Search results for "Synteny"
showing 10 items of 46 documents
Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream
2019
AbstractGilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding towards more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds (∼732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreambrowser. Homology-based functional annotation, …
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l.
2019
AbstractGene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-base…
TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens…
2019
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 ofShewanella putrefaciensand genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed …
The Evolution of Human Chromosome 7 Syntenies in Eutheria, with Special Attention to Primates
2004
Genetic and cytogenetic comparison in between man and non-human primates has largely contributed to the knowledge of the evolution of the Order Primates, and in particular of man. Recently, the "Chromosome painting" approach indicated a strong conservation of syntenies in Eutheria. At present, a more precise identification of breakpoints and evolutionary related rearrangements can be obtained by BAC and locus specific in situ hybridi- sation. In spite to this situation the evolutionary history of different human autosomes remains a dilemma; at the same time, high resolution banded chromosome analysis confirms to be a valuable tool for the preliminary detection of fine rearrangements. This r…
Reconstructing the Phylogeny of the Human Chromosome 4 Synteny using Comparative Karyology and Genomic Data Analysis
2010
Abstract This work focuses on the evolution of the architecture of human chromosome 4 (HSA4) through the analysis of chromosomal regions that have been conserved over time, and the comparison of regions that have been involved in different rearrangements in placental lineages. As with most elements of the human genome, HSA4 is considered to be evolutionarily stable. A more detailed analysis indicates that the syntenic association has been reshuffled by a series of rearrangements, yielding different chromosomes in various taxa. In its ancestral eutherian state, HSA4 has a syntenic association with HSA8p. We investigated the complex origin of this human chromosome using three different approa…
Isolation and differential expression of two isoforms of the ROBO2/Robo2 axon guidance receptor gene in humans and mice.
2006
AbstractExpression of Robo receptor molecules is important for axon guidance across the midline of the mammalian central nervous system. Here we describe novel isoform a of human ROBO2, which is initially strongly expressed in the fetal human brain but thereafter only weakly expressed in adult brain and a few other tissues. The known isoform b of ROBO2 shows a more or less ubiquitous expression pattern, suggesting diverse functional roles. The genomic structure and distinct expression patterns of Robo2a and Robo2b have been conserved in the mouse, but in contrast to human ROBO2a mouse Robo2a is also abundant in adult brain. Exons 1 and 2 of human ROBO2a lie in an inherently unstable DNA seg…
Comparative analysis of zebrafish nos2a and nos2b genes
2008
Abstract Nitric oxide synthase (NOS) produces nitric oxide (NO) from arginine. Three NOS isoforms have been identified in mammals, namely a neuronal (NOS1), an inducible (NOS2) and an endothelial (NOS3) enzyme. In zebrafish genome, one nos1 gene and two nos2 genes (nos2a and nos2b) were observed. We cloned zebrafish nos2a cDNA and compared nos2a and nos2b sequences, expression and inducibility. When analyzed by reverse transcription-PCR, the expression of nos2a remained very low during initial development, then increased at 96 hpf, while nos2b was expressed from 6 hpf and subsequently remained stable. Expression of nos2a is detected in the head, eye and gut regions by WISH experiments perfo…
The gene encoding the transcriptional repressor BERF-1 maps to a region of conserved synteny on mouse chromosome 16 and human chromosome 3 and a rela…
1999
We have recently identified and characterized a Kruppel-like zinc finger protein (BERF-1), that functions as a repressor of β enolase gene transcription. By interspecific backcross analysis the gene encoding BERF-1 was localized 4.7 cM proximal to the <i>Mtv6</i> locus on mouse chromosome 16, and an isolated pseudogene was localized to mouse chromosome 8, about 5.3 cM distal to the D8Mit4 marker. Nucleotide sequence identity and chomosome location indicate that the gene encoding BERF-1 is the mouse homologue (<i>Zfp148</i>) of ZNF148 localized to human chromosome 3q21, a common translocation site in acute myeloid leukemia patients.
Comparative architectural aspects of regions of conserved synteny on human chromosome 11p15.3 and mouse chromosome 7 (including genes WEE1 and LMO1)
2001
Human chromosome 11p15.3 is associated with chromosome aberrations in the Beckwith Wiedemann Syndrome and implicated in the pathogenesis of different tumor types including lung cancer and leukemias. To date, only single tumor-relevant genes with linkage to this region (e.g. LMO1) have been found suggesting that this region may harbor additional potential disease associated genes. Although this genomic area has been studied for years, the exact order of genes/chromosome markers between D11S572 and the WEE1 gene locus remained unclear. Using the FISH technique and PAC clones of the flanking markers we determined the order of the genomic markers. Based on these clones we established a PAC cont…
Chromosomal Dynamics in Cercopithecini Studied by Williams-Beuren probe mapping
2010
Chromosomal evolution in the tribe Cercopithecini and in related taxa is highly debated. Uncertainty in reconstruction is mainly related to the great genetic variability and polymorphism of the taxa. Recent molecular and karyological efforts individuate a split between genetically conservative, arbitrarily defi ned, “terrestrial” guenons and vervets, and genetically variable and derived “arboreal” guenons. We performed the mapping of WS loci probe (7q11.23) in order to verify the chromosomal dynamics of the genomes of three tree-dwelling species of the tribe: C. neglectus, C. mitis mitis, C. albogularis labiatus. Data from literature for the “ground-dwelling” Chlorocebus aethiops sabaeus ha…