Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle.

abstract：BACKGROUND:One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this f...

journal_title：BMC genomics

authors： Li F,Nellåker C,Yolken RH,Karlsson H

更新日期：2011-01-12 00:00:00

abstract：BACKGROUND:Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the famil...

journal_title：BMC genomics

authors： Cong Q,Borek D,Otwinowski Z,Grishin NV

更新日期：2015-08-27 00:00:00

abstract：BACKGROUND:Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. Often, crop improvement and management activities are segregated by crop type, thus preserving unique genome diversity and organization. Full interfertility is typically retained in crosses betwe...

journal_title：BMC genomics

authors： Galewski P,McGrath JM

更新日期：2020-03-02 00:00:00

abstract：BACKGROUND:Alternative σ factors are important transcriptional regulators in bacteria. While σ(B) has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σ(H) has not yet been well defined in Listeria, even though σ(H) c...

journal_title：BMC genomics

authors： Liu Y,Orsi RH,Boor KJ,Wiedmann M,Guariglia-Oropeza V

更新日期：2016-02-16 00:00:00

abstract：BACKGROUND:Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number ...

journal_title：BMC genomics

authors： Rusinov IS,Ershova AS,Karyagina AS,Spirin SA,Alexeevski AV

更新日期：2018-12-07 00:00:00

abstract：BACKGROUND:Neighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone m...

journal_title：BMC genomics

authors： Deng Y,Dai X,Xiang Q,Dai Z,He C,Wang J,Feng J

更新日期：2010-10-09 00:00:00

abstract：BACKGROUND:Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicate...

journal_title：BMC genomics

authors： De Maayer P,Chan WY,Rubagotti E,Venter SN,Toth IK,Birch PR,Coutinho TA

更新日期：2014-05-27 00:00:00

abstract：BACKGROUND:Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regressi...

journal_title：BMC genomics

authors： Gong P,Nan X,Barker ND,Boyd RE,Chen Y,Wilkins DE,Johnson DR,Suedel BC,Perkins EJ

更新日期：2016-03-08 00:00:00

abstract：BACKGROUND:Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross-talks between bacteria and human host to date. METHODS:In this work, ta...

journal_title：BMC genomics

authors： Mei S,Flemington EK,Zhang K

更新日期：2018-06-28 00:00:00

abstract：BACKGROUND:Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are develo...

journal_title：BMC genomics

authors： Guardia GD,Vêncio RZ,de Farias CR

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly anal...

journal_title：BMC genomics

authors： Williams D,Trimble WL,Shilts M,Meyer F,Ochman H

更新日期：2013-08-08 00:00:00

abstract：BACKGROUND:Oxidative stress is a consequence of normal and abnormal cellular metabolism and is linked to the development of human diseases. The effective functioning of the pathway responding to oxidative stress protects the cellular DNA against oxidative damage; conversely the failure of the oxidative stress response ...

journal_title：BMC genomics

authors： Sridharan S,Layek R,Datta A,Venkatraj J

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Tubulin isotypes and expression patterns are highly regulated in diverse organisms. The genome sequence of the protozoan parasite Leishmania major contains three distinct beta-tubulin loci. To investigate the diversity of beta-tubulin genes, we have compared the published genome sequence to draft genome sequ...

journal_title：BMC genomics

authors： Jackson AP,Vaughan S,Gull K

更新日期：2006-06-06 00:00:00

abstract：BACKGROUND:Sugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causing severe losses to the sugarcane industry. The use of PCR reference genes is essential to the no...

journal_title：BMC genomics

authors： Huang N,Ling H,Liu F,Su Y,Su W,Mao H,Zhang X,Wang L,Chen R,Que Y

更新日期：2018-06-19 00:00:00

abstract：BACKGROUND:Regions of the genome that are under evolutionary constraint across multiple species have previously been used to identify functional sequences in the human genome. Furthermore, it is known that there is an inverse relationship between evolutionary constraint and the allele frequency of a mutation segregatin...

journal_title：BMC genomics

authors： Hodgkinson A,Casals F,Idaghdour Y,Grenier JC,Hernandez RD,Awadalla P

更新日期：2013-07-23 00:00:00

abstract：BACKGROUND:Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great...

