11,165 results match your criteria BMC Genomics [Journal]


Correction to: STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plantparasitic nematode Bursaphelenchus xylophilus.

BMC Genomics 2018 Aug 10;19(1):603. Epub 2018 Aug 10.

Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

Following publication of the original article [1], the authors reported that one of the authors' names was erroneously changed during proofing and published incorrectly. In this Correction the incorrect and correct author name are shown. The original publication of this article has been corrected. Read More

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Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses.

BMC Genomics 2018 Aug 9;19(1):599. Epub 2018 Aug 9.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.

Background: Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family genes have been extensively studied under biotic and abiotic stresses, both in model and non-model plant species; however, information on their roles in cotton is still limited.

Results: A total of 64 putative LOX genes were identified in four cotton species (Gossypium (G. Read More

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August 2018
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Strategy for efficient generation of numerous full-length cDNA clones of classical swine fever virus for haplotyping.

BMC Genomics 2018 Aug 9;19(1):600. Epub 2018 Aug 9.

DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771, Kalvehave, Denmark.

Background: Direct molecular cloning of full-length cDNAs derived from viral RNA is an approach to identify the individual viral genomes within a virus population. This enables characterization of distinct viral haplotypes present during infection.

Results: In this study, we recover individual genomes of classical swine fever virus (CSFV), present in a pig infected with vKos that was rescued from a cDNA clone corresponding to the highly virulent CSFV Koslov strain. Read More

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August 2018
1 Read

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs.

BMC Genomics 2018 Aug 9;19(1):598. Epub 2018 Aug 9.

Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.

Background: Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs. Read More

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Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany.

BMC Genomics 2018 Aug 9;19(1):601. Epub 2018 Aug 9.

Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany.

Background: Resistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal ampC gene, acquisition of plasmid-encoded ampC genes, e.g. Read More

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August 2018
1 Read

RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants.

BMC Genomics 2018 Aug 9;19(1):602. Epub 2018 Aug 9.

Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.

Background: While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels.

Results: Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Read More

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Omics for understanding the tolerant mechanism of Trichoderma asperellum TJ01 to organophosphorus pesticide dichlorvos.

BMC Genomics 2018 Aug 8;19(1):596. Epub 2018 Aug 8.

Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, 236037, Anhui, China.

Backgroud: Though it is toxic to humans, dichlorvos is a widely used chemical pesticide and plays an important role in the control of plant pests. The application of a combination of the biocontrol agent Trichoderma with dichlorvos may reduce the need for chemical pesticides. Therefore, revealing the specific molecular mechanism of Trichoderma tolerance to dichlorvos has become particularly important. Read More

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DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq.

BMC Genomics 2018 Aug 8;19(1):597. Epub 2018 Aug 8.

Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel.

Background: Recent studies have described a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. However, the mechanism underlying naturally occurring transcriptional readthrough, as well as its regulatory consequences, still remain elusive. Read More

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Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes.

BMC Genomics 2018 Aug 7;19(1):593. Epub 2018 Aug 7.

Institute of Ecology and Evolution, University of Oregon, 5289 University of Oregon, Eugene, OR, 97403-5289, USA.

Background: Nematode sperm have unique and highly diverged morphology and molecular biology. In particular, nematode sperm contain subcellular vesicles known as membranous organelles that are necessary for male fertility, yet play a still unknown role in overall sperm function. Here we take a novel proteomic approach to characterize the functional protein complement of membranous organelles in two Caenorhabditis species: C. Read More

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Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.

BMC Genomics 2018 Aug 7;19(1):594. Epub 2018 Aug 7.

The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK.

Background: The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues.

Results: Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. Read More

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Gene editing in the context of an increasingly complex genome.

BMC Genomics 2018 Aug 8;19(1):595. Epub 2018 Aug 8.

Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK.

The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catalogued mutations across the primary carcinomas; whilst, for other diseases, we have identified the genetic variants with strongest association. Despite this, we are still awaiting the genetic revolution in healthcare to materialise and translate itself into the health benefits for which we had hoped. Read More

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Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns.

BMC Genomics 2018 Aug 7;19(1):592. Epub 2018 Aug 7.

Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain.

Background: Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating and potentially fatal disease. These 2 species show evidence of hybridisation in geographical areas where they are sympatric. Read More

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Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression.

BMC Genomics 2018 Aug 6;19(1):590. Epub 2018 Aug 6.

ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland.

