Multiple Rounds of Artificial Selection Promote Microbe Secondary Domestication-The Case of Cachaça Yeasts.

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：: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

authors： Gan P,Narusaka M,Kumakura N,Tsushima A,Takano Y,Narusaka Y,Shirasu K

更新日期：2016-05-22 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

authors： Fort P,Kajava AV,Delsuc F,Coux O

更新日期：2015-05-04 00:00:00

abstract：:Clashes between transcription and replication complexes can cause point mutations and chromosome rearrangements on heavily transcribed genes. In eukaryotic ribosomal RNA genes, the system that prevents transcription-replication conflicts also causes frequent copy number variation. Such fast mutational dynamics do not ...

journal_title：Genome biology and evolution

authors： Colizzi ES,Hogeweg P

更新日期：2019-11-01 00:00:00

abstract：:Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most...

journal_title：Genome biology and evolution

authors： Zhang F,Broughton RE

更新日期：2013-01-01 00:00:00

abstract：:Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here...

journal_title：Genome biology and evolution

authors： Assis R

更新日期：2019-01-01 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：:Chlorarachniophytes are unicellular marine algae with plastids (chloroplasts) of secondary endosymbiotic origin. Chlorarachniophyte cells retain the remnant nucleus (nucleomorph) and cytoplasm (periplastidial compartment, PPC) of the green algal endosymbiont from which their plastid was derived. To characterize the di...

journal_title：Genome biology and evolution

authors： Hopkins JF,Spencer DF,Laboissiere S,Neilson JA,Eveleigh RJ,Durnford DG,Gray MW,Archibald JM

更新日期：2012-01-01 00:00:00

abstract：:Many algal groups acquired complex plastids by the uptake of green and red algae through multiple secondary endosymbioses. As a result of gene loss and transfer during the endosymbiotic processes, algal endosymbiont nuclei disappeared in most cases. However, chlorarachniophytes and cryptophytes still possess a relict ...

journal_title：Genome biology and evolution

authors： Suzuki S,Shirato S,Hirakawa Y,Ishida K

更新日期：2015-05-22 00:00:00

abstract：:The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...

journal_title：Genome biology and evolution

authors： Li C,Wang Z,Zhang J

更新日期：2013-01-01 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：: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：:DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here, ...

journal_title：Genome biology and evolution

authors： Kvist J,Gonçalves Athanàsio C,Shams Solari O,Brown JB,Colbourne JK,Pfrender ME,Mirbahai L

更新日期：2018-08-01 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

authors： Lu MR,Lai CK,Liao BY,Tsai IJ

更新日期：2020-07-01 00:00:00

abstract：:Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene co...

journal_title：Genome biology and evolution

authors： Brockman SA,McFadden CS

更新日期：2012-01-01 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

authors： Link V,Aguilar-Gómez D,Ramírez-Suástegui C,Hurst LD,Cortez D

更新日期：2017-09-01 00:00:00

abstract：:The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be ass...

journal_title：Genome biology and evolution

authors： Arber W

更新日期：2011-01-01 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

authors： Öztürk B,Werner J,Meier-Kolthoff JP,Bunk B,Spröer C,Springael D

更新日期：2020-06-01 00:00:00

abstract：:Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2...

journal_title：Genome biology and evolution

authors： Lin YL,Gokcumen O

更新日期：2019-04-01 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

authors： Vegesna R,Tomaszkiewicz M,Ryder OA,Campos-Sánchez R,Medvedev P,DeGiorgio M,Makova KD

更新日期：2020-06-01 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

authors： Weissenbach J,Ilhan J,Bogumil D,Hülter N,Stucken K,Dagan T

更新日期：2017-01-01 00:00:00

abstract：:Bitter taste perception likely evolved as a protective mechanism against the ingestion of harmful compounds in food. The evolution of the taste receptor type 2 (TAS2R) gene family, which encodes the chemoreceptors that are directly responsible for the detection of bitter compounds, has therefore been of considerable i...

journal_title：Genome biology and evolution

authors： Davis JK,Lowman JJ,Thomas PJ,ten Hallers BF,Koriabine M,Huynh LY,Maney DL,de Jong PJ,Martin CL,NISC Comparative Sequencing Program.,Thomas JW

更新日期：2010-07-12 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

authors： Ogier JC,Pagès S,Bisch G,Chiapello H,Médigue C,Rouy Z,Teyssier C,Vincent S,Tailliez P,Givaudan A,Gaudriault S

更新日期：2014-06-05 00:00:00

abstract：:The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effect...

journal_title：Genome biology and evolution

authors： Nabholz B,Uwimana N,Lartillot N

更新日期：2013-01-01 00:00:00

abstract：:Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to p...

journal_title：Genome biology and evolution

authors： Ely ZA,Moon JM,Sliwoski GR,Sangha AK,Shen XX,Labella AL,Meiler J,Capra JA,Rokas A

更新日期：2019-09-01 00:00:00

abstract：:Plants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example is secreted fungal effector proteins and their host targets, w...

journal_title：Genome biology and evolution

authors： Schweizer G,Münch K,Mannhaupt G,Schirawski J,Kahmann R,Dutheil JY

更新日期：2018-02-01 00:00:00

abstract：:As most genes are shared between females and males, DNA methylation is assumed to play a crucial role in sex-biased gene expression. DNA methylation exclusively occurs at CpG dinucleotides, and therefore, we would expect that CpG density around transcription start sites (TSSs) relate to sex-biased gene expression. Her...

journal_title：Genome biology and evolution

authors： Tamagawa K,Makino T,Kawata M

更新日期：2017-05-01 00:00:00

abstract：:Cyanobacteria are dominant primary producers of various ecosystems and they colonize marine as well as freshwater and terrestrial habitats. On the basis of their oxygenic photosynthesis they are known to synthesize a high number of secondary metabolites, which makes them promising for biotechnological applications. St...

journal_title：Genome biology and evolution

authors： Will SE,Henke P,Boedeker C,Huang S,Brinkmann H,Rohde M,Jarek M,Friedl T,Seufert S,Schumacher M,Overmann J,Neumann-Schaal M,Petersen J

更新日期：2019-01-01 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

authors： Schuelke TA,Wu G,Westbrook A,Woeste K,Plachetzki DC,Broders K,MacManes MD

更新日期：2017-12-01 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

authors： Chang YL,Li WY,Miao H,Yang SQ,Li R,Wang X,Li WQ,Chen KM

更新日期：2016-02-23 00:00:00