12,969 results match your criteria BMC genomics[Journal]


Correction to: On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments.

BMC Genomics 2020 Jun 3;21(1):384. Epub 2020 Jun 3.

Department of Data Analysis and Mathematical Modeling, Ghent University, 9000, Ghent, Belgium.

An amendment to this paper has been published and can be accessed via the original article. Read More

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http://dx.doi.org/10.1186/s12864-020-6754-2DOI Listing

The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste.

BMC Genomics 2020 Jun 3;21(1):386. Epub 2020 Jun 3.

Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil.

Background: Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. Read More

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http://dx.doi.org/10.1186/s12864-020-06784-8DOI Listing

iTRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage.

BMC Genomics 2020 Jun 3;21(1):390. Epub 2020 Jun 3.

College of Food, Shihezi University, Xinjiang, 832000, China.

Background: Cantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in cantaloupe, a cold-sensitive cultivar, Golden Empress-308 (GE) and a cold-tolerant cultivar, Jia Shi-310 (JS), were selected in parallel for iTRAQ quantitative proteomic analysis.

Results: The two kinds of commercial cultivars were exposed to a temperature of 0. Read More

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http://dx.doi.org/10.1186/s12864-020-06797-3DOI Listing

Identification of genetic loci associated with higher resistance to pancreas disease (PD) in Atlantic salmon (Salmo salar L.).

BMC Genomics 2020 Jun 3;21(1):388. Epub 2020 Jun 3.

Benchmark Genetics Norway AS, Sandviksboder 3A, N-5035, Bergen, Norway.

Background: Pancreas disease (PD) is a contagious disease caused by salmonid alphavirus (SAV) with significant economic and welfare impacts on salmon farming. Previous work has shown that higher resistance against PD has underlying additive genetic components and can potentially be improved through selective breeding. To better understand the genetic basis of PD resistance in Atlantic salmon, we challenged 4506 smolts from 296 families of the SalmoBreed strain. Read More

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http://dx.doi.org/10.1186/s12864-020-06788-4DOI Listing

Distinctions between sex and time in patterns of DNA methylation across puberty.

BMC Genomics 2020 Jun 3;21(1):389. Epub 2020 Jun 3.

Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford, CA, 94305, USA.

Background: There are significant sex differences in human physiology and disease; the genomic sources of these differences, however, are not well understood. During puberty, a drastic neuroendocrine shift signals physical changes resulting in robust sex differences in human physiology. Here, we explore how shifting patterns of DNA methylation may inform these pathways of biological plasticity during the pubertal transition. Read More

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http://dx.doi.org/10.1186/s12864-020-06789-3DOI Listing

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family.

BMC Genomics 2020 Jun 3;21(1):387. Epub 2020 Jun 3.

Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.

Background: Lanthipeptides belong to the ribosomally synthesized and post-translationally modified peptide group of natural products and have a variety of biological activities ranging from antibiotics to antinociceptives. These peptides are cyclized through thioether crosslinks and can bear other secondary post-translational modifications. While lanthipeptide biosynthetic gene clusters can be identified by the presence of genes encoding characteristic enzymes involved in the post-translational modification process, locating the precursor peptides encoded within these clusters is challenging due to their short length and high sequence variability, which limits the high-throughput exploration of lanthipeptide biosynthesis. Read More

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http://dx.doi.org/10.1186/s12864-020-06785-7DOI Listing

Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus.

BMC Genomics 2020 Jun 3;21(1):383. Epub 2020 Jun 3.

College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China.

Background: Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of Ananas comosus var. Read More

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http://dx.doi.org/10.1186/s12864-020-6750-6DOI Listing

LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.

BMC Genomics 2020 Jun 3;21(1):385. Epub 2020 Jun 3.

Department of Clinical Sciences, Division of Reproduction, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.

Background: Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometrial function. Following in vitro culture, bEECs from three cows were either untreated (0) or exposed to 2 and 8 μg/mL LPS for 24 h. Read More

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http://dx.doi.org/10.1186/s12864-020-06777-7DOI Listing

Identification and characterization of male reproduction-related genes in pig (Sus scrofa) using transcriptome analysis.

BMC Genomics 2020 Jun 1;21(1):381. Epub 2020 Jun 1.

