Search results for "Genome"
showing 10 items of 1913 documents
Evidence for the Existence of a Pseudogene for the Large Subunit of Rubisco within the Chloroplast DNA of Norway Spruce (Picea Abies)
1998
Many hundreds of genes are involved in the synthesis, maintenance and degradation of chloroplasts. Although quite a number of these genes are located in the chloroplast genome, by far the greater proportion is present in the nuclear genome. The sizes of chloroplast DNAs (cpDNA) were estimated from restriction enzyme mapping studies and the complete sequences of different cpDNAs from diverse plant lineages have been determined to date (Marchantia polymorpha [1], Nicotiana tabacum [2], Oryza saliva [3], Epifagus virginiana [4], Euglena gracilis [5], Pinus thunbergii [6], Porphyra purpurea [7], Odontella sinensis [8], Zea mays [9], Chlorella vulgaris [10]).
Phylogeography of a Habitat Specialist with High Dispersal Capability: The Savi’s Warbler Locustella luscinioides
2012
In order to describe the influence of Pleistocene glaciations on the genetic structure and demography of a highly mobile, but specialized, passerine, the Savi's Warbler (Locustella luscinioides), mitochondrial DNA sequences (ND2) and microsatellites were analysed in c.330 individuals of 17 breeding and two wintering populations. Phylogenetic, population genetics and coalescent methods were used to describe the genetic structure, determine the timing of the major splits and model the demography of populations. Savi's Warblers split from its sister species c.8 million years ago and have two major haplotype groups that diverged in the early/middle Pleistocene. One of these clades originated in…
On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing
2013
One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing errors and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with …
Why are viral genomes so fragile? The bottleneck hypothesis
2021
If they undergo new mutations at each replication cycle, why are RNA viral genomes so fragile, with most mutations being either strongly deleterious or lethal? Here we provide theoretical and numerical evidence for the hypothesis that genetic fragility is partly an evolutionary response to the multiple population bottlenecks experienced by viral populations at various stages of their life cycles. Modelling within-host viral populations as multi-type branching processes, we show that mutational fragility lowers the rate at which Muller’s ratchet clicks and increases the survival probability through multiple bottlenecks. In the context of a susceptible-exposed-infectious-recovered epidemiolog…
On the complexity of the Saccharomyces bayanus taxon: Hybridization and potential hybrid speciation
2014
Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequenc…
From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses.
2012
Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown. Viruses are an ideal system for addressing this question because their evolution is fast enough to be observed in real time, and experimentally-determined mutation rates are abundant. This article provides statistically supported evidence that the mutation rate determines molecular evolution across all types of viruses. Properties of the viral genome such as its size and chemical composition are…
Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis.
2012
In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S…
A Critical Review of Statistical Methods for Twin Studies Relating Exposure to Early Life Health Conditions
2021
International audience; When investigating disease etiology, twin data provide a unique opportunity to control for confounding and disentangling the role of the human genome and exposome. However, using appropriate statistical methods is fundamental for exploiting such potential. We aimed to critically review the statistical approaches used in twin studies relating exposure to early life health conditions. We searched PubMed, Scopus, Web of Science, and Embase (2011–2021). We identified 32 studies and nine classes of methods. Five were conditional approaches (within-pair analyses): additive-common-erratic (ACE) models (11 studies), generalized linear mixed models (GLMMs, five studies), gene…
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
2000
The study of a few genes has permitted the identification of three elements that constitute a yeast polyadenylation signal: the efficiency element (EE), the positioning element and the actual site for cleavage and polyadenylation. In this paper we perform an analysis of oligonucleotide composition on the sequences located downstream of the stop codon of all yeast genes. Several oligonucleotide families appear over-represented with a high significance (referred to herein as"words"). The family with the highest over-representation includes the oligonucleotides shown experimentally to play a role as EEs. The word with the highest score is TATATA, followed, among others, by a series of singl…
Phylogenomics reveals deep molluscan relationships.
2011
Evolutionary relationships among the eight major lineages of Mollusca have remained unresolved despite their diversity and importance. Previous investigations of molluscan phylogeny, based primarily on nuclear ribosomal gene sequences1–3 or morphological data4, have been unsuccessful at elucidating these relationships. Recently, phylogenomic studies using dozens to hundreds of genes have greatly improved our understanding of deep animal relationships5. However, limited genomic resources spanning molluscan diversity has prevented use of a phylogenomic approach. Here we use transcriptome and genome data from all major lineages (except Monoplacophora) and recover a well-supported topology for …