11,833 results match your criteria BMC genomics[Journal]


Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion.

BMC Genomics 2019 Apr 16;20(1):300. Epub 2019 Apr 16.

Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinery Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.

Background: Temperate bacteriophages are capable of lysogenic conversion of new bacterial hosts. This phenomenon is often ascribed to "moron" elements that are acquired horizontally and transcribed independently from the rest of the phage genes. Whereas some bacterial species exhibit relatively little prophage-dependent phenotypic changes, other bacterial species such as Stenotrophomonas maltophilia appear to commonly adopt prophage genetic contributions. Read More

View Article

Download full-text PDF

Source
https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12864-019-5674-5DOI Listing
April 2019
1 Read

The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host.

BMC Genomics 2019 Apr 16;20(1):301. Epub 2019 Apr 16.

Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.

Background: Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5665-6DOI Listing

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.

BMC Genomics 2019 Apr 16;20(1):299. Epub 2019 Apr 16.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.

Background: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σ factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.

Results: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σ regulon in this bacterium. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5619-zDOI Listing

Selective translational usage of TSS and core promoters revealed by translatome sequencing.

BMC Genomics 2019 Apr 11;20(1):282. Epub 2019 Apr 11.

State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.

Background: In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive.

Results: In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5' isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. Read More

View Article

Download full-text PDF

Source
https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12864-019-5650-0DOI Listing
April 2019
1 Read

Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines.

BMC Genomics 2019 Apr 15;20(1):289. Epub 2019 Apr 15.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Background: Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5630-4DOI Listing
April 2019
1 Read

A cmap-enabled gene expression signature-matching approach identifies small-molecule inducers of accelerated cell senescence.

BMC Genomics 2019 Apr 15;20(1):290. Epub 2019 Apr 15.

Department of Molecular Genetics and Cell Biology and Ludwig Center for Metastasis Research, The University of Chicago, 929 East 57th Street, GCIS W522A, Chicago, IL, 60637, USA.

Background: Diverse stresses including genotoxic therapy can induce proliferating cancer cells to undergo cellular senescence and take on the characteristic phenotypes of replicative cellular aging. This accelerated or therapy-induced senescence has been alternatively proposed to contribute to therapeutic efficacy or resistance. Toward better understanding this cell state, we sought to define the core transcriptome of accelerated senescence in cancer cells. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5653-xDOI Listing

Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle.

BMC Genomics 2019 Apr 15;20(1):291. Epub 2019 Apr 15.

Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, Victoria, Australia.

Background: Identifying causative mutations or genes through which quantitative trait loci (QTL) act has proven very difficult. Using information such as gene expression may help to identify genes and mutations underlying QTL. Our objective was to identify regions associated both with production traits or fertility and with gene expression, in dairy cattle. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5656-7DOI Listing

An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS.

BMC Genomics 2019 Apr 11;20(1):285. Epub 2019 Apr 11.

Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.

Background: Two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are widely used in plant proteomics research. However, these two techniques cannot be simultaneously satisfied by traditional protein extraction methods when investigate cotton leaf proteome.

Results: Here, we evaluated the efficiency of three different protein extraction methods for 2-DE and LC-MS/MS analyses of total proteins obtained from cotton leaves. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5658-5DOI Listing

A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle.

BMC Genomics 2019 Apr 11;20(1):286. Epub 2019 Apr 11.

Animal Genomics, ETH Zurich, 8001, Zurich, Switzerland.

Background: Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of artificial insemination bulls. Two young Nordic Red bulls delivered sperm with low progressive motility (i.e. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5628-yDOI Listing
April 2019
1 Read

Effects of a previously selected antibiotic resistance on mutations acquired during development of a second resistance in Escherichia coli.

BMC Genomics 2019 Apr 11;20(1):284. Epub 2019 Apr 11.

Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.

Background: The effect of mutations conferring antibiotic resistance can depend on the genetic background. To determine if a previously de novo acquired antibiotic resistance influences the adaptation to a second antibiotic, antibiotic resistance was selected for by exposure to stepwise increasing sublethal levels of amoxicillin, enrofloxacin, kanamycin, or tetracycline. E. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5648-7DOI Listing

Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis.

BMC Genomics 2019 Apr 11;20(1):283. Epub 2019 Apr 11.

College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China.

Background: Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5646-9DOI Listing

Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat.

BMC Genomics 2019 Apr 11;20(1):287. Epub 2019 Apr 11.

The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China.

Background: The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives.

Results: We identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu, 29 in Aegilops tauschii, and 31 in Brachypodium distachyon. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5632-2DOI Listing
April 2019
2 Reads

Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis.

