the C. livia genome reference assembly and gene annotation dataset. (nih.gov)

Chromosome level reference genome for European flat oyster (Ostrea edulis L. (ed.ac.uk)
Dive into the research topics of 'Chromosome level reference genome for European flat oyster (Ostrea edulis L.)'. Together they form a unique fingerprint. (ed.ac.uk)

A gene-based map of the lentil genome has been developed that has been used to identify regions of conserved synteny with Medicago truncatula. (usda.gov)

Her research focus is on the evolution, assembly and data curation of protozoan parasite genomes, particularly Cryptosporidium, Toxoplasma gondii and Plasmodium. (wikipedia.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)
Construction of comprehensive, informative second generation linkage maps for three Conifer genomes. (le.ac.uk)

C) Genome synteny between isolates TAS7, B003, MA101 and 511-17. (figshare.com)

Human gene to disease annotations are now from the Alliance of Genome Resources. (jax.org)
Polymorphic sites tend to be sparse along the genome, however, so this approach requires some type of pooling of information across genomic positions, which can be difficult in the absence good-quality genomic annotations. (biorxiv.org)

I remember the difference between algorithms for global/local alignments but I don't remember using genome alignments. (biostars.org)
See VISTA's enhancer database , and pay attention to how they use the genome alignments to extract candidates. (biostars.org)
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)
UCSC genome browser offer downloads for pre-built alignments, in MAF format . (biostars.org)

In addition, fitCons scores indicate that 4.2-7.5% of nucleotides in the human genome have influenced fitness since the human-chimpanzee divergence, and, in contrast to several recent studies, they suggest that recent evolutionary turnover has had limited impact on the functional content of the genome. (biorxiv.org)
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)

In protostomes, comparative studies of the genomes of closely related dipterans ( Drosophila sp. (biomedcentral.com)

Here, we focus on reconstructing the gene order of ancestral genomes, a proble. (biomedcentral.com)

Sequencing of the A. oryzae genome was accomplished using the whole-genome shotgun (WGS) approach. (nature.com)
Systematic analysis of the chloroplast and its photosynthetic machinery has begun, using a combination of two-dimensional gels, mass spectroscopy, protein sequencing and genome databases. (biomedcentral.com)
The dog genome: survey sequencing and comparative analysis. (jcvi.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)
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)

The population of P. aeruginosa was diverse, with clonal expansions of XDR genomes belonging to MLSTs ST235, ST244, ST309 and ST773. (who.int)

2002. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. . (umd.edu)

The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. (biomedcentral.com)
A whole genome duplication event occurred 25 to 100 million years ago in the common ancestor of the salmonids. (biomedcentral.com)
Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event? (biomedcentral.com)
Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Saccharomyces cerevisiae . (biomedcentral.com)
This is clearly incompatible with an ancient genome duplication event in S. cerevisiae . (biomedcentral.com)
Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns. (biomedcentral.com)
The existence of an ancient whole-genome duplication (WGD) event in Saccharomyces cerevisiae [ 1 ] has been debated over the past several years. (biomedcentral.com)
These may include synteny (see this resource on yeast genome synteny ) or large-scale rearrangements: duplication, deletion, inversion. (biostars.org)

The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. (researchgate.net)

Timing and mechanism of ancient vertebrate genome duplications - the adventure of a hypothesis. (mpg.de)

2004. Gene synteny and evolution of genome architecture in trypanosomatids. . (umd.edu)
2012. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. . (umd.edu)
His recent research on Citrus tristeza virus has revealed its genome stability, unusual for an RNA virus, and the promiscuous recombination between viral strains as the major factor driving Citrus tristeza virus evolution. (bio5.org)

The blue bars at the bottom indicate the regions syntenic with A. fumigatus ( AF ) and A. nidulans ( AN ) genomes (see Methods). (nature.com)

The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain. (jax.org)

The characterization of BES provided insights on the rainbow trout genome. (biomedcentral.com)

The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. (biomedcentral.com)
2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes . (umd.edu)
This gene has no protein-coding homolog in any other genome but its presence is supported by evidence from expression and hybridization data. (ubc.ca)

Un-ambiguous orthologs were identified and synteny blocks anchored to these regions. (ubc.ca)
This means that in the chicken genome, all the duplicated regions will be clustered together, and there it will be more holes in the most repetitive regions. (biostars.org)

Genome Biol Evol;13(7)2021 07 06. (bvsalud.org)

Beyond the creation of databases, Kissinger focuses on the analysis and comparison of parasite genomes. (wikipedia.org)
Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. (frontiersin.org)

The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. (mdpi.com)
Most of the ST235 genomes formed a distinct lineage from global genomes, thus raising the possibility that they may be unique to the Philippines. (who.int)

Considerable progress has been achieved in Conifer genome mapping by the use of megagametophyte tissue and RAPDs (3). (le.ac.uk)

The expansion in genome size appears to be characteristic of the organisms closely related to A. oryzae , as the estimated genome size of its close relatives A. flavus (W. Nierman, personal communication) and Aspergillus niger 8 is comparable to that of A. oryzae . (nature.com)
Genome alignment obviously makes most sense for organisms that are more closely-related. (biostars.org)

Query contigs have been ordered based on synteny length to reference. (figshare.com)

At least 11 complete orf virus genomes are available, and at least 19 are available for the entire genus Parapoxvirus . (cdc.gov)

Find conserved synteny and genome rearrangements. (biostars.org)

1.1 Objectives The main objective of the proposed research is to improve our basic understanding of genome organisation in conifers. (le.ac.uk)

The JAX Synteny Browser for mouse-human comparative genomics. (jax.org)
Sorry for yet another basic question, but what exactly is a pairwise genome alignment between 2 organisms e.g. human/chicken. (biostars.org)
We have generated fitCons scores for three human cell types based on public data from EN-CODE. (biorxiv.org)

Anatomy7

Organisms28

Diseases4

Chemicals and Drugs14

Analytical, Diagnostic and Therapeutic Techniques and Equipment18

Phenomena and Processes79

Disciplines and Occupations3

Technology, Industry, Agriculture5

Information Science14

Health Care1

Genes18

Animal genomes2

Assemblies7

Sequence9

Species15

Sequences5

Rearrangement5

Chromosomes4

Biology3

Eukaryotic genomes1

Phylogenetic3

Chromatin1

Complete genome2

Computational2

Annotation1

Chromosome2

Medicago1

Assembly1

Linkage2

Isolates1

Annotations2

Alignments4

Functional2

Drosophila1

Gene order1

Sequencing6

Expansions1

Chordate1

Duplication8

Taxa1

Vertebrate1

Evolution3

Syntenic1

Strain1

Insights1

Protein3

Regions2

20211

Analysis2

Distinct2

Mapping1

Closely related2

Reference1

Genus1

Rearrangements1

Research1

Human3