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.

Background: The systematic interrogation of reproduction-related genes was key to gain a comprehensive understanding of the molecular mechanisms underlying male reproductive traits in mammals. Here, based on the data collected from the NCBI SRA database, this study first revealed the genes involved in porcine male reproduction as well their uncharacterized transcriptional characteristics.

Results: Results showed that the transcription of porcine genome was more widespread in testis than in other organs (the same for other mammals) and that testis had more tissue-specific genes (1210) than other organs. Read More

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http://dx.doi.org/10.1186/s12864-020-06790-wDOI Listing

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern.

BMC Genomics 2020 Jun 1;21(1):382. Epub 2020 Jun 1.

U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA.

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. Read More

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http://dx.doi.org/10.1186/s12864-020-06783-9DOI Listing

ncRI: a manually curated database for experimentally validated non-coding RNAs in inflammation.

BMC Genomics 2020 Jun 1;21(1):380. Epub 2020 Jun 1.

College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.

Background: Inflammation has been considered to be central to the onset, progression, and outcome of infectious diseases, especially as one of the hallmarks of cancer. Non-coding RNAs (ncRNAs), such as miRNAs and lncRNAs, have emerged as vital regulators in control of immune and inflammatory processes, and also play important roles in the inflammatory disease and immunotherapy.

Results: In this study, we presented a database ncRI, which documented experimentally verified ncRNAs in inflammatory diseases, from published articles. Read More

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http://dx.doi.org/10.1186/s12864-020-06794-6DOI Listing

Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species.

BMC Genomics 2020 Jun 1;21(1):379. Epub 2020 Jun 1.

State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.

Background: Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of FBPs has been reported in Gossypium species.

Results: A total of 41 FBP genes from four Gossypium species were identified and analyzed. Read More

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http://dx.doi.org/10.1186/s12864-020-6773-zDOI Listing

Discovering candidate imprinted genes and imprinting control regions in the human genome.

Authors:
Minou Bina

BMC Genomics 2020 May 31;21(1):378. Epub 2020 May 31.

Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN, 47907, USA.

Background: Genomic imprinting is a process thereby a subset of genes is expressed in a parent-of-origin specific manner. This evolutionary novelty is restricted to mammals and controlled by genomic DNA segments known as Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, I showed that in the mouse genome, the fully characterized ICRs/gDMRs often includes clusters of 2 or more of a set of composite-DNA-elements known as ZFBS-morph overlaps. Read More

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http://dx.doi.org/10.1186/s12864-020-6688-8DOI Listing

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum.

BMC Genomics 2020 May 29;21(1):376. Epub 2020 May 29.

Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.

Background: Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Read More

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http://dx.doi.org/10.1186/s12864-020-6764-0DOI Listing

Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries.

BMC Genomics 2020 May 29;21(1):377. Epub 2020 May 29.

Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada.

Background: Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. Read More

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http://dx.doi.org/10.1186/s12864-020-06780-yDOI Listing

MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression.

BMC Genomics 2020 May 29;21(1):375. Epub 2020 May 29.

Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan.

Background: DNA methylation is a major epigenetic modification involved in regulating gene expression. The effects of DNA methylation on gene expression differ by genomic location and vary across kingdoms, species and environmental conditions. To identify the functional regulatory roles of DNA methylation, the correlation between DNA methylation changes and alterations in gene expression is crucial. Read More

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http://dx.doi.org/10.1186/s12864-020-6722-xDOI Listing

Correction to: Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256.

BMC Genomics 2020 May 26;21(1):373. Epub 2020 May 26.

Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.

An amendment to this paper has been published and can be accessed via the original article. Read More

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http://dx.doi.org/10.1186/s12864-020-06781-xDOI Listing

Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica.

BMC Genomics 2020 May 26;21(1):374. Epub 2020 May 26.

Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada.

Background: Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica. Read More

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http://dx.doi.org/10.1186/s12864-020-6765-zDOI Listing

Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats.

BMC Genomics 2020 May 25;21(1):372. Epub 2020 May 25.

Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.

Background: The microscopic process of postnatal testicular development in early-puberty animals is poorly understood. Therefore, in this study, 21 male Yiling goats with average ages of 0, 30, 60, 90, 120, 150 and 180 days old (each age group comprised three goats) were used to study the changes in organs, tissues and transcriptomes during postnatal testicle development to obtain a broad and deep insight into the dynamic process of testicular transition from growth to spermatogenesis in early-puberty animals.