BMC Genomics 2019 Apr 11;20(1):288. Epub 2019 Apr 11.

MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.

Background: Reverse transcription quantitative PCR (RT-qPCR) is widely used for gene expression analysis in various organisms. Its accuracy largely relies on the stability of reference genes, making reference gene selection a vital step in RT-qPCR experiments. However, previous studies in mollusks only focused on the reference genes widely used in vertebrates. Read More

View Article

Download full-text PDF

Source
https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12864-019-5661-xDOI Listing
April 2019
1 Read

Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm.

BMC Genomics 2019 Apr 10;20(1):278. Epub 2019 Apr 10.

Istituto di Genomica Applicata, via J. Linussio 51, 33100, Udine, Italy.

Background: The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5645-xDOI Listing

Transcriptional changes in response to ketamine ester-analogs SN 35210 and SN 35563 in the rat brain.

BMC Genomics 2019 Apr 11;20(1):281. Epub 2019 Apr 11.

Waikato District Health Board, Pembroke Street, Hamilton, 3204, New Zealand.

Background: Ketamine ester analogs, SN 35210 and SN 35563, demonstrate different pharmacological profiles to ketamine in animal models. Both confer hypnosis with predictably rapid offset yet, paradoxically, SN35563 induces a prolonged anti-nociceptive state. To explore underlying mechanisms, broad transcriptome changes were measured and compared across four relevant target regions of the rat brain. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5649-6DOI Listing

Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots.

BMC Genomics 2019 Apr 11;20(1):280. Epub 2019 Apr 11.

Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.

Background: Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5651-zDOI Listing

DeepHistone: a deep learning approach to predicting histone modifications.

BMC Genomics 2019 Apr 4;20(Suppl 2):193. Epub 2019 Apr 4.

MOE Key Laboratory of Bioinformatics; Bioinformatics Division, Beijing National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China.

Motivation: Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage. However, high-throughput experimental techniques such as ChIP-seq are usually expensive and time-consuming, prohibiting the establishment of a histone modification landscape for hundreds of cell types across dozens of histone markers. These disadvantages have been appealing for computational methods to complement experimental approaches towards large-scale analysis of histone modifications. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5489-4DOI Listing

Improving the sensitivity of long read overlap detection using grouped short k-mer matches.

BMC Genomics 2019 Apr 4;20(Suppl 2):190. Epub 2019 Apr 4.

Electronic Engineering Department, City University of Hong Kong, Hong Kong SAR, China.

Background: Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than second-generation sequencing technologies such as Illumina. The increased read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and characterize the intra-species variations. It also holds the promise to decipher the community structure in complex microbial communities because long reads help metagenomic assembly. Read More

View Article

Download full-text PDF

Source
https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12864-019-5475-xDOI Listing
April 2019
1 Read

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis.

BMC Genomics 2019 Apr 4;20(Suppl 2):185. Epub 2019 Apr 4.

Department of Medicine, Stanford University School of Medicine, 269 Campus Dr., Stanford, CA, 94305, USA.

Background: Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities. Read More

View Article

Download full-text PDF

Source
https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12864-019-5469-8DOI Listing
April 2019
1 Read

MRCNN: a deep learning model for regression of genome-wide DNA methylation.

BMC Genomics 2019 Apr 4;20(Suppl 2):192. Epub 2019 Apr 4.

School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.

Background: Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence the cell differentiation which can possibly lead to cancer. Due to the involuted biochemical mechanism of DNA methylation, obtaining a precise prediction is a considerably tough challenge. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5488-5DOI Listing

Large-scale 3D chromatin reconstruction from chromosomal contacts.

BMC Genomics 2019 Apr 4;20(Suppl 2):186. Epub 2019 Apr 4.

Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR.

Background: Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C technology, which detects long-range chromosomal interactions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5470-2DOI Listing

Meta-network: optimized species-species network analysis for microbial communities.

BMC Genomics 2019 Apr 4;20(Suppl 2):187. Epub 2019 Apr 4.

Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.

Background: The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data mining methods become important and necessary to perform deep and comprehensive analysis. Among the various priorities for microbiome data mining, the examination of species-species co-occurrence patterns becomes one of the key themes in urgent need. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5471-1DOI Listing

A distance-type measure approach to the analysis of copy number variation in DNA sequencing data.

BMC Genomics 2019 Apr 4;20(Suppl 2):195. Epub 2019 Apr 4.

Department of Statistics and Biostatistics Center, The George Washington University, Rome Hall, 7th Floor, 801, 22nd Street NW, Washington D.C, 20052, USA.

