Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats.

abstract：BACKGROUND:Sacha Inchi (Plukenetia volubilis L., Euphorbiaceae) is a potential oilseed crop because the seeds of this plant are rich in unsaturated fatty acids (FAs). In particular, the fatty acid composition of its seed oil differs markedly in containing large quantities of α-linolenic acid (18C:3, a kind of ω-3 FAs)....

journal_title：BMC genomics

authors： Wang X,Xu R,Wang R,Liu A

更新日期：2012-12-20 00:00:00

abstract：BACKGROUND:The recently developed RNA interference (RNAi) technology has created an unprecedented opportunity which allows the function of individual genes in whole organisms or cell lines to be interrogated at genome-wide scale. However, multiple issues, such as off-target effects or low efficacies in knocking down ce...

journal_title：BMC genomics

authors： Wang L,Tu Z,Sun F

更新日期：2009-05-12 00:00:00

abstract：BACKGROUND:Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene tr...

journal_title：BMC genomics

authors： Gao S,Li L,Han X,Liu T,Jin P,Cai L,Xu M,Zhang T,Zhang F,Chen J,Yang J,Zhong K

更新日期：2021-01-11 00:00:00

abstract：BACKGROUND:The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related t...

journal_title：BMC genomics

authors： Shi W,Chen S,Kong X,Si L,Gong L,Zhang Y,Yu H

更新日期：2018-05-25 00:00:00

abstract：BACKGROUND:Fitness epistasis, the interaction effect of genes at different loci on fitness, makes an important contribution to adaptive evolution. Although fitness interaction evidence has been observed in model organisms, it is more difficult to detect and remains poorly understood in human populations as a result of ...

journal_title：BMC genomics

authors： Ni X,Zhou M,Wang H,He KY,Broeckel U,Hanis C,Kardia S,Redline S,Cooper RS,Tang H,Zhu X

更新日期：2020-07-11 00:00:00

abstract：BACKGROUND:In our previous study, Citrobacter werkmanii BF-6 was isolated from an industrial spoilage sample and demonstrated an excellent ability to form biofilms, which could be affected by various environmental factors. However, the genome sequence of this organism has not been reported so far. RESULTS:We report th...

journal_title：BMC genomics

authors： Zhou G,Peng H,Wang YS,Huang XM,Xie XB,Shi QS

更新日期：2017-10-10 00:00:00

abstract：BACKGROUND:Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity....

journal_title：BMC genomics

authors： Cantu D,Segovia V,MacLean D,Bayles R,Chen X,Kamoun S,Dubcovsky J,Saunders DG,Uauy C

更新日期：2013-04-22 00:00:00

abstract：BACKGROUND:Two-component systems (TCSs) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. TCS gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and m...

journal_title：BMC genomics

authors： Williams RH,Whitworth DE

更新日期：2010-12-20 00:00:00

abstract：BACKGROUND:The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found in fast neutron populations has been hindered, however, by the wide range of mutations generated and...

journal_title：BMC genomics

authors： Lemay MA,Torkamaneh D,Rigaill G,Boyle B,Stec AO,Stupar RM,Belzile F

更新日期：2019-08-06 00:00:00

abstract：BACKGROUND:Genomic inversion is one type of structural variations (SVs) and is known to play an important biological role. An established problem in sequence data analysis is calling inversions from high-throughput sequence data. It is more difficult to detect inversions because they are surrounded by duplication or ot...

journal_title：BMC genomics

authors： Wu Z,Wu Y,Gao J

更新日期：2020-03-05 00:00:00

abstract：BACKGROUND:Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplas...

journal_title：BMC genomics

authors： Do TD,Vuong TD,Dunn D,Clubb M,Valliyodan B,Patil G,Chen P,Xu D,Nguyen HT,Shannon JG

更新日期：2019-04-25 00:00:00

abstract：BACKGROUND:Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnan...

journal_title：BMC genomics

authors： Zheng J,Liu L,Wang J,Jin Q

更新日期：2013-11-11 00:00:00

abstract：BACKGROUND:Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleur...

journal_title：BMC genomics

authors： Castanera R,Pérez G,López L,Sancho R,Santoyo F,Alfaro M,Gabaldón T,Pisabarro AG,Oguiza JA,Ramírez L

更新日期：2014-12-05 00:00:00

abstract：BACKGROUND:Transporter proteins are one of an organism's primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general...

journal_title：BMC genomics

authors： Giuliani SE,Frank AM,Corgliano DM,Seifert C,Hauser L,Collart FR

更新日期：2011-06-15 00:00:00

abstract：BACKGROUND:Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have...

