Abstract:
:The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels-mostly in the plasticity region near the vap pathogencity island (PAI)-defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
MacArthur I,Anastasi E,Alvarez S,Scortti M,Vázquez-Boland JAdoi
10.1093/gbe/evx057subject
Has Abstractpub_date
2017-05-01 00:00:00pages
1241-1247issue
5issn
1759-6653pii
3078089journal_volume
9pub_type
杂志文章abstract::Arbuscular mycorrhizal fungi (AMF) represent an ecologically important and evolutionarily intriguing group of symbionts of land plants, currently thought to have propagated clonally for over 500 Myr. AMF produce multinucleate spores and may exchange nuclei through anastomosis, but meiosis has never been observed in th...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr089
更新日期:2011-01-01 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::All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome a...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv068
更新日期:2015-05-04 00:00:00
abstract::Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male dete...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv128
更新日期:2015-07-02 00:00:00
abstract::Aspergillus ochraceoroseus and Aspergillus rambellii were isolated from soil detritus in Taï National Park, Ivory Coast, Africa. The Type strain for each species happens to be the only representative ever sampled. Both species secrete copious amounts of aflatoxin B1 and sterigmatocystin, because each of their genomes ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv246
更新日期:2015-12-03 00:00:00
abstract::SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, De...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw029
更新日期:2016-02-12 00:00:00
abstract::Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy042
更新日期:2018-04-01 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::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::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::Although the morphological and physiological changes involved in pregnancy in live-bearing reptiles are well studied, the genetic mechanisms that underlie these changes are not known. We used the viviparous African Ocellated Skink, Chalcides ocellatus, as a model to identify a near complete gene expression profile ass...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs013
更新日期:2012-01-01 00:00:00
abstract::This study investigated long-term substitution rate differences using three calibration points, divergences between lobe-finned vertebrates and ray-finned fish, between mammals and sauropsids, and between holosteans (gar and bowfin) and teleost fish with amino acid sequence data of 625 genes for 25 bony vertebrates. T...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy125
更新日期:2018-07-01 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::Recent whole-genome approaches to microbial phylogeny have emphasized partitioning genes into functional classes, often focusing on differences between a stable core of genes and a variable shell. To rigorously address the effects of partitioning and combining genes in genome-level analyses, we developed a novel techn...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr121
更新日期:2012-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small RNA molecules involved in the regulation of mammalian gene expression. Together with other transcription regulators, miRNAs modulate the expression of genes and thereby potentially contribute to tissue and species diversity. To identify miRNAs that are differentially expressed between tiss...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs033
更新日期:2012-01-01 00:00:00
abstract::Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy177
更新日期:2018-09-01 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::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::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::Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic an...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt195
更新日期:2013-01-01 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::The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of N...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu202
更新日期:2014-09-10 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
abstract::Vomeronasal sensitivity is important for detecting intraspecific pheromonal cues as well as environmental odorants and is involved in mating, social interaction, and other daily activities of many vertebrates. Two large families of seven-transmembrane G-protein-coupled receptors, V1rs and V2rs, bind to various ligands...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr039
更新日期:2011-01-01 00:00:00
abstract::In 1957, an invasive and highly defensive honey bee began to spread across Brazil. In the previous year, Brazilian researchers hoped to produce a subtropical-adapted honey bee by crossing local commercial honey bees (of European origin) with a South African honey bee subspecies (Apis mellifera scutellata; an A-lineage...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa128
更新日期:2020-08-01 00:00:00
abstract::We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampy...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy219
更新日期:2018-12-01 00:00:00
abstract::OAS (2'-5'-oligoadenylate synthases) proteins and cyclic GMP-AMP synthase (cGAS, gene symbol: MB21D1) patrol the cytoplasm for the presence of foreign nucleic acids. Upon binding to double-stranded RNA or double-stranded DNA, OAS proteins and cGAS produce nucleotide second messengers to activate RNase L and STING (sti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv046
更新日期:2015-03-09 00:00:00
abstract::Gibbons (Hylobatidae) shared a common ancestor with the other hominoids only 15-18 million years ago. Nevertheless, gibbons show very distinctive features that include heavily rearranged chromosomes. Previous observations indicate that this phenomenon may be linked to the attenuated epigenetic repression of transposab...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs048
更新日期:2012-01-01 00:00:00
abstract::To fulfill their physiological functions, bile acids are conjugated with amino acids. In humans, conjugation is catalyzed by bile acid coenzyme A: amino acid N-acyltransferase (BAAT), an enzyme with a highly conserved catalytic triad in its active site. Interestingly, the conjugated amino acids are highly variable amo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz238
更新日期:2019-11-01 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