Abstract:
:Gene duplication is the primary source of new genes, but the mechanisms underlying the functional divergence and retention of duplicate genes are not well understood. Because eukaryotic proteins are localized to subcellular structures and localization can be altered by a single amino acid replacement, it was recently proposed that protein subcellular relocalization (PSR) plays an important role in the functional divergence and retention of duplicate genes. Although numerous examples of distinct subcellular localizations of paralogous proteins have been reported, it is unknown whether PSR occurs more frequently after gene duplication than without duplication. By analyzing experimentally determined and computationally predicted genome-wide protein subcellular localization data of the budding yeast Saccharomyces cerevisiae and two other fungi (Schizosaccharomyces pombe and Kluyveromyces waltii), we show that even singleton genes have an appreciable rate of relocalization in evolution and that duplicate genes do not relocalize more frequently than singletons. These results suggest that subcellular relocalization is unlikely to have been a major mechanism for duplicate gene retention and functional divergence at the genomic scale.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Qian W,Zhang Jdoi
10.1093/gbe/evp021subject
Has Abstractpub_date
2009-07-22 00:00:00pages
198-204issn
1759-6653journal_volume
1pub_type
信件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::The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary pr...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy198
更新日期:2018-11-01 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::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::A major mode of gene expression evolution is based on changes in cis-regulatory elements (CREs) whose function critically depends on the presence of transcription factor-binding sites (TFBS). Because CREs experience extensive TFBS turnover even with conserved function, alignment-based studies of CRE sequence evolution...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evp010
更新日期:2009-05-25 00:00:00
abstract::Macroevolutionary trends exhibited by retroviruses are complex and not entirely understood. The sloth endogenized foamy-like retrovirus (SloEFV), which demonstrates incongruence in virus-host evolution among extant sloths (Order Folivora), has not been investigated heretofore in any extinct sloth lineages and its prem...
journal_title:Genome biology and evolution
pub_type: 杂志文章
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更新日期:2016-02-14 00:00:00
abstract::Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Unlike other Xenorhabdus species, Xenorhabdus poinarii is avirulent when injected into insects in the ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
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更新日期:2014-06-05 00:00:00
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 cont...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy103
更新日期:2018-06-01 00:00:00
abstract::Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species' genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw206
更新日期:2016-10-05 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::Geosmithia morbida is an emerging fungal pathogen which serves as a model for examining the evolutionary processes behind pathogenicity because it is one of two known pathogens within a genus of mostly saprophytic, beetle-associated, fungi. This pathogen causes thousand cankers disease in black walnut trees and is vec...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx242
更新日期:2017-12-01 00:00:00
abstract::Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid a...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy165
更新日期:2018-09-01 00:00:00
abstract::Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multitissue transcriptome data set from great tit (Parus major), we analyzed patterns of molecular evolution between two pas...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu157
更新日期:2014-08-01 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::The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expressio...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz029
更新日期:2019-03-01 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::Throughout the animal kingdom chemical senses are one of the primary means by which organisms make sense of their environment. To achieve perception of complex chemosensory stimuli large repertoires of olfactory and gustatory receptors are employed in bony vertebrates, which are characterized by high evolutionary dyna...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evz002
更新日期:2019-02-01 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::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::Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw047
更新日期:2017-02-01 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::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::Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity, and the rate of adaptation. Nevertheless,...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz243
更新日期:2019-11-01 00:00:00
abstract::Plasma membrane NADPH oxidases (NOXs) are key producers of reactive oxygen species under both normal and stress conditions in plants and they form functional subfamilies. Studies of these subfamilies indicated that they show considerable evolutionary selection. We performed a comparative genomic analysis that identifi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw035
更新日期:2016-02-23 00:00:00
abstract::Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to be greater than that of the mitochondrial genome. This assumption is based on early, pioneering studies of land plant molecular evolution, which uncovered higher rates of synonymous substitution in plastid versus mitochondrial ...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evv069
更新日期:2015-04-13 00:00:00
abstract::Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,2...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw138
更新日期:2016-08-25 00:00:00
abstract::The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu195
更新日期:2014-09-04 00:00:00
abstract::Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv126
更新日期:2015-07-01 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::Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs056
更新日期:2012-01-01 00:00:00