Background: The expression of microRNAs (miRNAs) is essential for the proper development of the mammalian embryo. A maternal exposure to endocrine disrupting chemicals during preimplantation bears the potential for transgenerational inheritance of disease through the epigenetic perturbation of the developing embryo. A comprehensive assembly of embryo-specific miRNAs and respective isoforms (isomiR) is lacking to date. Read More

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August 2018
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Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus.

BMC Genomics 2018 Aug 6;19(1):586. Epub 2018 Aug 6.

Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.

Background: Allopolyploids require rapid genetic and epigenetic modifications to reconcile two or more sets of divergent genomes. To better understand the fate of duplicate genes following genomic mergers and doubling during allopolyploid formation, in this study, we explored the global gene expression patterns in resynthesized allotetraploid Brassica napus (AACC) and its diploid parents B. rapa (AA) and B. Read More

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Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave.

BMC Genomics 2018 Aug 6;19(1):588. Epub 2018 Aug 6.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.

Background: Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. Read More

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August 2018
3.99 Impact Factor

Genome-based analysis for the identification of genes involved in o-xylene degradation in Rhodococcus opacus R7.

BMC Genomics 2018 Aug 6;19(1):587. Epub 2018 Aug 6.

Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.

Background: Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a powerhouse of numerous degradation functions, due to their ability to metabolize a wide range of organic molecules including aliphatic, aromatic, polycyclic aromatic compounds (PAHs), phenols, and nitriles. In accordance with their immense catabolic diversity, Rhodococcus spp. Read More

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August 2018
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Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat.

BMC Genomics 2018 Aug 6;19(1):591. Epub 2018 Aug 6.

Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 362D Plant Sciences Hall, Lincoln, NE, 68583, USA.

Background: Synthetic hexaploid wheat (SHW) is a reconstitution of hexaploid wheat from its progenitors (Triticum turgidum ssp. durum L.; AABB x Aegilops tauschii Coss. Read More

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Modeling of the GC content of the substituted bases in bacterial core genomes.

BMC Genomics 2018 Aug 6;19(1):589. Epub 2018 Aug 6.

Norwegian Institute of Public Health, Lovisenberggata 8, P.O. Box 4404, 0403, Oslo, Norway.

Background: The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strains. We also wanted to explore whether sbGC for each strain was associated with the corresponding species' core genome GC content (cgGC). Read More

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Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl.

BMC Genomics 2018 Aug 6;19(1):585. Epub 2018 Aug 6.

Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127, Bologna, Italy.

Background: Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options for controlling this disease are very limited and rely primarily on the use of bactericidal compounds, such as copper, and resistance inducers. Read More

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Correction to: Multiple functions of CREB-binding protein during postembryonic development: identification of target genes.

BMC Genomics 2018 Aug 6;19(1):584. Epub 2018 Aug 6.

Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY, 40546, USA.

Following the publication of this article [1], the authors found that the primers listed for CREB-binding protein were not correct. This mistake occurred during assembly of the primer table and the authors apologize for this error. This correction does not change the data included in the paper, their interpretation nor the conclusions drawn. Read More

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Comparative transcriptomics reveals suppressed expression of genes related to auxin and the cell cycle contributes to the resistance of cucumber against Meloidogyne incognita.

BMC Genomics 2018 Aug 3;19(1):583. Epub 2018 Aug 3.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.

Background: Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infection, the exact regulation mechanism of M. incognita-resistance in cucumber remains elusive. Read More

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August 2018
2 Reads

MHC class II restricted neoantigen peptides predicted by clonal mutation analysis in lung adenocarcinoma patients: implications on prognostic immunological biomarker and vaccine design.

BMC Genomics 2018 Aug 3;19(1):582. Epub 2018 Aug 3.

Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, 32224, USA.

Background: Mutant peptides presented by MHC (major histocompatibility complex) Class II in cancer are important targets for cancer immunotherapy. Both animal studies and clinical trials in cancer patients showed that CD4 T cells specific to tumor-derived mutant peptides are essential for the efficacy of immune checkpoint blockade therapy by PD1 antibody.

Results: In this study, we analyzed the next generation sequencing data of 147 lung adenocarcinoma patients from The Cancer Genome Atlas and predicted neoantigens presented by MHC Class I and Class II molecules. Read More

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August 2018
4 Reads

Gene expression analysis indicates reduced memory and cognitive functions in the hippocampus and increase in synaptic reorganization in the frontal cortex 3 weeks after MDMA administration in Dark Agouti rats.

BMC Genomics 2018 Aug 2;19(1):580. Epub 2018 Aug 2.

Department of Pharmacodynamics, Semmelweis University, Nagyvarad ter 4., Budapest, H-1089, Hungary.

