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 mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Taylor-Brown A,Pillonel T,Greub G,Vaughan L,Nowak B,Polkinghorne Adoi
10.1093/gbe/evy195subject
Has Abstractpub_date
2018-10-01 00:00:00pages
2587-2595issue
10issn
1759-6653pii
5092419journal_volume
10pub_type
杂志文章abstract::In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx155
更新日期:2017-09-01 00:00:00
abstract::We previously discovered that lagging strand genes evolve faster in Bacillus subtilis (and potentially other bacteria). Lagging strand genes are transcribed in the head-on orientation with respect to DNA replication, leading to collisions between the two machineries that stall replication and can destabilize genomes. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw274
更新日期:2016-12-01 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::Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt129
更新日期:2013-01-01 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::The Arabidopsis DA1 genes appear to have multiple functions in regulating organ size and abiotic stress response, but the biological roles of its closely related genes remain unknown. Evolutionary analyses might provide some clues to aid in an understanding of their functional diversification. In this work, we charact...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu076
更新日期:2014-04-01 00:00:00
abstract::The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A. mellifera nest in concealed cavities. Additionally, the worker and reproducti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz277
更新日期:2020-01-01 00:00:00
abstract::Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv008
更新日期:2015-01-18 00:00:00
abstract::Convergent evolution, a process by which organisms evolved independently to have similar traits, provides opportunities to understand adaptation. The bacterial genus Mycoplasma contains multiple species that evolved independently to become ruminant pathogens, which represents an interesting study system for investigat...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy172
更新日期:2018-08-01 00:00:00
abstract::Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom....
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq032
更新日期:2010-07-19 00:00:00
abstract::The ribonuclease (RNase) A superfamily is a vertebrate-specific gene family. Because of a massive expansion that occurred during the early mammalian evolution, extant mammals in general have much more RNase genes than nonmammalian vertebrates. Mammalian RNases have been associated with diverse physiological functions ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt161
更新日期:2013-01-01 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::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::The family Actinomycetaceae comprises several important pathogens that impose serious threat to human health and cause substantial infections of economically important animals. However, the phylogeny and evolutionary dynamic of this family are poorly characterized. Here, we provide detailed description of the genome c...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu211
更新日期:2014-09-22 00:00:00
abstract::All vertically transmitted bacterial symbionts undergo a process of genome reduction over time, resulting in tiny, gene-dense genomes. Comparison of genomes of ancient bacterial symbionts gives only limited information about the early stages in the transition from a free-living to symbiotic lifestyle because many chan...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr002
更新日期:2011-01-01 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::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::Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz183
更新日期:2019-09-01 00:00:00
abstract::Nested genes are the most common form of protein-coding overlap in eukaryotic genomes. Previous studies have shown that nested genes accumulate rapidly over evolutionary time, typically via the insertion of short young duplicate genes into long introns. However, the evolutionary relationship between nested genes remai...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evw237
更新日期:2016-10-23 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::Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given t...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz129
更新日期:2019-07-01 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::Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with d...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa088
更新日期:2020-06-01 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::Explaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct time-scales on potentially interdependent traits, can benefit from ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz182
更新日期:2019-09-01 00:00:00
abstract::Insertion sequences (ISs) are mobile genetic elements in bacterial genomes. In general, intergenic IS elements are probably less deleterious for their hosts than intragenic ISs, simply because they have a lower likelihood of disrupting native genes. However, since promoters, Shine-Dalgarno sequences, and transcription...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evq040
更新日期:2010-01-01 00:00:00
abstract::The loss of Y-linked genes during sex chromosome evolution creates a potentially deleterious low gene dosage in males. Recent studies have reported different strategies of dosage compensation. Unfortunately, most of these studies investigated taxa with comparatively old sex chromosome systems, which may limit insights...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv013
更新日期:2015-01-23 00:00:00
abstract::Parasites are sometimes able to manipulate the behavior of their hosts. However, the molecular cues underlying this phenomenon are poorly documented. We previously reported that the parasitoid wasp Leptopilina boulardi which develops from Drosophila larvae is often infected by an inherited DNA virus. In addition to be...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw277
更新日期:2016-12-01 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::Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene clu...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt041
更新日期:2013-01-01 00:00:00