Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness.

abstract：BACKGROUND:Cattle and other ruminants have evolved the ability to derive most of their metabolic energy requirement from otherwise indigestible plant matter through a symbiotic relationship with plant fibre degrading microbes within a specialised fermentation chamber, the rumen. The genetic changes underlying the evolu...

journal_title：BMC genomics

authors： Wheeler TT,Hood KA,Maqbool NJ,McEwan JC,Bingle CD,Zhao S

更新日期：2007-03-15 00:00:00

abstract：BACKGROUND:Maternal undernutrition leads to an increased risk of metabolic disorders in offspring including obesity and insulin resistance, thought to be due to a programmed thrifty phenotype which is inappropriate for a subsequent richer nutritional environment. In a rat model, both male and female offspring of undern...

journal_title：BMC genomics

authors： Ellis PJ,Morris TJ,Skinner BM,Sargent CA,Vickers MH,Gluckman PD,Gilmour S,Affara NA

更新日期：2014-01-21 00:00:00

abstract：BACKGROUND:The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequen...

journal_title：BMC genomics

authors： Kazakov AE,Rajeev L,Chen A,Luning EG,Dubchak I,Mukhopadhyay A,Novichkov PS

更新日期：2015-11-10 00:00:00

abstract：BACKGROUND:Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although transcriptomic and proteomic studies around the nematode life cycle have greatly enhanced our knowl...

journal_title：BMC genomics

authors： Luck AN,Anderson KG,McClung CM,VerBerkmoes NC,Foster JM,Michalski ML,Slatko BE

更新日期：2015-11-11 00:00:00

abstract：BACKGROUND:Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characterize the molecular processes associated with regeneration, we compared gene expression levels in hin...

journal_title：BMC genomics

authors： Turk R,Sterrenburg E,de Meijer EJ,van Ommen GJ,den Dunnen JT,'t Hoen PA

更新日期：2005-07-13 00:00:00

abstract：BACKGROUND:Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal re...

journal_title：BMC genomics

authors： Pornsukarom S,van Vliet AHM,Thakur S

更新日期：2018-11-06 00:00:00

abstract：BACKGROUND:NGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads. The other k-mers are called weak k-mers. A solid k-mer does not likely contain errors, while a weak k-...

journal_title：BMC genomics

authors： Zhao L,Xie J,Bai L,Chen W,Wang M,Zhang Z,Wang Y,Zhao Z,Li J

更新日期：2018-12-31 00:00:00

abstract：BACKGROUND:Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elemen...

journal_title：BMC genomics

authors： Karlsen C,Hjerde E,Klemetsen T,Willassen NP

更新日期：2017-04-20 00:00:00

abstract：BACKGROUND:Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for ...

journal_title：BMC genomics

authors： Salinero KK,Keller K,Feil WS,Feil H,Trong S,Di Bartolo G,Lapidus A

更新日期：2009-08-03 00:00:00

abstract：BACKGROUND:Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysing these data sets. RESULTS:DAWN (Diversity Among Wheat geNomes) integrates data from the T. aes...

journal_title：BMC genomics

authors： Watson-Haigh NS,Suchecki R,Kalashyan E,Garcia M,Baumann U

更新日期：2018-12-17 00:00:00

abstract：BACKGROUND:Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have ana...

journal_title：BMC genomics

authors： Sczyrba A,Beckstette M,Brivanlou AH,Giegerich R,Altmann CR

更新日期：2005-09-14 00:00:00

abstract：BACKGROUND:Hypoxia Inducible Factor (HIF) regulates a cascade of transcriptional events in response to decreased oxygenation, acting from the cellular to the physiological level. This response is evolutionarily conserved, allowing the use of zebrafish (Danio rerio) as a model for studying the hypoxic response. Activati...

journal_title：BMC genomics

authors： Greenald D,Jeyakani J,Pelster B,Sealy I,Mathavan S,van Eeden FJ

更新日期：2015-11-11 00:00:00

abstract：BACKGROUND:Dimethylsulfoniopropionate (DMSP) is a small sulphur compound which is produced in prodigious amounts in the oceans and plays a pivotal role in the marine sulfur cycle. Until recently, DMSP was believed to be synthesized exclusively by photosynthetic organisms; however we now know that corals and specific ba...

journal_title：BMC genomics

authors： Aguilar C,Raina JB,Motti CA,Fôret S,Hayward DC,Lapeyre B,Bourne DG,Miller DJ

更新日期：2017-08-14 00:00:00

abstract：BACKGROUND:Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers...

journal_title：BMC genomics

authors： Aguirre de Cárcer D,Angly FE,Alcamí A

更新日期：2014-11-18 00:00:00

abstract：BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...

journal_title：BMC genomics

authors： Baksa I,Nagy T,Barta E,Havelda Z,Várallyay É,Silhavy D,Burgyán J,Szittya G

更新日期：2015-12-01 00:00:00

abstract：BACKGROUND:Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes der...

