Search results for "Genome"

CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species

2023

The increasing availability of high-quality genomic, annotation and phenotypic data for different species contrasts with the lack of general software for comparative genomics that integrates these data types in a statistically sound framework in order to produce biologically meaningful knowledge. In this work, we present CALANGO (Comparative AnaLysis with ANnotation-based Genomic cOmponentes), a first-principles comparative genomics tool to search for annotation terms, such as GO terms or Pfam domain IDs, associated with a quantitative variable used to rank species data, after correcting for phylogenetic relatedness. This information can be used to annotate genomes at any level, including p…

2015

Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of in…

A multi-phase multi-objective genome-scale model shows diverse redox balance strategies in yeasts

2021

Yeasts constitute over 1500 species with great potential for biotechnology. Still, the yeastSaccharomyces cerevisiaedominates industrial applications and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabolic specificity in batch cultures. Here we propose a multi-phase multi-objective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic mod…

Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola.

2005

The study of three genomes of the aphid endosymbiont Buchnera aphidicola has revealed an extraordinary stasis: conservation of gene order and genetic composition of the chromosome, while the chromosome size and number of genes has reduced. The reduction in genome size appears to be ongoing since some lineages we now know to have even smaller chromosomes than the first B. aphidicola analysed. The current sequencing by our group of one of these smaller genomes with an estimated size of 450 kb, and its comparison with the other three available genomes provide insights into the nature of processes involved in shrinkage. We discuss whether B. aphidicola might be driven to extinction and be repla…

Evolution of reduced prokaryotic genomes and the minimal cell concept: Variations on a theme

2010

Prokaryotic genomes of endosymbionts and parasites are examples of naturally evolved minimal cells, the study of which can shed light on life in its minimum form. Their diverse biology, their lack of a large set of orthologous genes and the existence of essential linage (and environmentally) specific genes all illustrate the diversity of genes building up naturally evolved minimal cells. This conclusion is reinforced by the fact that sometimes the same essential function is performed by genes from different evolutionary origins. Nevertheless, all cells perform a set of life-essential functions however different their cell machinery and environment in which they thrive. An upcoming challenge…

Snapshot liver transcriptome in hepatocellular carcinoma

2012

Lately, advances in high throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at different levels of cancer biology such as genome, epigenome, transcriptome, proteome, and others. Among the diverse biological layers, the transcriptome has been most extensively studied especially due to the successful and broad introduction of the microarray technology. The future prospect of broad disposability of deep sequencing technology will furthermore lead to a more sensitive detection of lowly expressed transcripts and to an increase in the number of newly identified transcripts, but also to increase the discovery and characterizati…

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…

Factors Behind Junk DNA in Bacteria

2012

Although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding DNA, this view has dramatically changed in recent years. The increase of available complete bacterial genomes has revealed that many species present abundant repetitive DNA (i.e., insertion sequences, prophages or paralogous genes) and that many of these sequences are not functional but can have evolutionary consequences as concerns the adaptation to specialized host-related ecological niches. Comparative genomics analyses with close relatives that live in non-specialized environments reveal the nature and fate of this bacterial junk DNA. In addition, the…

Genome Instability in DNA Viruses

2016

Genome instability generally refers to the appearance of a high frequency of mutations in a single genome, including point mutations, insertions/deletions, or major rearrangements. DNA viruses usually show greater genome stability than RNA viruses. However, recent genome-wide molecular evolution and experimental studies have shown that DNA viruses can exhibit rapid sequence changes that are often found in loci involved in dynamic host–virus interactions. In fact, DNA viruses are capable of promoting genome instability specifically at certain genes, thus boosting diversity wherein needed. We review some of the molecular mechanisms underlying genomic instability in prokaryotic and eukaryotic …

Bacterial endosymbionts of insects: insights from comparative genomics.

2004

The development of molecular techniques for the study of uncultured bacteria allowed the extensive study of the widespread association between insects and intracellular symbiotic bacteria. Most of the bacterial endosymbionts involved in such associations are gamma-proteobacteria, closely related to Escherichia coli. In recent years, five genomes from insect endosymbionts have been sequenced, allowing the performance of extensive genome comparative analysis that, as a complement of phylogenetic studies, and analysis on individual genes, can help to understand the different traits of this particular association, including how the symbiotic process is established, the explanation of the specia…