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, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we describe 15 SINEs, among which 13 are novel, that have a similar 66-bp central region and therefore constitute a new SINE superfamily, MetaSINEs. MetaSINEs are distributed from fish to cnidarians, suggesting their common evolutionary origin at least 640 Ma. Because the 3' tails of MetaSINEs are variable, these SINEs most likely survived by changing their partner long interspersed elements for retrotransposition during evolution. Furthermore, we examined the presence of members of other SINE superfamilies in bivalve genomes and characterized eight new SINEs belonging to the CORE-SINEs, V-SINEs, and DeuSINEs, in addition to the MetaSINEs. The broad distribution of bivalve SINEs suggests that at least three SINEs originated in the common ancestor of Bivalvia. Our comparative analysis of the central domains of the SINEs revealed that, in each superfamily, only a restricted region is shared among all of its members. Because the functions of the central domains of the SINE superfamilies remain unknown, such structural information of SINE superfamilies will be useful for future experimental and comparative analyses to reveal why they have been retained in metazoan genomes during evolution.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Nishihara H,Plazzi F,Passamonti M,Okada Ndoi
10.1093/gbe/evw029subject
Has Abstractpub_date
2016-02-12 00:00:00pages
528-39issue
3issn
1759-6653pii
evw029journal_volume
8pub_type
杂志文章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::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::Analysis of more than 150 Clostridium botulinum Group II type E genomes identified a small fraction (6%) where neurotoxin-encoding genes were located on plasmids. Seven closely related (134-144 kb) neurotoxigenic plasmids of subtypes E1, E3, and E10 were characterized; all carried genes associated with plasmid mobilit...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw017
更新日期:2016-03-02 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::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::One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the main...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw219
更新日期:2016-10-12 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::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::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::Klebsiella pneumoniae clonal group (CG) 258, comprising sequence types (STs) 258, 11, and closely related variants, is associated with dissemination of the K. pneumoniae carbapenemase (KPC). Hospital outbreaks of KPC CG258 infections have been observed globally and are very difficult to treat. As a consequence, there ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv062
更新日期:2015-04-10 00:00:00
abstract::Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we i...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa065
更新日期:2020-04-01 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::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::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::The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu288
更新日期:2015-01-09 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::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::Many organisms have a global mechanism for dosage compensation (DC) operating along the entire male X chromosome, which equalizes gene expression on the male X with that on the two Xs in females and/or on autosomes. At the initial stage of sex chromosome evolution, however, gene-by-gene (or localized) DC may also be n...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy148
更新日期:2018-08-01 00:00:00
abstract::Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homol...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy059
更新日期:2018-03-01 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::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::It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a compa...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv209
更新日期:2015-11-01 00:00:00
abstract::Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meni...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu094
更新日期:2014-05-06 00:00:00
abstract::Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx169
更新日期:2017-09-01 00:00:00
abstract::Experimental evolution allows the observation of change over time as laboratory populations evolve in response to novel, controlled environments. Microbial evolution experiments take advantage of cryopreservation to archive experimental populations in glycerol media, creating a frozen, living "fossil" record. Prior re...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa121
更新日期:2020-08-01 00:00:00
abstract::The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr047
更新日期:2011-01-01 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::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::Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N2O) emissions. Despite extensive efforts, fungal contributions to N2O emissions remain uncertain. For example, the majority of N2O emitted from antibiotic-ame...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy187
更新日期:2018-09-01 00:00:00
abstract::Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled th...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa108
更新日期:2020-07-01 00:00:00