Background: 3,4-methylenedioxymethamphetamine (MDMA, "ecstasy") is a widely used entactogenic drug known to impair cognitive functions on the long-run. Both hippocampal and frontal cortical regions have well established roles in behavior, memory formation and other cognitive tasks and damage of these regions is associated with altered behavior and cognitive functions frequently described in otherwise healthy MDMA users. Meanwhile, in post-traumatic stress disorder (PTSD) patients seem to benefit from therapeutic application of the drug, where damage in hippocampal cue extinction may play a role. Read More

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eQTL discovery and their association with severe equine asthma in European Warmblood horses.

BMC Genomics 2018 Aug 2;19(1):581. Epub 2018 Aug 2.

Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland.

Background: Severe equine asthma, also known as recurrent airway obstruction (RAO), is a debilitating, performance limiting, obstructive respiratory condition in horses that is phenotypically similar to human asthma. Past genome wide association studies (GWAS) have not discovered coding variants associated with RAO, leading to the hypothesis that causative variant(s) underlying the signals are likely non-coding, regulatory variant(s). Regions of the genome containing variants that influence the number of expressed RNA molecules are expression quantitative trait loci (eQTLs). Read More

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August 2018
2 Reads

Dietary supplementation with olive mill wastewaters induces modifications on chicken jejunum epithelial cell transcriptome and modulates jejunum morphology.

BMC Genomics 2018 Aug 2;19(1):576. Epub 2018 Aug 2.

Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126, Perugia, Italy.

Background: The Mediterranean diet is considered one of the healthier food habits and olive oil is one of its key components. Olive oil polyphenols are known to induce beneficial effects in several pathological conditions, such as inflammatory bowel disease, and to contrast the proliferation of cancer cells or hypercholesterolemia. Polyphenols are also present in waste products derived from the olive industry: olive mill wastewaters (OMWW) are rich in polyphenols and there is an increasing interest in using OMWW in animal nutrition. Read More

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August 2018
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Virulence-related comparative transcriptomics of infectious and non-infectious chlamydial particles.

BMC Genomics 2018 Aug 2;19(1):575. Epub 2018 Aug 2.

Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11A, 07745, Jena, Germany.

Background: Members of the phylum Chlamydiae are obligate intracellular pathogens of humans and animals and have a serious impact on host health. They comprise several zoonotic species with varying disease outcomes and prevalence. To investigate differences in virulence, we focused on Chlamydia psittaci, C. Read More

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August 2018
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A map of gene expression in neutrophil-like cell lines.

BMC Genomics 2018 Aug 1;19(1):573. Epub 2018 Aug 1.

Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.

Background: Human neutrophils are central players in innate immunity, a major component of inflammatory responses, and a leading model for cell motility and chemotaxis. However, primary neutrophils are short-lived, limiting their experimental usefulness in the laboratory. Thus, human myeloid cell lines have been characterized for their ability to undergo neutrophil-like differentiation in vitro. Read More

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Imbalance learning for the prediction of N-Methylation sites in mRNAs.

BMC Genomics 2018 Aug 1;19(1):574. Epub 2018 Aug 1.

Advanced Analytics Institute, Faculty of Engineering and Information Technology, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007, Australia.

Background: N-methyladenosine (mA) is an important epigenetic modification which plays various roles in mRNA metabolism and embryogenesis directly related to human diseases. To identify mA in a large scale, machine learning methods have been developed to make predictions on mA sites. However, there are two main drawbacks of these methods. Read More

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Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization.

BMC Genomics 2018 Aug 2;19(1):578. Epub 2018 Aug 2.

School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.

Background: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. Read More

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Genome-wide identification and characterization of the 14-3-3 family in Vitis vinifera L. during berry development and cold- and heat-stress response.

BMC Genomics 2018 Aug 2;19(1):579. Epub 2018 Aug 2.

Beijing Key Laboratory of Grape Sciences and Enology, Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, People's Republic of China.

Background: The 14-3-3 family of ubiquitous proteins in eukaryotes plays important roles in the regulation of various plant biological processes. However, less information is known about this family in grape fruit.

Results: To investigate the characteristics and functions of 14-3-3 in grape, a total of 11 14-3-3 proteins were identified. Read More

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August 2018
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Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.

BMC Genomics 2018 Aug 2;19(1):577. Epub 2018 Aug 2.

Department of Zoology, University of Oxford, Oxford, United Kingdom.

Background: Human cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCMV cultures but have also been observed in vivo. Thus, the assembly of HCMV whole genomes from technologies producing shorter than 500 bp sequences is technically challenging. Read More

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August 2018
1 Read

Effects of liquid cultivation on gene expression and phenotype of C. elegans.

