Abstract:
:Amoebiasis is the third-most common cause of mortality worldwide from a parasitic disease. Although the primary etiological agent of amoebiasis is the obligate human parasite Entamoeba histolytica, other members of the genus Entamoeba can infect humans and may be pathogenic. Here, we present the first annotated reference genome for Entamoeba moshkovskii, a species that has been associated with human infections, and compare the genomes of E. moshkovskii, E. histolytica, the human commensal Entamoeba dispar, and the nonhuman pathogen Entamoeba invadens. Gene clustering and phylogenetic analyses show differences in expansion and contraction of families of proteins associated with host or bacterial interactions. They intimate the importance to parasitic Entamoeba species of surface-bound proteins involved in adhesion to extracellular membranes, such as the Gal/GalNAc lectin and members of the BspA and Ariel1 families. Furthermore, E. dispar is the only one of the four species to lack a functional copy of the key virulence factor cysteine protease CP-A5, whereas the gene's presence in E. moshkovskii is consistent with the species' potentially pathogenic nature. Entamoeba moshkovskii was found to be more diverse than E. histolytica across all sequence classes. The former is ∼200 times more diverse than latter, with the four E. moshkovskii strains tested having a most recent common ancestor nearly 500 times more ancient than the tested E. histolytica strains. A four-haplotype test indicates that these E. moshkovskii strains are not the same species and should be regarded as a species complex.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Wilson IW,Weedall GD,Lorenzi H,Howcroft T,Hon CC,Deloger M,Guillén N,Paterson S,Clark CG,Hall Ndoi
10.1093/gbe/evz009subject
Has Abstractpub_date
2019-03-01 00:00:00pages
688-705issue
3issn
1759-6653pii
5298318journal_volume
11pub_type
杂志文章abstract::The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can c...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr110
更新日期:2011-01-01 00:00:00
abstract::It is often unavoidable to combine data from different sequencing centers or sequencing platforms when compiling data sets with a large number of individuals. However, the different data are likely to contain specific systematic errors that will appear as SNPs. Here, we devise a method to detect systematic errors in c...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy199
更新日期:2018-10-01 00:00:00
abstract::Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,2...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw138
更新日期:2016-08-25 00:00:00
abstract::Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability o...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy081
更新日期:2018-04-01 00:00:00
abstract::Cyanobacteria are dominant primary producers of various ecosystems and they colonize marine as well as freshwater and terrestrial habitats. On the basis of their oxygenic photosynthesis they are known to synthesize a high number of secondary metabolites, which makes them promising for biotechnological applications. St...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy275
更新日期:2019-01-01 00:00:00
abstract::Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx085
更新日期:2017-05-01 00:00:00
abstract::Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid a...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy165
更新日期:2018-09-01 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::Members from Colletotrichum genus adopt a diverse range of lifestyles during infection of plants and represent a group of agriculturally devastating pathogens. In this study, we present the draft genome of Colletotrichum incanum from the spaethianum clade of Colletotrichum and the comparative analyses with five other ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw089
更新日期:2016-05-22 00:00:00
abstract::Protein metabolism is one of the most costly processes in the cell and is therefore expected to be under the effective control of natural selection. We stimulated yeast strains to overexpress each single gene product to approximately 1% of the total protein content. Consistent with previous reports, we found that exce...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt154
更新日期:2013-01-01 00:00:00
abstract::The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 45...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu138
更新日期:2014-06-19 00:00:00
abstract::The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy251
更新日期:2019-01-01 00:00:00
abstract::Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw047
更新日期:2017-02-01 00:00:00
abstract::It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of gene...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt178
更新日期:2013-01-01 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::The genus Claviceps has been known for centuries as an economically important fungal genera for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, m...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa267
更新日期:2021-01-29 00:00:00
abstract::Adaptive prediction is a capability of diverse organisms, including microbes, to sense a cue and prepare in advance to deal with a future environmental challenge. Here, we investigated the timeframe over which adaptive prediction emerges when an organism encounters an environment with novel structure. We subjected yea...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx116
更新日期:2017-06-01 00:00:00
abstract::Plants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example is secreted fungal effector proteins and their host targets, w...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy023
更新日期:2018-02-01 00:00:00
abstract::Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochon...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx225
更新日期:2017-11-01 00:00:00
abstract::Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0-3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning m...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy195
更新日期:2018-10-01 00:00:00
abstract::The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which, Rab3-interacting molecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channels in vitro via a PDZ domain that binds to the extreme C-termi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa097
更新日期:2020-08-01 00:00:00
abstract::Hemerythrins and hemocyanins are respiratory proteins present in some of the most ecologically diverse animal lineages; however, the precise evolutionary history of their enzymatic domains (hemerythrin, hemocyanin M, and tyrosinase) is still not well understood. We survey a wide dataset of prokaryote and eukaryote gen...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt102
更新日期:2013-01-01 00:00:00
abstract::Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model s...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy085
更新日期:2018-04-01 00:00:00
abstract::The process of transcription is highly stochastic leading to cell-to-cell variations and noise in gene expression levels. However, key essential genes have to be precisely expressed at the correct amount and time to ensure proper cellular development and function. Studies in yeast and bacterial systems have shown that...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv179
更新日期:2015-09-04 00:00:00
abstract::North Borneo (NB) is home to more than 40 native populations. These natives are believed to have undergone local adaptation in response to environmental challenges such as the mosquito-abundant tropical rainforest. We attempted to trace the footprints of natural selection from the genomic data of NB native populations...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa207
更新日期:2020-12-06 00:00:00
abstract::Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolut...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa110
更新日期:2020-07-01 00:00:00
abstract::Bacteriophage flux can cause the majority of genetic diversity in free-living bacteria. This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. However, recent studie...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr007
更新日期:2011-01-01 00:00:00
abstract::The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metaz...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt052
更新日期:2013-01-01 00:00:00
abstract::The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt091
更新日期:2013-01-01 00:00:00
abstract::Coliphage phi1, which was isolated for phage therapy in the Republic of Georgia, is closely related to the T-like myovirus RB49. The approximately 275 open reading frames encoded by each phage have an average level of amino acid identity of 95.8%. RB49 lacks 7 phi1 genes while 10 phi1 genes are missing from RB49. Most...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq006
更新日期:2010-02-01 00:00:00