Abstract：
:Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to have the most compositionally homogeneous genome of all amniotes sequenced thus far, a homogeneity exceeding that for the frog Xenopus. Based on a Bayesian algorithm, Anolis has smaller and less GC-rich isochores compared with human and chicken. Correlates generally associated with GC-rich isochores, including shorter introns and higher gene density, have all but disappeared from the Anolis genome. Using genic GC as a proxy for isochore structure so as to compare with other vertebrates, we found that GC content has substantially decreased in the lineage leading to Anolis since diverging from the common ancestor of Reptilia ∼275 Ma, perhaps reflecting weakened or reversed GC-biased gene conversion, a nonadaptive substitution process that is thought to be important in the maintenance and trajectory of isochore evolution. Our results demonstrate that GC composition in Anolis is not associated with important features of genome structure, including gene density and intron size, in contrast to patterns seen in mammal and bird genomes.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Fujita MK,Edwards SV,Ponting CPdoi
10.1093/gbe/evr072subject
Has Abstractpub_date
2011-01-01 00:00:00pages
974-84issn
1759-6653pii
evr072journal_volume
3pub_type
杂志文章abstract：:Many algal groups acquired complex plastids by the uptake of green and red algae through multiple secondary endosymbioses. As a result of gene loss and transfer during the endosymbiotic processes, algal endosymbiont nuclei disappeared in most cases. However, chlorarachniophytes and cryptophytes still possess a relict ...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evv096
更新日期：2015-05-22 00:00:00
abstract：:The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relat...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evx245
更新日期：2018-01-01 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 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：:Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by mult...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evw042
更新日期：2016-03-23 00:00:00
abstract：:Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and "Candidatus Methanomethylophilus alvus," provide in...
journal_title：Genome biology and evolution
pub_type： 信件
doi：10.1093/gbe/evt128
更新日期：2013-01-01 00:00:00
abstract：:piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. More...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evaa064
更新日期：2020-05-01 00:00:00
abstract：:Intronic DNA is a major component of eukaryotic genes and genomes and can be subject to selective constraint and have functions in gene regulation. Intron size is of particular interest given that it is thought to be the target of a variety of evolutionary forces and has been suggested to be linked ultimately to vario...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evs070
更新日期：2012-01-01 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：:In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evw010
更新日期：2016-01-23 00:00:00
abstract：:Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here...
journal_title：Genome biology and evolution
pub_type： 信件
doi：10.1093/gbe/evy245
更新日期：2019-01-01 00:00:00
abstract：:Mitochondrial DNA (mtDNA) mutations underlie a variety of human genetic disorders and are associated with the aging process. mtDNA polymorphisms are widely used in a variety of evolutionary applications. Although mtDNA mutation spectra are known to differ between distantly related model organisms, the extent to which ...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evp055
更新日期：2009-12-23 00:00:00
abstract：:Mitochondrial evolution has given rise to a complex array of organelles, ranging from classical aerobic mitochondria to mitochondrial remnants known as hydrogenosomes and mitosomes. The latter are found in anaerobic eukaryotes, and these highly derived organelles often retain only scant evidence of their mitochondrial...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evq015
更新日期：2010-07-12 00:00:00
abstract：:Pathogens and hosts are in an ongoing arms race and genes involved in host-pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, ...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evv092
更新日期：2015-05-19 00:00:00
abstract：:"Candidatus Endomicrobium trichonymphae" (Bacteria; Elusimicrobia) is an obligate intracellular symbiont of the cellulolytic protist genus Trichonympha in the termite gut. A previous genome analysis of "Ca Endomicrobium trichonymphae" phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in the...
journal_title：Genome biology and evolution
pub_type： 信件
doi：10.1093/gbe/evw227
更新日期：2016-10-13 00:00:00
abstract：:Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evz099
更新日期：2019-06-01 00:00:00
abstract：:Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evy010
更新日期：2018-01-01 00:00:00
abstract：:The evolution of heterogametic sex chromosomes is often-but not always-accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) s...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evv156
更新日期：2015-09-02 00:00:00
abstract：:Mitochondrial (mt) genomes are intensively studied in Ascomycota and Basidiomycota, but they are poorly documented in basal fungal lineages. In this study, we sequenced the complete mtDNA of Rhizophagus sp. DAOM 213198, a close relative to Rhizophagus irregularis, a widespread, ecologically and economical relevant spe...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evu268
更新日期：2014-12-19 00:00:00
abstract：:Only few studies on snake venoms were dedicated to deeply characterize the toxin secretion of animals from the Colubridae family, despite the fact that they represent the majority of snake diversity. As a consequence, some evolutionary trends observed in venom proteins that underpinned the evolutionary histories of sn...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evw149
更新日期：2016-08-16 00:00:00
abstract：:Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evw254
更新日期：2017-01-01 00:00:00
abstract：:Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations b...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evt065
更新日期：2013-01-01 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：: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：: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：:Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mut...
journal_title：Genome biology and evolution
pub_type： 杂志文章,评审
doi：10.1093/gbe/evy252
更新日期：2019-01-01 00:00:00
abstract：:The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard tha...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evt100
更新日期：2013-01-01 00:00:00
abstract：:The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host im...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evy124
更新日期：2018-09-01 00:00:00
abstract：:The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic in...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evx249
更新日期：2017-12-01 00:00:00
abstract：:Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer's yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high quality long read genomes of non-domesticated yeast strains isolated from primeval forests...
journal_title：Genome biology and evolution
pub_type： 杂志文章
doi：10.1093/gbe/evab001
更新日期：2021-01-11 00:00:00