BMC Genomics 2018 Jul 31;19(1):562. Epub 2018 Jul 31.

Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE, 19711, USA.

Background: Liquid cultures have been commonly used in space, toxicology, and pharmacology studies of Caenorhabditis elegans. However, the knowledge about transcriptomic alterations caused by liquid cultivation remains limited. Moreover, the impact of different genotypes in rapid adaptive responses to environmental changes (e. Read More

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July 2018
2 Reads

Identification of microRNAs in response to aluminum stress in the roots of Tibetan wild barley and cultivated barley.

BMC Genomics 2018 Jul 31;19(1):560. Epub 2018 Jul 31.

Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.

Background: Barley is relatively sensitive to Aluminum (Al) toxicity among cereal crops, but shows a wide genotypic difference in Al tolerance. The well-known Al-tolerant mechanism in barley is related to Al exclusion mediated by a citrate transporter HvAACT1 (Al-activated citrate transporter 1). A 1-kb insertion in the promoter region of HvAACT1 gene results in a dramatic increase of its expression level, which only occurs in some Al-tolerant cultivars. Read More

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Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800.

BMC Genomics 2018 Jul 31;19(1):559. Epub 2018 Jul 31.

Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann Straße 3, 06120, Halle, Germany.

Background: Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F lines derived from intercrossing eight recently released European winter wheat cultivars.

Results: Genotyping WM-800 with 7849 SNPs revealed a low mean genetic similarity of 59. Read More

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ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference.

BMC Genomics 2018 Jul 31;19(1):563. Epub 2018 Jul 31.

National Institute of Dental and Craniofacial Research, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20816, USA.

Background: Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution. Optimization of molecular protocols has enabled the molecular biologist to produce next-generation sequencing libraries in several hours, leaving the analysis of sequencing data as the primary obstacle to wide-scale deployment of accessibility profiling assays. To address this obstacle we have developed an optimized and efficient pipeline for the analysis of ATAC-seq and DNase1-seq data. Read More

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July 2018
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Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures.

BMC Genomics 2018 Jul 31;19(1):561. Epub 2018 Jul 31.

Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic.

Background: In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.

Results: Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Read More

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Correction to: Detect tissue heterogeneity in gene expression data with BioQC.

BMC Genomics 2018 Jul 30;19(1):558. Epub 2018 Jul 30.

Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.

After the publication of this work [1], a mistake was noticed in the Eq. 1. Given an m  ×  n expression matrix with m genes and samples of n tissues, the correct definition of the Gini index for gene i is. Read More

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July 2018
1 Read

Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.

BMC Genomics 2018 Jul 28;19(1):556. Epub 2018 Jul 28.

Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.

Background: Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. Read More

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July 2018
2 Reads

Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola.

BMC Genomics 2018 Jul 28;19(1):557. Epub 2018 Jul 28.

State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.

Background: Colletotrichum is a fungal genus in Ascomycota that contain many plant pathogens. Among all Colletotrichum genomes that have been sequenced, C. fructicola contains the largest number of candidate virulence factors, such as plant cell wall degrading enzymes, secondary metabolite (SM) biosynthetic enzymes, secreted proteinases, and small secreted proteins. Read More

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Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera).

BMC Genomics 2018 Jul 27;19(1):554. Epub 2018 Jul 27.

Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.

Background: Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying this phenomenon is still obscure. Read More

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Understanding the role of interactions between host and Mycobacterium tuberculosis under hypoxic condition: an in silico approach.

BMC Genomics 2018 Jul 27;19(1):555. Epub 2018 Jul 27.

Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Limited, Pune, India.

Background: Mycobacterium tuberculosis infection in humans is often associated with extended period of latency. To adapt to the hostile hypoxic environment inside a macrophage, M. tuberculosis cells undergo several physiological and metabolic changes. Read More

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July 2018
1 Read

STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plant-parasitic nematode Bursaphelenchus xylophilus.

BMC Genomics 2018 Jul 27;19(1):553. Epub 2018 Jul 27.

Cell and Molecular Sciences Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.

Background: Plant-parasitic nematodes cause severe damage to a wide range of crop and forest species worldwide. The migratory endoparasitic nematode, Bursaphelenchus xylophilus, (pinewood nematode) is a quarantine pathogen that infects pine trees and has a hugely detrimental economic impact on the forestry industry. Under certain environmental conditions large areas of infected trees can be destroyed, leading to damage on an ecological scale. Read More

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July 2018
1 Read

CIGene: a literature-based online resource for cancer initiation genes.

