Abstract:
:Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Andres J,Arsène-Ploetze F,Barbe V,Brochier-Armanet C,Cleiss-Arnold J,Coppée JY,Dillies MA,Geist L,Joublin A,Koechler S,Lassalle F,Marchal M,Médigue C,Muller D,Nesme X,Plewniak F,Proux C,Ramírez-Bahena MH,Schenowitz Cdoi
10.1093/gbe/evt061subject
Has Abstractpub_date
2013-01-01 00:00:00pages
934-53issue
5issn
1759-6653pii
evt061journal_volume
5pub_type
杂志文章abstract::The evolution of a mechanically resilient epidermis was a key adaptation in the transition of amniotes to a fully terrestrial lifestyle. Skin appendages usually form via a specialized type of programmed cell death known as cornification which is characterized by the formation of an insoluble cornified envelope (CE). M...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz054
更新日期:2019-03-01 00:00:00
abstract::The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effect...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt083
更新日期:2013-01-01 00:00:00
abstract::Klebsiella pneumoniae clonal group (CG) 258, comprising sequence types (STs) 258, 11, and closely related variants, is associated with dissemination of the K. pneumoniae carbapenemase (KPC). Hospital outbreaks of KPC CG258 infections have been observed globally and are very difficult to treat. As a consequence, there ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv062
更新日期:2015-04-10 00:00:00
abstract::The propensity of protein sites to be occupied by any of the 20 amino acids is known as site-specific amino acid preferences (SSAP). Under the assumption that SSAP are conserved among homologs, they can be used to parameterize evolutionary models for the reconstruction of accurate phylogenetic trees. However, simulati...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy261
更新日期:2019-01-01 00:00:00
abstract::Macroevolutionary trends exhibited by retroviruses are complex and not entirely understood. The sloth endogenized foamy-like retrovirus (SloEFV), which demonstrates incongruence in virus-host evolution among extant sloths (Order Folivora), has not been investigated heretofore in any extinct sloth lineages and its prem...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw023
更新日期:2016-02-14 00:00:00
abstract::Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-in...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw014
更新日期:2016-03-09 00:00:00
abstract::Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isol...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa085
更新日期:2020-06-01 00:00:00
abstract::Wolbachia is a widely distributed intracellular bacterial endosymbiont among invertebrates. The wStriCN, the Wolbachia strain that naturally infects an agricultural pest Laodelphax striatellus, has a "Jekyll and Hyde" mode of infection pattern with positive and negative effects: It not only kills many offspring by ind...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa006
更新日期:2020-02-01 00:00:00
abstract::Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragr...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw117
更新日期:2016-06-13 00:00:00
abstract::Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and loss...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw013
更新日期:2016-02-09 00:00:00
abstract::Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs056
更新日期:2012-01-01 00:00:00
abstract::A long-standing mystery of genomic/transcriptomic structure involves spliced leader trans-splicing (SLTS), in which short RNA "tags" transcribed from a distinct genomic locus is added near the 5' end of RNA transcripts by the spliceosome. SLTS has been observed in diverse eukaryotes in a phylogenetic pattern implying ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz217
更新日期:2019-10-01 00:00:00
abstract::Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa159
更新日期:2020-09-01 00:00:00
abstract::Nucleomorphs are the remnant nuclei of algal endosymbionts that were engulfed by nonphotosynthetic host eukaryotes. These peculiar organelles are found in cryptomonad and chlorarachniophyte algae, where they evolved from red and green algal endosymbionts, respectively. Despite their independent origins, cryptomonad an...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq082
更新日期:2011-01-01 00:00:00
abstract::Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic re...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu159
更新日期:2014-07-28 00:00:00
abstract::The globin gene family encodes oxygen-binding hemeproteins conserved across the major branches of multicellular life. The origins and evolutionary histories of complete globin repertoires have been established for many vertebrates, but there remain major knowledge gaps for ray-finned fish. Therefore, we used phylogene...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw266
更新日期:2017-01-01 00:00:00
abstract::Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa152
更新日期:2020-11-03 00:00:00
abstract::Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems. However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv108
更新日期:2015-05-28 00:00:00
abstract::Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force l...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw097
更新日期:2016-06-03 00:00:00
abstract::Amoebae have been considered as a genetic "melting pot" for its symbionts, facilitating genetic exchanges of the bacteria that co-inhabit the same host. To test the "melting pot" hypothesis, we analyzed six genomes of amoeba endosymbionts within Rickettsiales, four of which belong to Holosporaceae family and two to Ca...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx246
更新日期:2017-11-01 00:00:00
abstract::Genomic analysis of many nonmodel species has uncovered an incredible diversity of sex chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of sex chromosome evolution. Classic theory predicts that sex chromosomes originate from a pair of homologous ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa081
更新日期:2020-06-01 00:00:00
abstract::Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homol...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy059
更新日期:2018-03-01 00:00:00
abstract::The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity f...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv219
更新日期:2015-11-11 00:00:00
abstract::The major human pathogens Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major are collectively known as the Tritryps. The initial comparative analysis of their genomes has uncovered that Tritryps share a great number of genes, but repetitive DNA seems to be extremely variable between them. However, the in-dept...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evz017
更新日期:2019-02-01 00:00:00
abstract::The presence of spliceosomal introns in eukaryotic genes poses a major puzzle for the study of genome evolution. Intron densities vary enormously among distant lineages. However, the mechanisms driving intron gains are poorly understood and very few intron gains and losses have been documented over short evolutionary ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs091
更新日期:2012-01-01 00:00:00
abstract::Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despit...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu261
更新日期:2014-12-04 00:00:00
abstract::Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx270
更新日期:2018-01-01 00:00:00
abstract::Human-specific small insertions and deletions (HS indels, with lengths <100 bp) are reported to be ubiquitous in the human genome. However, whether these indels contribute to human-specific traits remains unclear. Here we employ a modified McDonald-Kreitman (MK) test and a combinatorial population genetics approach to...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evp041
更新日期:2009-10-20 00:00:00
abstract::Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we d...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx268
更新日期:2018-01-01 00:00:00
abstract::RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx046
更新日期:2017-04-01 00:00:00