Background: The next generation sequencing technology allows us to obtain a large amount of short DNA sequence (DNA-seq) reads at a genome-wide level. DNA-seq data have been increasingly collected during the recent years. Count-type data analysis is a widely used approach for DNA-seq data. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5491-xDOI Listing

A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.

BMC Genomics 2019 Apr 4;20(Suppl 2):188. Epub 2019 Apr 4.

Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.

Background: Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNPs are detectable from the tumor. Many hospitals have developed their own panels that include clinically important SNPs. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5473-zDOI Listing

Signal enrichment with strain-level resolution in metagenomes using topological data analysis.

BMC Genomics 2019 Apr 4;20(Suppl 2):194. Epub 2019 Apr 4.

Computational Biology Center, IBM T. J. Watson Research Center, Yorktown Heights, NY, USA.

Background: A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of the challenges is in distinguishing between similar organisms due to rampant multiple possible assignments of sequencing reads, resulting in false positive identifications. We map the problem to a topological data analysis (TDA) framework that extracts information from the geometric structure of data. Read More

View Article

Download full-text PDF

Source
https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12864-019-5490-yDOI Listing
April 2019
4 Reads

Microbiota in the apical root canal system of tooth with apical periodontitis.

BMC Genomics 2019 Apr 4;20(Suppl 2):189. Epub 2019 Apr 4.

Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.

Background: Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as well as their changes responding to dental therapy, are of utmost importance to understand the pathogensis of the apical periodontitis and establishing effective antimicrobial therapeutic strategies. This study aims to uncover the composition and diversity of microbiota associated to the root apex to identify the relevant bacteria highly involved in AP, with the consideration of root apex samples from the infected teeth (with/without root canal treatment), healthy teeth as well as the healthy oral. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5474-yDOI Listing

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller.

BMC Genomics 2019 Apr 4;20(Suppl 2):184. Epub 2019 Apr 4.

Delft University of Technology, Mekelweg 4, Delft, 2628 CD, The Netherlands.

Background: Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far been difficult to accelerate effectively on GPUs. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5468-9DOI Listing

Estimating the total genome length of a metagenomic sample using k-mers.

BMC Genomics 2019 Apr 4;20(Suppl 2):183. Epub 2019 Apr 4.

MOE Key Laboratory of Bioinformatics Division and Center for Synthetic & System Biology, BNRIST, Beijing, 100084, China.

Background: Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5467-xDOI Listing

ENIGMA: an enterotype-like unigram mixture model for microbial association analysis.

BMC Genomics 2019 Apr 4;20(Suppl 2):191. Epub 2019 Apr 4.

Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan.

Background: One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as "enterotype", which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5476-9DOI Listing
April 2019
1 Read

Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues.

BMC Genomics 2019 Apr 4;20(Suppl 2):221. Epub 2019 Apr 4.

Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai, China.

Background: Epigenome is highly dynamic during the early stages of embryonic development. Epigenetic modifications provide the necessary regulation for lineage specification and enable the maintenance of cellular identity. Given the rapid accumulation of genome-wide epigenomic modification maps across cellular differentiation process, there is an urgent need to characterize epigenetic dynamics and reveal their impacts on differential gene regulation. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5472-0DOI Listing
April 2019
1 Read

TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data.

BMC Genomics 2019 Apr 4;20(Suppl 2):224. Epub 2019 Apr 4.

Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.

Background: Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However, the analysis of time series scRNA-seq data could be compromised by 1) distortion created by assorted sources of data collection and generation across time samples and 2) inheritance of cell-to-cell variations by stochastic dynamic patterns of gene expression. This calls for the development of an algorithm able to visualize time series scRNA-seq data in order to reveal latent structures and uncover dynamic transition processes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5477-8DOI Listing

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.

BMC Genomics 2019 Apr 8;20(1):275. Epub 2019 Apr 8.

Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

Background: The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5642-0DOI Listing

RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.

BMC Genomics 2019 Apr 8;20(1):276. Epub 2019 Apr 8.

School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.

Background: RNA-protein 3D complex structure prediction is still challenging. Recently, a template-based approach PRIME is proposed in our team to build RNA-protein 3D complex structure models with a higher success rate than computational docking software. However, scoring function of RNA alignment algorithm SARA in PRIME is size-dependent, which limits its ability to detect templates in some cases. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5631-3DOI Listing

Genome-wide associations and functional gene analyses for endoparasite resistance in an endangered population of native German Black Pied cattle.

BMC Genomics 2019 Apr 8;20(1):277. Epub 2019 Apr 8.

Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390, Gießen, Germany.