BMC Genomics 2018 Jul 25;19(1):552. Epub 2018 Jul 25.

Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, People's Republic of China.

Background: Cancer initiation genes (CIGs) are genes that can directly promote cell proliferation or induce cancer. There are thousands of published studies identifying various CIGs; however, no systematic collection or description is available.

Results: To construct a CIG reference for genetic screening, we have collected 177 human genes curated from 1507 PubMed abstracts. Read More

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Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower.

BMC Genomics 2018 Jul 24;19(1):548. Epub 2018 Jul 24.

State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu, 611137, China.

Background: The flower of the safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine for the ability to improve cerebral blood flow. Flavonoids are the primary bioactive components in safflower, and their biosynthesis has attracted widespread interest. Read More

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Transcriptome analysis and identification of genes related to terpenoid biosynthesis in Cinnamomum camphora.

BMC Genomics 2018 Jul 24;19(1):550. Epub 2018 Jul 24.

Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.

Background: Cinnamomum camphora has been cultivated as an economically important tree for its medicinal and aromatic properties. Selective breeding has produced Cinnamomum plants for special uses, including spice strains with characteristic flavors and aromas and high-potency medicinal cultivars. The molecular biology underlying terpenoid biosynthesis is still unexplored. Read More

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Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project.

BMC Genomics 2018 Jul 24;19(1):551. Epub 2018 Jul 24.

Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.

Background: Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify strongly associated variants in genome-wide association studies. The Tohoku Medical Megabank (TMM) project was established to support the development of precision medicine, together with the whole-genome sequencing of 1070 human genomes from individuals in the Miyagi region (Northeast Japan) and the construction of the 1070 Japanese genome reference panel (1KJPN). Here, we investigated the performance of 1KJPN for genotype imputation of Japanese samples not included in the TMM project and compared it with other population reference panels. Read More

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A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16).

BMC Genomics 2018 Jul 24;19(1):549. Epub 2018 Jul 24.

Department of Biochemistry and Molecular Biology, University of Nevada, Reno, MS330, Howard Building, Reno, NV, 89557, USA.

Background: In flowering plants, the male gametophyte (pollen) is one of the most vulnerable cells to temperature stress. In Arabidopsis thaliana, a pollen-specific Cyclic Nucleotide-Gated cation Channel 16 (cngc16), is required for plant reproduction under temperature-stress conditions. Plants harboring a cncg16 knockout are nearly sterile under conditions of hot days and cold nights. Read More

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July 2018
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RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes.

BMC Genomics 2018 Jul 20;19(1):546. Epub 2018 Jul 20.

Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, NMS 5.324, Austin, TX, 78712, USA.

Background: Although different quality controls have been applied at different stages of the sample preparation and data analysis to ensure both reproducibility and reliability of RNA-seq results, there are still limitations and bias on the detectability for certain differentially expressed genes (DEGs). Whether the transcriptional dynamics of a gene can be captured accurately depends on experimental design/operation and the following data analysis processes. The workflow of subsequent data processing, such as reads alignment, transcript quantification, normalization, and statistical methods for ultimate identification of DEGs can influence the accuracy and sensitivity of DEGs analysis, producing a certain number of false-positivity or false-negativity. Read More

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July 2018
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Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening.

BMC Genomics 2018 Jul 20;19(1):545. Epub 2018 Jul 20.

National Center of Colorectal Disease, Nanjing Municipal Hospital of Chinese Medicine, The Third Affiliated Hospital, Nanjing University of Chinese Medicine, Nanjing, 210001, China.

Background: Lung cancer is a major cause of cancer-related mortality worldwide, and around two-thirds of patients have metastasis at diagnosis. Thus, detecting lung cancer at an early stage could reduce mortality. Aberrant levels of circulating small non-coding RNAs (small ncRNAs) are potential diagnostic or prognostic markers for lung cancer. Read More

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July 2018
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Antennal transcriptome analysis of the chemosensory gene families in Carposina sasakii (Lepidoptera: Carposinidae).

BMC Genomics 2018 Jul 20;19(1):544. Epub 2018 Jul 20.

Research Institute of Pomology, Chinese Academy of Agricultural Sciences, 98 South Street, Xinghai, Xingcheng, 125100, Liaoning, China.

Background: The peach fruit moth, Carposina sasakii Matsumura (Lepidoptera: Carposinidae), poses a serious threat to a variety of fruits and causes significant economic loss owing to difficulties in its prevention and control. The olfactory sense is generally acknowledged to be a novel target for pest control. However, a systematic study of the olfactory genes expressed in C. Read More

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July 2018
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