Expansion and Functional Divergence of the SHORT VEGETATIVE PHASE (SVP) Genes in Eudicots.

abstract：:Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer's yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high quality long read genomes of non-domesticated yeast strains isolated from primeval forests...

journal_title：Genome biology and evolution

authors： Bendixsen DP,Gettle N,Gilchrist C,Zhang Z,Stelkens R

更新日期：2021-01-11 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

authors： Irwin NAT,Keeling PJ

更新日期：2019-03-01 00:00:00

abstract：:The mechanistic basis of regulatory variation and the prevailing evolutionary forces shaping that variation are known to differ between sexes and between chromosomes. Regulatory variation of gene expression can be due to functional changes within a gene itself (cis) or in other genes elsewhere in the genome (trans). T...

journal_title：Genome biology and evolution

authors： Graze RM,McIntyre LM,Morse AM,Boyd BM,Nuzhdin SV,Wayne ML

更新日期：2014-04-01 00:00:00

abstract：:By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are le...

journal_title：Genome biology and evolution

authors： Evangelisti AM,Conant GC

更新日期：2010-01-01 00:00:00

abstract：:In the experimental evolution of microbes such as Escherichia coli, many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus ea...

journal_title：Genome biology and evolution

authors： Sprouffske K,Aguilar-Rodríguez J,Wagner A

更新日期：2016-05-09 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

authors： Bankoff RJ,Jerjos M,Hohman B,Lauterbur ME,Kistler L,Perry GH

更新日期：2017-07-01 00:00:00

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

authors： Campos PF,Andrade-Silva D,Zelanis A,Paes Leme AF,Rocha MM,Menezes MC,Serrano SM,Junqueira-de-Azevedo Ide L

更新日期：2016-08-16 00:00:00

abstract：:In general, proteins do not work alone; they form macromolecular complexes to play fundamental roles in diverse cellular functions. On the basis of their iterative clustering procedure and frequency of occurrence in the macromolecular complexes, the protein subunits have been categorized as core and attachment. Core p...

journal_title：Genome biology and evolution

authors： Chakraborty S,Ghosh TC

更新日期：2013-01-01 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

authors： Meisel RP,Scott JG,Clark AG

更新日期：2015-07-02 00:00:00

abstract：:Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trema...

journal_title：Genome biology and evolution

authors： Zajac N,Zoller S,Seppälä K,Moi D,Dessimoz C,Jokela J,Hartikainen H,Glover N

更新日期：2021-01-23 00:00:00

abstract：:Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. Recently, an antibiotic-resistant strain of this serovar was implicated in a large 2011 multistate outbreak resulting from consumption of contaminated ground turkey that involved 136 confirmed...

journal_title：Genome biology and evolution

authors： Hoffmann M,Zhao S,Pettengill J,Luo Y,Monday SR,Abbott J,Ayers SL,Cinar HN,Muruvanda T,Li C,Allard MW,Whichard J,Meng J,Brown EW,McDermott PF

更新日期：2014-05-01 00:00:00

abstract：:Different genes and proteins evolve at very different rates. To identify the factors that explain these differences is an important aspect of research in molecular evolution. One such factor is the role a protein plays in a large molecular network. Here, we analyze the evolutionary rates of enzyme-coding genes in the ...

journal_title：Genome biology and evolution

authors： Aguilar-Rodríguez J,Wagner A

更新日期：2018-11-01 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

authors： Vance KW,Woodcock DJ,Reid JE,Bretschneider T,Ott S,Koentges G

更新日期：2015-09-04 00:00:00

abstract：:Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a si...

journal_title：Genome biology and evolution

authors： Bitarello BD,de Filippo C,Teixeira JC,Schmidt JM,Kleinert P,Meyer D,Andrés AM

更新日期：2018-03-01 00:00:00

abstract：:Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf ...

journal_title：Genome biology and evolution

authors： Arakawa T,Kagami H,Katsuyama T,Kitazaki K,Kubo T

更新日期：2020-12-06 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

authors： Doroghazi JR,Buckley DH

更新日期：2011-01-01 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

authors： Mahajan S,Bachtrog D

更新日期：2015-01-18 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

authors： Goo SM,Cho S

更新日期：2013-01-01 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

authors： Wolf JB,Künstner A,Nam K,Jakobsson M,Ellegren H

更新日期：2009-08-13 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

authors： Tomala K,Korona R

更新日期：2013-01-01 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

authors： Lang D,Weiche B,Timmerhaus G,Richardt S,Riaño-Pachón DM,Corrêa LG,Reski R,Mueller-Roeber B,Rensing SA

更新日期：2010-07-19 00:00:00

abstract：:Mitochondrial evolution has given rise to a complex array of organelles, ranging from classical aerobic mitochondria to mitochondrial remnants known as hydrogenosomes and mitosomes. The latter are found in anaerobic eukaryotes, and these highly derived organelles often retain only scant evidence of their mitochondrial...

journal_title：Genome biology and evolution

authors： Pérez-Brocal V,Shahar-Golan R,Clark CG

更新日期：2010-07-12 00:00:00

abstract：:RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded p...

journal_title：Genome biology and evolution

authors： Dong S,Zhao C,Zhang S,Wu H,Mu W,Wei T,Li N,Wan T,Liu H,Cui J,Zhu R,Goffinet B,Liu Y

更新日期：2019-11-01 00:00:00

abstract：:The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors...

journal_title：Genome biology and evolution

authors： Jackman SD,Warren RL,Gibb EA,Vandervalk BP,Mohamadi H,Chu J,Raymond A,Pleasance S,Coope R,Wildung MR,Ritland CE,Bousquet J,Jones SJ,Bohlmann J,Birol I

更新日期：2015-12-08 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

authors： Bertelli C,Cissé OH,Rusconi B,Kebbi-Beghdadi C,Croxatto A,Goesmann A,Collyn F,Greub G

更新日期：2016-08-25 00:00:00

abstract：:The question on the patterns and limits of reduction of plastid genomes in nonphotosynthetic plants and the reasons of their conservation is one of the intriguing topics in plant genome evolution. Here, we report sequencing and analysis of plastid genome in nonphotosynthetic orchids Epipogium aphyllum and Epipogium ro...

journal_title：Genome biology and evolution

authors： Schelkunov MI,Shtratnikova VY,Nuraliev MS,Selosse MA,Penin AA,Logacheva MD

更新日期：2015-01-28 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

authors： Piekut T,Wong YY,Walker SE,Smith CL,Gauberg J,Harracksingh AN,Lowden C,Novogradac BB,Cheng HM,Spencer GE,Senatore A

更新日期：2020-08-01 00:00:00

abstract：:It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of gene...

journal_title：Genome biology and evolution

authors： Hernández-López A,Chabrol O,Royer-Carenzi M,Merhej V,Pontarotti P,Raoult D

更新日期：2013-01-01 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

authors： Fares MA,Sabater-Muñoz B,Toft C

更新日期：2017-05-01 00:00:00

abstract：:The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host im...

journal_title：Genome biology and evolution

authors： Glander S,He F,Schmitz G,Witten A,Telschow A,de Meaux J

更新日期：2018-09-01 00:00:00