Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism.

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：: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：: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

authors： Hayes K,Barton HJ,Zeng K

更新日期：2020-03-01 00:00:00

abstract：:The family Actinomycetaceae comprises several important pathogens that impose serious threat to human health and cause substantial infections of economically important animals. However, the phylogeny and evolutionary dynamic of this family are poorly characterized. Here, we provide detailed description of the genome c...

journal_title：Genome biology and evolution

authors： Zhao K,Li W,Kang C,Du L,Huang T,Zhang X,Wu M,Yue B

更新日期：2014-09-22 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

authors： R Marcelino V,Cremen MC,Jackson CJ,Larkum AA,Verbruggen H

更新日期：2016-10-05 00:00:00

abstract：:Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model s...

journal_title：Genome biology and evolution

authors： Chen ZH,Zhang M,Lv FH,Ren X,Li WR,Liu MJ,Nam K,Bruford MW,Li MH

更新日期：2018-04-01 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

authors： Irwin NAT,Keeling PJ

更新日期：2019-03-01 00:00:00

abstract：:The root-knot nematodes (genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding...

journal_title：Genome biology and evolution

authors： Szitenberg A,Salazar-Jaramillo L,Blok VC,Laetsch DR,Joseph S,Williamson VM,Blaxter ML,Lunt DH

更新日期：2017-10-01 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

authors： Murillo T,Ramírez-Vargas G,Riedel T,Overmann J,Andersen JM,Guzmán-Verri C,Chaves-Olarte E,Rodríguez C

更新日期：2018-03-01 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：: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

authors： Takezaki N

更新日期：2018-07-01 00:00:00

abstract：:Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abioti...

journal_title：Genome biology and evolution

authors： Mohd-Assaad N,McDonald BA,Croll D

更新日期：2018-04-01 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

authors： Tomala K,Korona R

更新日期：2013-01-01 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

authors： Kent BN,Salichos L,Gibbons JG,Rokas A,Newton IL,Clark ME,Bordenstein SR

更新日期：2011-01-01 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

authors： Baymann F,Schoepp-Cothenet B,Lebrun E,van Lis R,Nitschke W

更新日期：2012-01-01 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

authors： Jiang X,Tang H,Ye Z,Lynch M

更新日期：2017-02-01 00:00:00

abstract：:The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatale...

journal_title：Genome biology and evolution

authors： Luo Y,Ma PF,Li HT,Yang JB,Wang H,Li DZ

更新日期：2016-04-06 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

authors： Smith DR

更新日期：2015-04-13 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：:Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model ...

journal_title：Genome biology and evolution

authors： Riba A,Fumagalli MR,Caselle M,Osella M

更新日期：2020-11-03 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

authors： Nishihara H,Plazzi F,Passamonti M,Okada N

更新日期：2016-02-12 00:00:00

abstract：:Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of geni...

journal_title：Genome biology and evolution

authors： Smith DR,Hua J,Archibald JM,Lee RW

更新日期：2013-01-01 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

authors： Otto W,Stadler PF,López-Giraldéz F,Townsend JP,Lynch VJ,Wagner GP

更新日期：2009-05-25 00:00:00

abstract：:Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with ...

journal_title：Genome biology and evolution

authors： Lynch M,Bost D,Wilson S,Maruki T,Harrison S

更新日期：2014-04-30 00:00:00

abstract：:Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lo...

journal_title：Genome biology and evolution

authors： Huylmans AK,Toups MA,Macon A,Gammerdinger WJ,Vicoso B

更新日期：2019-04-01 00:00:00

abstract：:Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given t...

journal_title：Genome biology and evolution

authors： Díaz-Viraqué F,Pita S,Greif G,de Souza RCM,Iraola G,Robello C

更新日期：2019-07-01 00:00:00

abstract：:Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. ...

journal_title：Genome biology and evolution

authors： Coimbra NDR,Goes-Neto A,Azevedo V,Ouangraoua A

更新日期：2020-04-01 00:00:00

abstract：:Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile ...

journal_title：Genome biology and evolution

authors： Hill PL,Burridge CP,Ezaz T,Wapstra E

更新日期：2018-04-01 00:00:00

abstract：:The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity f...

journal_title：Genome biology and evolution

authors： Tang H,Bomhoff MD,Briones E,Zhang L,Schnable JC,Lyons E

更新日期：2015-11-11 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