Results: The inflection point of testicular weight was at 119 days postpartum (dpp), and the testicular weight increased rapidly from 119 dpp to 150 dpp. Read More

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http://dx.doi.org/10.1186/s12864-020-6767-xDOI Listing
May 2020
3.986 Impact Factor

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen.

BMC Genomics 2020 May 20;21(1):369. Epub 2020 May 20.

Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.

Background: Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. Read More

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http://dx.doi.org/10.1186/s12864-020-06778-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7238557PMC

Genome-wide characterization of the SPL gene family involved in the age development of Jatropha curcas.

BMC Genomics 2020 May 20;21(1):368. Epub 2020 May 20.

Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou, 510520, China.

Background: SPL (SQUAMOSA-promoter binding protein-like) proteins form a large family of plant-specific transcription factors that play essential roles in various aspects of plant growth and development. They are potentially important candidates for genetic improvement of agronomic traits. However, there were limited information about the SPL genes in Jatropha curcas, an important biofuel plant. Read More

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http://dx.doi.org/10.1186/s12864-020-06776-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7238634PMC

Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods.

BMC Genomics 2020 May 20;21(1):370. Epub 2020 May 20.

Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA.

Background: Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. One area of interest is determining genes showing signals of coevolution, which can also indicate potential functional similarity, analogous to co-expression analysis often performed across conditions for a single species. Read More

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http://dx.doi.org/10.1186/s12864-020-6761-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240986PMC

Correction to: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae).

BMC Genomics 2020 May 20;21(1):371. Epub 2020 May 20.

Department of Ecology and Evolution Biophore, University of Lausanne, Lausanne, Switzerland.

An amendment to this paper has been published and can be accessed via the original article. Read More

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http://dx.doi.org/10.1186/s12864-020-06782-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240987PMC

Transposable element persistence via potential genome-level ecosystem engineering.

BMC Genomics 2020 May 19;21(1):367. Epub 2020 May 19.

Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.

Background: The nuclear genomes of eukaryotes vary enormously in size, with much of this variability attributable to differential accumulation of transposable elements (TEs). To date, the precise evolutionary and ecological conditions influencing TE accumulation remain poorly understood. Most previous attempts to identify these conditions have focused on evolutionary processes occurring at the host organism level, whereas we explore a TE ecology explanation. Read More

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http://dx.doi.org/10.1186/s12864-020-6763-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236351PMC

Metabolic and transcriptomic analysis of two Cucurbita moschata germplasms throughout fruit development.

BMC Genomics 2020 May 15;21(1):365. Epub 2020 May 15.

Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.

Background: Pumpkins (Cucurbita moschata; Cucurbitaceae) are valued for their fruits and seeds and are rich in nutrients. Carotenoids and sugar contents, as main feature of pumpkin pulp, are used to determine the fruit quality.

Results: Two pumpkin germplasms, CMO-X and CMO-E, were analyzed regarding the essential quality traits such as dry weight, soluble solids, organic acids, carotenoids and sugar contents. Read More

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http://dx.doi.org/10.1186/s12864-020-6774-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227267PMC
May 2020
3.986 Impact Factor

An integrated software for virus community sequencing data analysis.

BMC Genomics 2020 May 15;21(1):363. Epub 2020 May 15.

Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.

Background: A virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases. However automatic and dedicated pipeline for interpreting virus community sequencing data has not been developed yet.

Results: We developed Quasispecies Analysis Package (QAP), an integrated software platform to address the problems associated with making biological interpretations from massive viral population sequencing data. Read More

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http://dx.doi.org/10.1186/s12864-020-6744-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227348PMC

PretiMeth: precise prediction models for DNA methylation based on single methylation mark.

BMC Genomics 2020 May 15;21(1):364. Epub 2020 May 15.

School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China.

