High rate of large deletions in Caenorhabditis briggsae mitochondrial genome mutation processes.

abstract：:Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired sh...

journal_title：Genome biology and evolution

authors： Guo W,Grewe F,Cobo-Clark A,Fan W,Duan Z,Adams RP,Schwarzbach AE,Mower JP

更新日期：2014-03-01 00:00:00

abstract：:Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally...

journal_title：Genome biology and evolution

authors： Glinsky GV

更新日期：2016-09-19 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

authors： Sykes T,Yates S,Nagy I,Asp T,Small I,Studer B

更新日期：2017-02-01 00:00:00

abstract：:Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two ...

journal_title：Genome biology and evolution

authors： Luchetti A,Plazzi F,Mantovani B

更新日期：2017-06-01 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：:Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV...

journal_title：Genome biology and evolution

authors： Simons ND,Eick GN,Ruiz-Lopez MJ,Hyeroba D,Omeja PA,Weny G,Zheng H,Shankar A,Frost SDW,Jones JH,Chapman CA,Switzer WM,Goldberg TL,Sterner KN,Ting N

更新日期：2019-06-01 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：: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：: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：: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：: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

abstract：:Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophu...

journal_title：Genome biology and evolution

authors： García-Pérez R,Ibáñez C,Godínez JM,Aréchiga N,Garin I,Pérez-Suárez G,de Paz O,Juste J,Echevarría JE,Bravo IG

更新日期：2014-01-01 00:00:00

abstract：:Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chloro...

journal_title：Genome biology and evolution

authors： Miller SR,Wood AM,Blankenship RE,Kim M,Ferriera S

更新日期：2011-01-01 00:00:00

abstract：:piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. More...

journal_title：Genome biology and evolution

authors： Kofler R

更新日期：2020-05-01 00:00:00

abstract：:The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard tha...

journal_title：Genome biology and evolution

authors： Kelly JK,Koseva B,Mojica JP

更新日期：2013-01-01 00:00:00

abstract：:The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic in...

journal_title：Genome biology and evolution

authors： Freese HM,Sikorski J,Bunk B,Scheuner C,Meier-Kolthoff JP,Spröer C,Gram L,Overmann J

更新日期：2017-12-01 00:00:00

abstract：:Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morph...

journal_title：Genome biology and evolution

authors： Huang Z,Duan W,Song X,Tang J,Wu P,Zhang B,Hou X

更新日期：2015-12-31 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：:The study of microbe domestication has witnessed major advances that contribute to a better understanding of the emergence of artificially selected phenotypes and set the foundations of their rational improvement for biotechnology. Several features make Saccharomyces cerevisiae an ideal model for such a study, notably...

journal_title：Genome biology and evolution

authors： Barbosa R,Pontes A,Santos RO,Montandon GG,de Ponzzes-Gomes CM,Morais PB,Gonçalves P,Rosa CA,Sampaio JP

更新日期：2018-08-01 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：: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：:Campylobacter sputorum is a nonthermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase neg...

journal_title：Genome biology and evolution

authors： Miller WG,Yee E,Chapman MH,Bono JL

更新日期：2017-06-01 00:00:00

abstract：:Parasites are sometimes able to manipulate the behavior of their hosts. However, the molecular cues underlying this phenomenon are poorly documented. We previously reported that the parasitoid wasp Leptopilina boulardi which develops from Drosophila larvae is often infected by an inherited DNA virus. In addition to be...

journal_title：Genome biology and evolution

authors： Lepetit D,Gillet B,Hughes S,Kraaijeveld K,Varaldi J

更新日期：2016-12-01 00:00:00

abstract：:Constitutive defense mechanisms are critical to the understanding of defense mechanisms in conifers because they constitute the first barrier to attacks by insect pests. In interior spruce, trees that are putatively resistant and susceptible to attacks by white pine weevil (Pissodes strobi) typically exhibit constitut...

journal_title：Genome biology and evolution

authors： Verne S,Jaquish B,White R,Ritland C,Ritland K

更新日期：2011-01-01 00:00:00

abstract：:Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by mult...

journal_title：Genome biology and evolution

authors： Reyes-Bermudez A,Villar-Briones A,Ramirez-Portilla C,Hidaka M,Mikheyev AS

更新日期：2016-03-23 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：:Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly...

journal_title：Genome biology and evolution

authors： Abascal F,Tress ML,Valencia A

更新日期：2015-04-29 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：:Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, howe...

journal_title：Genome biology and evolution

authors： Naidoo T,Xu J,Vicente M,Malmström H,Soodyall H,Jakobsson M,Schlebusch CM

更新日期：2020-07-01 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