journal_title：BMC genomics

authors： Settles AM,Holding DR,Tan BC,Latshaw SP,Liu J,Suzuki M,Li L,O'Brien BA,Fajardo DS,Wroclawska E,Tseung CW,Lai J,Hunter CT 3rd,Avigne WT,Baier J,Messing J,Hannah LC,Koch KE,Becraft PW,Larkins BA,McCarty DR

更新日期：2007-05-09 00:00:00

abstract：BACKGROUND:Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue predi...

journal_title：BMC genomics

authors： Rane RV,Oakeshott JG,Nguyen T,Hoffmann AA,Lee SF

更新日期：2017-08-31 00:00:00

abstract：BACKGROUND:The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the geno...

journal_title：BMC genomics

authors： Prunier J,Pelgas B,Gagnon F,Desponts M,Isabel N,Beaulieu J,Bousquet J

更新日期：2013-06-01 00:00:00

abstract：BACKGROUND:Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on singl...

journal_title：BMC genomics

authors： Genini S,Badaoui B,Sclep G,Bishop SC,Waddington D,Pinard van der Laan MH,Klopp C,Cabau C,Seyfert HM,Petzl W,Jensen K,Glass EJ,de Greeff A,Smith HE,Smits MA,Olsaker I,Boman GM,Pisoni G,Moroni P,Castiglioni B,Cremon

更新日期：2011-05-11 00:00:00

abstract：BACKGROUND:Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphis...

journal_title：BMC genomics

authors： Li X,Gao W,Guo H,Zhang X,Fang DD,Lin Z

更新日期：2014-12-01 00:00:00

abstract：BACKGROUND:In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be d...

journal_title：BMC genomics

authors： Xiang H,Li X,Dai F,Xu X,Tan A,Chen L,Zhang G,Ding Y,Li Q,Lian J,Willden A,Guo Q,Xia Q,Wang J,Wang W

更新日期：2013-09-23 00:00:00

abstract：BACKGROUND:We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS:By using simulated and real datasets we showed that our tool, based on read count approac...

journal_title：BMC genomics

authors： Magi A,Pippucci T,Sidore C

更新日期：2017-09-21 00:00:00

abstract：BACKGROUND:The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of ...

journal_title：BMC genomics

authors： Li H,Sharma A,Ming W,Sun X,Liu H

更新日期：2020-09-23 00:00:00

abstract：BACKGROUND:Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clin...

journal_title：BMC genomics

authors： Samarasinghe SR,Samaranayake N,Kariyawasam UL,Siriwardana YD,Imamura H,Karunaweera ND

更新日期：2018-11-28 00:00:00

abstract：BACKGROUND:Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the p...

journal_title：BMC genomics

authors： Zimmerman SJ,Aldridge CL,Oyler-McCance SJ

更新日期：2020-06-01 00:00:00

abstract：BACKGROUND:In clinical and basic research custom panels for transcript profiling are gaining importance because only project specific informative genes are interrogated. This approach reduces costs and complexity of data analysis and allows multiplexing of samples. Polymerase-chain-reaction (PCR) based TaqMan assays ha...

journal_title：BMC genomics

authors： Zhang JD,Schindler T,Küng E,Ebeling M,Certa U

更新日期：2014-07-05 00:00:00

abstract：BACKGROUND:Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only t...

journal_title：BMC genomics

authors： Lafontaine I,Dujon B

更新日期：2010-04-22 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:We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we transferred this respiratory phenotype in the presence of up to 50 g/L glucose to a yeast strai...

journal_title：BMC genomics

authors： Bonander N,Ferndahl C,Mostad P,Wilks MD,Chang C,Showe L,Gustafsson L,Larsson C,Bill RM

更新日期：2008-07-31 00:00:00

abstract：BACKGROUND:It has been shown previously that aminocoumarin antibiotics such as novobiocin lead to immediate downregulation of recA expression and thereby inhibit the SOS response, mutation frequency and recombination capacity in Staphylococcus aureus. Aminocoumarins function by inhibiting the ATPase activity of DNA gyr...

journal_title：BMC genomics

authors： Schröder W,Bernhardt J,Marincola G,Klein-Hitpass L,Herbig A,Krupp G,Nieselt K,Wolz C

更新日期：2014-04-16 00:00:00

abstract：BACKGROUND:RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular i...

journal_title：BMC genomics

authors： Fu Y,Wu PH,Beane T,Zamore PD,Weng Z

更新日期：2018-07-13 00:00:00