Background: The computational prediction of methylation levels at single CpG resolution is promising to explore the methylation levels of CpGs uncovered by existing array techniques, especially for the 450 K beadchip array data with huge reserves. General prediction models concentrate on improving the overall prediction accuracy for the bulk of CpG loci while neglecting whether each locus is precisely predicted. This leads to the limited application of the prediction results, especially when performing downstream analysis with high precision requirements. Read More

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http://dx.doi.org/10.1186/s12864-020-6768-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227319PMC

Identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam) with SSR linkage maps.

BMC Genomics 2020 May 15;21(1):366. Epub 2020 May 15.

Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.

Background: Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to root rot have not yet been reported, and the biological mechanisms of resistance remain unclear in sweetpotato. Read More

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http://dx.doi.org/10.1186/s12864-020-06775-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229581PMC

Intron and gene size expansion during nervous system evolution.

BMC Genomics 2020 May 14;21(1):360. Epub 2020 May 14.

Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Background: The evolutionary radiation of animals was accompanied by extensive expansion of gene and genome sizes, increased isoform diversity, and complexity of regulation.

Results: Here we show that the longest genes are enriched for expression in neuronal tissues of diverse vertebrates and of invertebrates. Additionally, we show that neuronal gene size expansion occurred predominantly through net gains in intron size, with a positional bias toward the 5' end of each gene. Read More

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http://dx.doi.org/10.1186/s12864-020-6760-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222433PMC

Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian.

BMC Genomics 2020 May 14;21(1):361. Epub 2020 May 14.

Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Woodward Hall, Room 381A, Charlotte, NC, 28223, USA.

Background: Animals have specific molecular, physiological, and behavioral responses to light that are influenced by wavelength and intensity. Predictable environmental changes - predominantly solar and lunar cycles - drive endogenous daily oscillations by setting internal pacemakers, otherwise known as the circadian clock. Cnidarians have been a focal group to discern the evolution of light responsiveness due to their phylogenetic position as a sister phylum to bilaterians and broad range of light-responsive behaviors and physiology. Read More

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http://dx.doi.org/10.1186/s12864-020-6766-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222589PMC

Phylogenomic incongruence in Ceratocystis: a clue to speciation?

BMC Genomics 2020 May 14;21(1):362. Epub 2020 May 14.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.

Background: The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g. Read More

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http://dx.doi.org/10.1186/s12864-020-6772-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222570PMC

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.

BMC Genomics 2020 May 13;21(1):359. Epub 2020 May 13.

Department of Biology, Duke University, Biological Sciences Building, 124 Science Drive, Durham, NC, 27708, USA.

Background: Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype.

Results: We used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. Read More

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http://dx.doi.org/10.1186/s12864-020-6752-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222330PMC

Linkage mapping and genome-wide association study reveals conservative QTL and candidate genes for Fusarium rot resistance in maize.

BMC Genomics 2020 May 12;21(1):357. Epub 2020 May 12.

College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.

Background: Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned.

Result: To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred lines (RIL) population and one panel of inbred lines were used to map quantitative trait loci (QTL) for resistance. Read More

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http://dx.doi.org/10.1186/s12864-020-6733-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218626PMC

ICGEC: a comparative method for measuring epigenetic conservation of genes via the integrated signal from multiple histone modifications between cell types.

BMC Genomics 2020 May 12;21(1):356. Epub 2020 May 12.

College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.

Background: Histone post-translational modifications play crucial roles in epigenetic regulation of gene expression and are known to be associated with the phenotypic differences of different cell types. Therefore, it is of fundamental importance to dissect the genes and pathways involved in such a phenotypic variation at the level of epigenetics. However, the existing comparative approaches are largely based on the differences, especially the absolute difference in the levels of individual histone modifications of genes under contrasting conditions. Read More

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http://dx.doi.org/10.1186/s12864-020-6771-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216622PMC

Evolution of Fusarium tricinctum and Fusarium avenaceum mitochondrial genomes is driven by mobility of introns and of a new type of palindromic microsatellite repeats.

BMC Genomics 2020 May 12;21(1):358. Epub 2020 May 12.

INRAE, MycSA, F-33882, Villenave d'Ornon, France.

Background: Increased contamination of European and Asian wheat and barley crops with "emerging" mycotoxins such as enniatins or beauvericin, produced by Fusarium avenaceum and Fusarium tricinctum, suggest that these phylogenetically close species could be involved in future food-safety crises.