journal_title：BMC genomics

authors： Park KD,Park J,Ko J,Kim BC,Kim HS,Ahn K,Do KT,Choi H,Kim HM,Song S,Lee S,Jho S,Kong HS,Yang YM,Jhun BH,Kim C,Kim TH,Hwang S,Bhak J,Lee HK,Cho BW

更新日期：2012-09-12 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:The Engrailed Homology 1 (EH1) motif is a small region, believed to have evolved convergently in homeobox and forkhead containing proteins, that interacts with the Drosophila protein groucho (C. elegans unc-37, Human Transducin-like Enhancers of Split). The small size of the motif makes its reliable identifi...

journal_title：BMC genomics

authors： Copley RR

更新日期：2005-11-27 00:00:00

abstract：BACKGROUND:The variability in gene organization and architecture of green algal mitochondrial genomes is only recently being studied on a finer taxonomic scale. Sequenced mt genomes from the chlorophycean orders Volvocales and Sphaeropleales exhibit considerable variation in size, content, and structure, even among clo...

journal_title：BMC genomics

authors： Farwagi AA,Fučíková K,McManus HA

更新日期：2015-10-21 00:00:00

abstract：BACKGROUND:Bacterial vaginosis (BV) is an ecological disorder of the vaginal microbiota that affects millions of women annually, and is associated with numerous adverse health outcomes including pre-term birth and the acquisition of sexually transmitted infections. However, little is known about the overall structure a...

journal_title：BMC genomics

authors： Ling Z,Kong J,Liu F,Zhu H,Chen X,Wang Y,Li L,Nelson KE,Xia Y,Xiang C

更新日期：2010-09-07 00:00:00

abstract：BACKGROUND:RNA-Seq is now widely used as a research tool. Choices must be made whether to use paired-end (PE) or single-end (SE) sequencing, and whether to use strand-specific or non-specific (NS) library preparation kits. To date there has been no analysis of the effect of these choices on identifying differentially e...

journal_title：BMC genomics

authors： Corley SM,MacKenzie KL,Beverdam A,Roddam LF,Wilkins MR

更新日期：2017-05-23 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are mobile genetic sequences that randomly propagate within their host's genome. This mobility has the potential to affect gene transcription and cause disease. However, TEs are technically challenging to identify, which complicates efforts to assess the impact of TE insertions on...

journal_title：BMC genomics

authors： Kvikstad EM,Piazza P,Taylor JC,Lunter G

更新日期：2018-02-01 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:Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex interplay then takes place between the macrophage (MPhi) striving to eliminate the pathogen and the pa...

journal_title：BMC genomics

authors： Guerfali FZ,Laouini D,Guizani-Tabbane L,Ottones F,Ben-Aissa K,Benkahla A,Manchon L,Piquemal D,Smandi S,Mghirbi O,Commes T,Marti J,Dellagi K

更新日期：2008-05-21 00:00:00

abstract：BACKGROUND:Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shift...

journal_title：BMC genomics

authors： Lu Y,Boswell M,Boswell W,Salinas RY,Savage M,Reyes J,Walter S,Marks R,Gonzalez T,Medrano G,Warren WC,Schartl M,Walter RB

更新日期：2020-11-11 00:00:00

abstract：BACKGROUND:With the development of several new technologies using synthetic biology, it is possible to engineer genetically intractable organisms including Mycoplasma mycoides subspecies capri (Mmc), by cloning the intact bacterial genome in yeast, using the host yeast's genetic tools to modify the cloned genome, and s...

journal_title：BMC genomics

authors： Chandran S,Noskov VN,Segall-Shapiro TH,Ma L,Whiteis C,Lartigue C,Jores J,Vashee S,Chuang RY

更新日期：2014-12-24 00:00:00

abstract：BACKGROUND:Malaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome of Plasmodium falciparum as i...

journal_title：BMC genomics

authors： van Biljon R,van Wyk R,Painter HJ,Orchard L,Reader J,Niemand J,Llinás M,Birkholtz LM

更新日期：2019-12-03 00:00:00

abstract：BACKGROUND:Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecolo...

journal_title：BMC genomics

authors： Scully ED,Geib SM,Carlson JE,Tien M,McKenna D,Hoover K

更新日期：2014-12-12 00:00:00

abstract：BACKGROUND:Genotyping-by-sequencing (GBS) is becoming an attractive alternative to array-based methods for genotyping individuals for a large number of single nucleotide polymorphisms (SNPs). Costs can be lowered by reducing the mean sequencing depth, but this results in genotype calls of lower quality. A common analys...

journal_title：BMC genomics

authors： Dodds KG,McEwan JC,Brauning R,Anderson RM,van Stijn TC,Kristjánsson T,Clarke SM

更新日期：2015-12-09 00:00:00

abstract：BACKGROUND:Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April in Hainan, China. To harvest pitayas with high economic value in the winter season, it is necessary t...

journal_title：BMC genomics

authors： Xiong R,Liu C,Xu M,Wei SS,Huang JQ,Tang H

更新日期：2020-04-29 00:00:00