Search results for "Genomic organization"
showing 10 items of 23 documents
Southern and fluorescent in situ hybridization detect three RAPD-generated PCR products useful as introgression markers in Petunia
1999
Fluorescent in situ hybridization (FISH) was used to reveal the intrachromosomal organization of 11 RAPD markers localized on the genetic map of Petunia hybrida. The cloned RAPD markers were analyzed by means of Southern hybridization to determine their level of sequence repetition and their specificity in different Petunia species with 2n=14 and 18 chromosomes. The same probes were then used in FISH experiments. Most of the RAPD clones studied showed high sequence repetition and no species specificity. Moreover, FISH analysis showed that these probes could belong to multilocus families as evidenced by the multiple FISH signals dispersed throughout the genome and present on every chromosome…
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis
2013
International audience; The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but thi…
A Network Model for the Correlation between Epistasis and Genomic Complexity
2008
The study of genetic interactions (epistasis) is central to the understanding of genome organization and evolution. A general correlation between epistasis and genomic complexity has been recently shown, such that in simpler genomes epistasis is antagonistic on average (mutational effects tend to cancel each other out), whereas a transition towards synergistic epistasis occurs in more complex genomes (mutational effects strengthen each other). Here, we use a simple network model to identify basic features explaining this correlation. We show that, in small networks with multifunctional nodes, lack of redundancy, and absence of alternative pathways, epistasis is antagonistic on average. In c…
New Insights into the Genome Organization of Yeast Killer Viruses Based on “Atypical” Killer Strains Characterized by High-Throughput Sequencing
2017
Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii. All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed. The few discrepancies between viral variants were mostly located aro…
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.
2018
Abstract Motivation The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data. Results PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic spec…
Co-regulation of paralog genes in the three-dimensional chromatin architecture.
2016
Paralog genes arise from gene duplication events during evolution, which often lead to similar proteins that cooperate in common pathways and in protein complexes. Consequently, paralogs show correlation in gene expression whereby the mechanisms of co-regulation remain unclear. In eukaryotes, genes are regulated in part by distal enhancer elements through looping interactions with gene promoters. These looping interactions can be measured by genome-wide chromatin conformation capture (Hi-C) experiments, which revealed self-interacting regions called topologically associating domains (TADs). We hypothesize that paralogs share common regulatory mechanisms to enable coordinated expression acco…
Related haloarchaeal pleomorphic viruses contain different genome types
2012
Archaeal viruses have been the subject of recent interest due to the diversity discovered in their virion architectures. Recently, a new group of haloarchaeal pleomorphic viruses has been discovered. It is distinctive in terms of the virion morphology and different genome types (ssDNA/dsDNA) harboured by rather closely related representatives. To date there are seven isolated viruses belonging to this group. Most of these share a cluster of five conserved genes, two of which encode major structural proteins. Putative proviruses and proviral remnants containing homologues of the conserved gene cluster were also identified suggesting a long-standing relationship of these viruses with their ho…
Evidence of Genomic Instability in Campylobacter jejuni Isolated from Poultry
1998
ABSTRACT Poultry isolates of Campylobacter jejuni derived from a survey of meat processing batches were genotyped by pulsed-field gel electrophoresis (PFGE) of chromosomal DNA to establish the clonal relationships between single-colony isolates. In the majority of batches studied, one or two genotype patterns predominated. However, in one batch (batch A), 21 single-colony isolates gave 14 different PFGE genotypes. The banding patterns obtained with Sma I were sufficiently different to distinguish between genotypes, although the patterns also produced many common bands. The question of whether these isolates represented different clones or had a common clonal ancestry was addressed by additi…
Cloning and characterization of the genes encoding the malolactic enzyme and the malate permease of Leuconostoc oenos
1996
Using degenerated primers from conserved regions of the protein sequences of malic enzymes, we amplified a 324-bp DNA fragment by PCR from Leuconostoc oenos and used this fragment as a probe for screening a Leuconostoc oenos genomic bank. Of the 2,990 clones in the genomic bank examined, 7 with overlapping fragments were isolated by performing colony hybridization experiments. Sequencing 3,453 bp from overlapping fragments revealed two open reading frames that were 1,623 and 942 nucleotides long and were followed by a putative terminator structure. The first deduced protein (molecular weight, 59,118) is very similar (level of similarity, 66%) to the malolactic enzyme of Lactococcus lactis; …
Different genomic organization and expression of immunoglobulin light-chain isotypes in the rainbow trout.
2000
cDNA studies have distinguished two isotypes of the rainbow trout (Oncorhynchus mykiss) immunoglobulin (Ig) light chain (designated L1 and L2). This study characterized genomic clones of these isotypes. L1 genes are arranged in clusters with single copies of variable (V), joining (J), and constant (C) segments. The transcriptional orientation of the V genes is opposite to that of the J and C segments, indicating that the V genes must be rearranged by inversion. L2 is also organized in clusters, consisting of two or three V, one J, and one C exon, all in the same transcriptional orientation. L1 and L2 of rainbow trout are similar to the previously identified cod and catfish clusters. Repeat …