Results: The mitochondrial genomes of F. tricinctum strain INRA104 and F. Read More

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http://dx.doi.org/10.1186/s12864-020-6770-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218506PMC

Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis.

BMC Genomics 2020 May 11;21(1):351. Epub 2020 May 11.

Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow, 119334, Russia.

Background: The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. Read More

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http://dx.doi.org/10.1186/s12864-020-6759-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216553PMC

The seasonal development dynamics of the yak hair cycle transcriptome.

BMC Genomics 2020 May 11;21(1):355. Epub 2020 May 11.

Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.

Background: Mammalian hair play an important role in mammals' ability to adapt to changing climatic environments. The seasonal circulation of yak hair helps them adapt to high altitude but the regulation mechanisms of the proliferation and differentiation of hair follicles (HFs) cells during development are still unknown. Here, using time series data for transcriptome and hormone contents, we systematically analyzed the mechanism regulating the periodic expression of hair development in the yak and reviewed how different combinations of genetic pathways regulate HFs development and cycling. Read More

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http://dx.doi.org/10.1186/s12864-020-6725-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216598PMC
May 2020
3.986 Impact Factor

Transcriptome profiling of human thymic CD4+ and CD8+ T cells compared to primary peripheral T cells.

BMC Genomics 2020 May 11;21(1):350. Epub 2020 May 11.

Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0450, Oslo, Norway.

Background: The thymus is a highly specialized organ of the immune system where T cell precursors develop and differentiate into self-tolerant CD4+ or CD8+ T cells. No studies to date have investigated how the human transcriptome profiles differ, between T cells still residing in the thymus and T cells in the periphery.

Results: We have performed high-throughput RNA sequencing to characterize the transcriptomes of primary single positive (SP) CD4+ and CD8+ T cells from infant thymic tissue, as well as primary CD4+ and CD8+ T cells from infant and adult peripheral blood, to enable the comparisons across tissues and ages. Read More

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http://dx.doi.org/10.1186/s12864-020-6755-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216358PMC

Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment.

BMC Genomics 2020 May 11;21(1):348. Epub 2020 May 11.

Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.

Background: Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and globally alter microbial community and metabolic capacities.

Results: Consistently, we found host DNA contents (HDCs), calculated as the percentage of metagenomic sequencing reads mapped to the host genome, were significantly elevated in patients of CRC and Crohn's disease (CD). Read More

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http://dx.doi.org/10.1186/s12864-020-6749-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216530PMC

Optimized breeding strategies to harness genetic resources with different performance levels.

BMC Genomics 2020 May 11;21(1):349. Epub 2020 May 11.

GQE - Le Moulon, INRAE, University Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France.

Background: The narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient strategy is required to broaden the genetic base of commercial breeding programs while not compromising short-term variety release. Optimal cross selection aims at identifying the optimal set of crosses that balances the expected genetic value and diversity. Read More

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http://dx.doi.org/10.1186/s12864-020-6756-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216646PMC

Assessment of databases to determine the validity of β- and γ-carbonic anhydrase sequences from vertebrates.

BMC Genomics 2020 May 11;21(1):352. Epub 2020 May 11.

Faculty of Medicine and Health Technology, Tampere University, FI-33520, Tampere, Finland.

Background: The inaccuracy of DNA sequence data is becoming a serious problem, as the amount of molecular data is multiplying rapidly and expectations are high for big data to revolutionize life sciences and health care. In this study, we investigated the accuracy of DNA sequence data from commonly used databases using carbonic anhydrase (CA) gene sequences as generic targets. CAs are ancient metalloenzymes that are present in all unicellular and multicellular living organisms. Read More

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http://dx.doi.org/10.1186/s12864-020-6762-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216627PMC

High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize.

BMC Genomics 2020 May 11;21(1):353. Epub 2020 May 11.

Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.

Background: The fluctuation of nitrogen (N) contents profoundly affects the root growth and architecture in maize by altering the expression of thousands of genes. The differentially expressed genes (DEGs) in response to N have been extensively reported. However, information about the effects of N variation on the alternative splicing in genes is limited. Read More

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http://dx.doi.org/10.1186/s12864-020-6769-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216474PMC

Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements.

BMC Genomics 2020 May 11;21(1):354. Epub 2020 May 11.