Background: Gastrointestinal nematodes (GIN), liver flukes (Fasciola hepatica) and bovine lungworms (Dictyocaulus viviparus) are the most important parasitic agents in pastured dairy cattle. Endoparasite infections are associated with reduced milk production and detrimental impacts on female fertility, contributing to economic losses in affected farms. In quantitative-genetic studies, the heritabilities for GIN and F. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5659-4DOI Listing

Diversity and recombination analysis of Cotton leaf curl Multan virus: a highly emerging begomovirus in northern India.

BMC Genomics 2019 Apr 6;20(1):274. Epub 2019 Apr 6.

Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia (Central University), New Delhi, 110025, India.

Background: Cotton leaf curl disease (CLCuD), caused by begomoviruses in association with satellite molecules, is a major threat to cotton production causing enormous losses to cotton crop in most of the cotton growing countries including Indian subcontinent. In this study, isolates of begomovirus and satellite molecules associated with CLCuD were collected from North India (Haryana, New Delhi). They were amplified employing rolling circle replication mechanism, cloned, sequenced and, their phylogenetic and recombination analysis was performed. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5640-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451280PMC
April 2019
1 Read

Comparative genomics reveals a lack of evidence for pigeons as a main source of stx-carrying Escherichia coli causing disease in humans and the common existence of hybrid Shiga toxin-producing and enteropathogenic E. coli pathotypes.

BMC Genomics 2019 Apr 5;20(1):271. Epub 2019 Apr 5.

Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.

Background: Wild birds, in particular pigeons are considered a natural reservoir for stx-carrying E. coli. An extensive comparison of isolates from pigeons and humans from the same region is lacking, which hampers justifiable conclusions on the epidemiology of these pathogens. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5635-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451237PMC
April 2019
2 Reads

L-lactate induces specific genome wide alterations of gene expression in cultured bovine granulosa cells.

BMC Genomics 2019 Apr 5;20(1):273. Epub 2019 Apr 5.

Institute of Reproductive Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.

Background: Previously, we could show that L-lactate affects cultured bovine granulosa cells (GC) in a specific manner driving the cells into an early pre-ovulatory phenotype. Here we studied genome wide effects in L-lactate-treated GC to further elucidate the underlying mechanisms that are responsible for the L-lactate induced transformation. Cultured estrogen producing GC treated either with L-lactate or vehicle control were subjected to mRNA microarray analysis. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5657-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451254PMC

Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3.

BMC Genomics 2019 Apr 5;20(1):272. Epub 2019 Apr 5.

Department of Medicine, Division of Infectious Diseases, Wright Fleming Wing, St Mary's Campus, Imperial College London, Norfolk Place, London, W2 1PG, UK.

Background: The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well documented in several animal species, but their genetic variation and biological mechanism is less well understood, particularly in avian species.

Results: Here we report the complete sequence of the domestic chicken Gallus gallus IFITM locus from a wide variety of chicken breeds to examine the detailed pattern of genetic variation of the locus on chromosome 5, including the flanking genes ATHL1 and B4GALNT4. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5621-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451222PMC

Marker genes as predictors of shared genomic function.

BMC Genomics 2019 Apr 4;20(1):268. Epub 2019 Apr 4.

Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Rd, Rudman Hall, Durham, NH, 03824, USA.

Background: Although high-throughput marker gene studies provide valuable insight into the diversity and relative abundance of taxa in microbial communities, they do not provide direct measures of their functional capacity. Recently, scientists have shown a general desire to predict functional profiles of microbial communities based on phylogenetic identification inferred from marker genes, and recent tools have been developed to link the two. However, to date, no large-scale examination has quantified the correlation between the marker gene based taxonomic identity and protein coding gene conservation. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5641-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449922PMC

Comparative transcriptome analyses revealed different heat stress responses in high- and low-GS Brassica alboglabra sprouts.

BMC Genomics 2019 Apr 4;20(1):269. Epub 2019 Apr 4.

Joint FAFU-Dalhousie Lab, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Background: Chinese kale (Brassica alboglabra) contains high nutritional elements and functional molecules, especially anticarcinogenic and antioxidant glucosinolates (GS), which was highly affected by environment temperature. To investigate the link of GS biosynthesis with heat stress response in Chinese kale, global transcription profiles of high-GS line (HG), low-GS line (LG), high-GS line under heat stress (HGT) and low-GS line under heat stress (LGT) were analyzed.

Results: Based on three biological replicates of each RNA sequencing data, 3901, 4062 and 2396 differentially expressed genes in HG vs HGT, LG vs LGT and HGT vs LGT were obtained, respectively. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5652-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450006PMC
April 2019
3 Reads

Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens.