journal_title：BMC genomics

authors： Velie BD,Lillie M,Fegraeus KJ,Rosengren MK,Solé M,Wiklund M,Ihler CF,Strand E,Lindgren G

更新日期：2019-02-04 00:00:00

abstract：BACKGROUND:The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to ide...

journal_title：BMC genomics

authors： Salisbury J,Hutchison KW,Graber JH

更新日期：2006-03-16 00:00:00

abstract：BACKGROUND:Identification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgn...

journal_title：BMC genomics

authors： Tu Q,Lin L

更新日期：2016-08-17 00:00:00

abstract：BACKGROUND:Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the b...

journal_title：BMC genomics

authors： Pannebakker BA,Cook N,van den Heuvel J,van de Zande L,Shuker DM

更新日期：2020-07-20 00:00:00

abstract：BACKGROUND:Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease f...

journal_title：BMC genomics

authors： Tremblay DC,Alexander G Jr,Moseley S,Chadwick BP

更新日期：2010-11-15 00:00:00

abstract：BACKGROUND:Designing sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig, it is necessary to increase knowledge on its immune system and to produce efficient tools dedicate...

journal_title：BMC genomics

authors： Gao Y,Flori L,Lecardonnel J,Esquerré D,Hu ZL,Teillaud A,Lemonnier G,Lefèvre F,Oswald IP,Rogel-Gaillard C

更新日期：2010-05-11 00:00:00

abstract：BACKGROUND:The genetic mechanisms underlying hemangioblastoma development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays and droplet digital PCR analysis to detect copy number variations (CNVs) in total of 45 hemangioblastoma tumors. RESULTS:We identified 94 CNVs with a m...

journal_title：BMC genomics

authors： Mehrian-Shai R,Yalon M,Moshe I,Barshack I,Nass D,Jacob J,Dor C,Reichardt JK,Constantini S,Toren A

更新日期：2016-01-14 00:00:00

abstract：BACKGROUND:Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and s...

journal_title：BMC genomics

authors： Narsai R,Wang C,Chen J,Wu J,Shou H,Whelan J

更新日期：2013-02-12 00:00:00

abstract：BACKGROUND:Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuti...

journal_title：BMC genomics

authors： Deng CH,Plummer KM,Jones DAB,Mesarich CH,Shiller J,Taranto AP,Robinson AJ,Kastner P,Hall NE,Templeton MD,Bowen JK

更新日期：2017-05-02 00:00:00

abstract：BACKGROUND:Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity,...

journal_title：BMC genomics

authors： English AC,Salerno WJ,Hampton OA,Gonzaga-Jauregui C,Ambreth S,Ritter DI,Beck CR,Davis CF,Dahdouli M,Ma S,Carroll A,Veeraraghavan N,Bruestle J,Drees B,Hastie A,Lam ET,White S,Mishra P,Wang M,Han Y,Zhang F,Stankie

更新日期：2015-04-11 00:00:00

abstract：BACKGROUND:Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the protein secretory pathway of this biotechnologically relevant fungus, we undertook genome-wide analyse...

journal_title：BMC genomics

authors： Aguiar TQ,Ribeiro O,Arvas M,Wiebe MG,Penttilä M,Domingues L

更新日期：2014-12-18 00:00:00

abstract：BACKGROUND:Genome-wide association studies show that most human traits and diseases are caused by a combination of environmental and genetic causes, with each one of these having a relatively small effect. In contrast, most therapies based on macromolecules like antibodies, antisense oligonucleotides or peptides focus ...

journal_title：BMC genomics

authors： Varela MA

更新日期：2015-07-18 00:00:00

abstract：BACKGROUND:Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant specie...

journal_title：BMC genomics

authors： De Paola D,Cattonaro F,Pignone D,Sonnante G

更新日期：2012-01-24 00:00:00

abstract：BACKGROUND:Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study ...

journal_title：BMC genomics

authors： Li GH,Chen HC,Liu JL,Luo WL,Xie DS,Luo SB,Wu TQ,Akram W,Zhong YJ

更新日期：2019-05-07 00:00:00

abstract：BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...

journal_title：BMC genomics

authors： Lehnert EM,Burriesci MS,Pringle JR

更新日期：2012-06-22 00:00:00