Abstract:
:We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Guillory WX,Onyshchenko A,Ruck EC,Parks M,Nakov T,Wickett NJ,Alverson AJdoi
10.1093/gbe/evy103subject
Has Abstractpub_date
2018-06-01 00:00:00pages
1504-1515issue
6issn
1759-6653pii
5020725journal_volume
10pub_type
杂志文章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::Natural products from microbes have provided humans with beneficial antibiotics for millennia. However, a decline in the pace of antibiotic discovery exerts pressure on human health as antibiotic resistance spreads, a challenge that may better faced by unveiling chemical diversity produced by microbes. Current microbi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw125
更新日期:2016-07-02 00:00:00
abstract::Conservation of function can be accompanied by obvious similarity of homologous sequences which may persist for billions of years (Iyer LM, Leipe DD, Koonin EV, Aravind L. 2004. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 146:11-31.). However, presumably homologous segments of ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt023
更新日期:2013-01-01 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::Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two-component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cu...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy213
更新日期:2019-01-01 00:00:00
abstract::Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insert...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw302
更新日期:2017-02-01 00:00:00
abstract::Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of posit...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx199
更新日期:2017-10-01 00:00:00
abstract::Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether and how this occurs is limited. Here, we present an analysis of the great tit (Parus ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa044
更新日期:2020-03-01 00:00:00
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::Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called "selfish" genetic elements will proliferate when the host e...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv116
更新日期:2015-06-24 00:00:00
abstract::Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagasca...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx140
更新日期:2017-07-01 00:00:00
abstract::Chaperonins promote protein folding and are known to play a role in the maintenance of cellular stability under stress conditions. The group I bacterial chaperonin complex comprises GroEL, that forms a barrel-like oligomer, and GroES that forms the lid. In most eubacteria the GroES/GroEL chaperonin is encoded by a sin...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw287
更新日期:2017-01-01 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::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::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::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::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::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::Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired sh...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu046
更新日期:2014-03-01 00:00:00
abstract::Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evp030
更新日期:2009-08-13 00:00:00
abstract::Tandem repeats (TRs) are highly dynamic regions of the genome. Mutations at these loci represent a significant source of genetic variation and can facilitate rapid adaptation. Bumblebees are important pollinating insects occupying a wide range of habitats. However, to date, molecular mechanisms underlying the potentia...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy244
更新日期:2018-12-01 00:00:00
abstract::Dosage compensation--equalizing gene expression levels in response to differences in gene dose or copy number--is classically considered to play a critical role in the evolution of heteromorphic sex chromosomes. As the X and Y diverge through degradation and gene loss on the Y (or the W in female-heterogametic ZW taxa...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr036
更新日期:2011-01-01 00:00:00
abstract::Because of its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy086
更新日期:2018-05-01 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::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 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::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::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::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::Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw185
更新日期:2016-09-19 00:00:00