BMC Genomics 2019 Apr 4;20(1):270. Epub 2019 Apr 4.

Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L. K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St Petersburg, 196601, Russia.

Background: The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great potential in meeting demands of local food producers, commercial farmers and biotechnology sector of specific pathogen-free (SPF) eggs, the former valuing the breed for its egg weight (EW), EL, age at first egg (AFE), body weight (BW), and the latter for its yield of extraembryonic fluid (YEF) in 12.5-day embryos, ratio of extraembryonic fluid to egg weight, and embryo mass. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5605-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449956PMC

Comparative transcriptome analysis and ChIP-sequencing reveals stage-specific gene expression and regulation profiles associated with pollen wall formation in Brassica rapa.

BMC Genomics 2019 Apr 3;20(1):264. Epub 2019 Apr 3.

Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China.

Background: Genic male sterility (GMS) line is an important approach to utilize heterosis in Brassica rapa, one of the most widely cultivated vegetable crops in Northeast Asia. However, the molecular genetic mechanisms of GMS remain to be largely unknown.

Results: Detailed phenotypic observation of 'Bcajh97-01A/B', a B. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5637-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446297PMC
April 2019
1 Read

ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels.

BMC Genomics 2019 Apr 3;20(1):267. Epub 2019 Apr 3.

School of Computer Science, University of Waterloo, Waterloo, ON, Canada.

Background: Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains challenging due to the magnitude of the datasets and the intrinsic problems associated with classification. The need exists for an approach and software tool that addresses the limitations of existing alignment-based methods, as well as the challenges of recently proposed alignment-free methods.

Results: We propose a novel combination of supervised Machine Learning with Digital Signal Processing, resulting in ML-DSP: an alignment-free software tool for ultrafast, accurate, and scalable genome classification at all taxonomic levels. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5571-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448311PMC

De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar 'Tieguanyin' compared with cultivar 'Benshan'.

BMC Genomics 2019 Apr 3;20(1):265. Epub 2019 Apr 3.

College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

Background: The two original plants of the oolong tea cultivar ('Tieguanyin') are "Wei shuo" 'Tieguanyin'-TGY (Wei) and "Wang shuo" 'Tieguanyin'-TGY (Wang). Another cultivar, 'Benshan' (BS), is similar to TGY in its aroma, taste, and genetic make-up, but it lacks the "Yin Rhyme" flavor. We aimed to identify differences in biochemical characteristics and gene expression among these tea plants. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5643-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446291PMC
April 2019
1 Read

Rapid evolution of a retro-transposable hotspot of ovine genome underlies the alteration of BMP2 expression and development of fat tails.

BMC Genomics 2019 Apr 2;20(1):261. Epub 2019 Apr 2.

Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

Background: Sheep have developed the ability to store fat in their tails, which is a unique way of reserving energy to survive a harsh environment. However, the mechanism underlying this adaptive trait remains largely unsolved.

Results: In the present study, we provide evidence for the genetic determinants of fat tails, based on whole genome sequences of 89 individual sheep. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5620-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445056PMC
April 2019
3 Reads
3.986 Impact Factor

OMICfpp: a fuzzy approach for paired RNA-Seq counts.

BMC Genomics 2019 Apr 2;20(1):259. Epub 2019 Apr 2.

Universidad de Valencia. Departamento de Estadística e Investigación Operativa, Avda. Vicent Andrés Estellés, 1, Burjasot, 46100, Spain.

Background: RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The major problem in statistical analysis of RNA-Seq and in the omics data in general, is the small sample size with respect to the large number of variables. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5496-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444640PMC

Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA.

BMC Genomics 2019 Apr 2;20(1):262. Epub 2019 Apr 2.

Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia, CEP 45662-900, Brazil.

Background: The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). Read More

View Article

Download full-text PDF

Source
https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12864-019-5576-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444444PMC
April 2019
3 Reads

Predicting male fertility in dairy cattle using markers with large effect and functional annotation data.

BMC Genomics 2019 Apr 2;20(1):258. Epub 2019 Apr 2.

Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.

Background: Fertility is among the most important economic traits in dairy cattle. Genomic prediction for cow fertility has received much attention in the last decade, while bull fertility has been largely overlooked. The goal of this study was to assess genomic prediction of dairy bull fertility using markers with large effect and functional annotation data. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5644-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444482PMC

QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations.

BMC Genomics 2019 Apr 2;20(1):260. Epub 2019 Apr 2.

The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Background: The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5610-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444683PMC
April 2019
1 Read