GEOMAR, Helmholtz Centre for Ocean Research, Marine Evolutionary Ecology, Duesternbrooker Weg 20, 24105, Kiel, Germany.

Background: Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. Read More

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http://dx.doi.org/10.1186/s12864-020-6735-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216594PMC

Comparative genomics of whole-cell pertussis vaccine strains from India.

BMC Genomics 2020 May 7;21(1):345. Epub 2020 May 7.

Serum Institute of India Pvt. Ltd, Pune, Maharashtra, 411028, India.

Background: Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of Bordetella pertussis has been reported as one of the contributing factors for the resurgence of the disease. Our current knowledge of B. Read More

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http://dx.doi.org/10.1186/s12864-020-6724-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204287PMC

The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak.

BMC Genomics 2020 May 7;21(1):347. Epub 2020 May 7.

State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China.

Background: The Intramuscular fat (IMF) content in meat products, which is positively correlated with meat quality, is an important trait considered by consumers. The regulation of IMF deposition is species specific. However, the IMF-deposition-related mRNA and non-coding RNA and their regulatory network in yak (Bos grunniens) remain unknown. Read More

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http://dx.doi.org/10.1186/s12864-020-6757-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203869PMC

Genome-wide association analyses identify known and novel loci for teat number in Duroc pigs using single-locus and multi-locus models.

BMC Genomics 2020 May 7;21(1):344. Epub 2020 May 7.

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China.

Background: More teats are necessary for sows to nurse larger litters to provide immunity and nutrient for piglets prior to weaning. Previous studies have reported the strong effect of an insertion mutation in the Vertebrae Development Associated (VRTN) gene on Sus scrofa chromosome 7 (SSC7) that increased the number of thoracic vertebrae and teat number in pigs. We used genome-wide association studies (GWAS) to map genetic markers and genes associated with teat number in two Duroc pig populations with different genetic backgrounds. Read More

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http://dx.doi.org/10.1186/s12864-020-6742-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204245PMC

The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma.

BMC Genomics 2020 May 7;21(1):346. Epub 2020 May 7.

Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK.

Background: Reference genome and transcriptome assemblies of helminths have reached a level of completion whereby secondary analyses that rely on accurate gene estimation or syntenic relationships can be now conducted with a high level of confidence. Recent public release of the v.3 assembly of the mouse bile-duct tapeworm, Hymenolepis microstoma, provides chromosome-level characterisation of the genome and a stabilised set of protein coding gene models underpinned by bioinformatic and empirical data. Read More

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http://dx.doi.org/10.1186/s12864-020-6710-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204028PMC

Differential expression pattern of the proteome in response to cadmium stress based on proteomics analysis of wheat roots.

BMC Genomics 2020 May 7;21(1):343. Epub 2020 May 7.

College of Agronomy, Northwest A&F University, Yangling, 712100, China.

Background: Heavy metal cadmium (Cd) is a common environmental pollutant in soils, which has an negative impacts on crop growth and development. At present, cadmium has become a major soil and water heavy metal pollutant, which not only causes permanent and irreversible health problems for humans, but also causes a significant reduction in crop yields.

Results: This study examined the chemical forms of Cd in the roots of two wheat varieties (M1019 and Xinong20) by continuous extraction and analyzed differences in distribution characteristics of Cd in the root cell wall, cytoplasm, and organelles by elemental content determination and subcellular separation. Read More

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http://dx.doi.org/10.1186/s12864-020-6716-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203821PMC

Correction to: The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics.

BMC Genomics 2020 May 6;21(1):342. Epub 2020 May 6.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

An amendment to this paper has been published and can be accessed via the original article. Read More

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http://dx.doi.org/10.1186/s12864-020-6753-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7201704PMC

The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster.

BMC Genomics 2020 May 4;21(1):341. Epub 2020 May 4.

Department of Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA.

Background: Genetic association studies that seek to explain the inheritance of complex traits typically fail to explain a majority of the heritability of the trait under study. Thus, we are left with a gap in the map from genotype to phenotype. Several approaches have been used to fill this gap, including those that attempt to map endophenotype such as the transcriptome, proteome or metabolome, that underlie complex traits. Read More

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http://dx.doi.org/10.1186/s12864-020-6739-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7199327PMC