Comparative Genomic Analysis of Acanthamoeba Endosymbionts Highlights the Role of Amoebae as a "Melting Pot" Shaping the Rickettsiales Evolution.

abstract：:Mitochondrial (mt) genomes are intensively studied in Ascomycota and Basidiomycota, but they are poorly documented in basal fungal lineages. In this study, we sequenced the complete mtDNA of Rhizophagus sp. DAOM 213198, a close relative to Rhizophagus irregularis, a widespread, ecologically and economical relevant spe...

journal_title：Genome biology and evolution

authors： Nadimi M,Stefani FO,Hijri M

更新日期：2014-12-19 00:00:00

abstract：:The propensity of protein sites to be occupied by any of the 20 amino acids is known as site-specific amino acid preferences (SSAP). Under the assumption that SSAP are conserved among homologs, they can be used to parameterize evolutionary models for the reconstruction of accurate phylogenetic trees. However, simulati...

journal_title：Genome biology and evolution

authors： Ferrada E

更新日期：2019-01-01 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：:Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats...

journal_title：Genome biology and evolution

authors： Zoldoš V,Biruš I,Muratovic E,Šatovic Z,Vojta A,Robin O,Pustahija F,Bogunic F,Vicic Bockor V,Siljak-Yakovlev S

更新日期：2018-01-01 00:00:00

abstract：:Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to...

journal_title：Genome biology and evolution

authors： Fujita MK,Edwards SV,Ponting CP

更新日期：2011-01-01 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：:In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive...

journal_title：Genome biology and evolution

authors： De Maeyer D,Weytjens B,De Raedt L,Marchal K

更新日期：2016-01-23 00:00:00

abstract：:Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and...

journal_title：Genome biology and evolution

authors： Coronado-Zamora M,Salvador-Martínez I,Castellano D,Barbadilla A,Salazar-Ciudad I

更新日期：2019-05-01 00:00:00

abstract：:Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here...

journal_title：Genome biology and evolution

authors： Sarver BA,Demboski JR,Good JM,Forshee N,Hunter SS,Sullivan J

更新日期：2017-01-01 00:00:00

abstract：:Positive selection and purifying selection reduce levels of variation at linked neutral loci. One consequence of these processes is that the amount of neutral diversity and the meiotic recombination rate are predicted to be positively correlated across the genome-a prediction met in some species but not others. To bet...

journal_title：Genome biology and evolution

authors： Kartje ME,Jing P,Payseur BA

更新日期：2020-04-01 00:00:00

abstract：:Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availabil...

journal_title：Genome biology and evolution

authors： Wilhelmsson PKI,Mühlich C,Ullrich KK,Rensing SA

更新日期：2017-12-01 00:00:00

abstract：:Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (blac...

journal_title：Genome biology and evolution

authors： Thorpe P,Escudero-Martinez CM,Cock PJA,Eves-van den Akker S,Bos JIB

更新日期：2018-10-01 00:00:00

abstract：:The loss of Y-linked genes during sex chromosome evolution creates a potentially deleterious low gene dosage in males. Recent studies have reported different strategies of dosage compensation. Unfortunately, most of these studies investigated taxa with comparatively old sex chromosome systems, which may limit insights...

journal_title：Genome biology and evolution

authors： Schultheiß R,Viitaniemi HM,Leder EH

更新日期：2015-01-23 00:00:00

abstract：:The evolution of heterogametic sex chromosomes is often-but not always-accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) s...

journal_title：Genome biology and evolution

authors： Walters JR,Hardcastle TJ,Jiggins CD

更新日期：2015-09-02 00:00:00

abstract：:Tandem repeats (TRs) are highly dynamic regions of the genome. Mutations at these loci represent a significant source of genetic variation and can facilitate rapid adaptation. Bumblebees are important pollinating insects occupying a wide range of habitats. However, to date, molecular mechanisms underlying the potentia...

journal_title：Genome biology and evolution

authors： Zhao X,Su L,Schaack S,Sadd BM,Sun C

更新日期：2018-12-01 00:00:00

abstract：:Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems. However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small ...

journal_title：Genome biology and evolution

authors： Gottlieb Y,Lalzar I,Klasson L

更新日期：2015-05-28 00:00:00

abstract：:The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of N...

journal_title：Genome biology and evolution

authors： Morris AG,Heinze A,Chan EK,Smith AB,Hayes VM

更新日期：2014-09-10 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：: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：: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

authors： Vandewege MW,Mangum SF,Gabaldón T,Castoe TA,Ray DA,Hoffmann FG

更新日期：2016-02-09 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：: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

authors： Moore GG,Mack BM,Beltz SB

更新日期：2015-12-03 00:00:00

abstract：:Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mut...

journal_title：Genome biology and evolution

authors： Katju V,Bergthorsson U

更新日期：2019-01-01 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：:Adaptive prediction is a capability of diverse organisms, including microbes, to sense a cue and prepare in advance to deal with a future environmental challenge. Here, we investigated the timeframe over which adaptive prediction emerges when an organism encounters an environment with novel structure. We subjected yea...

journal_title：Genome biology and evolution

authors： López García de Lomana A,Kaur A,Turkarslan S,Beer KD,Mast FD,Smith JJ,Aitchison JD,Baliga NS

更新日期：2017-06-01 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：:The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary ...

journal_title：Genome biology and evolution

authors： Wetzel ME,Olsen GJ,Chakravartty V,Farrand SK

更新日期：2015-11-19 00:00:00

abstract：:Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustai...

journal_title：Genome biology and evolution

authors： Boon E,Halary S,Bapteste E,Hijri M

更新日期：2015-01-07 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：:Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0-3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning m...

journal_title：Genome biology and evolution

authors： Taylor-Brown A,Pillonel T,Greub G,Vaughan L,Nowak B,Polkinghorne A

更新日期：2018-10-01 00:00:00