20,453 results match your criteria Genomics [Journal]


Sex differences in gene regulation in the dorsal root ganglion after nerve injury.

BMC Genomics 2019 Feb 19;20(1):147. Epub 2019 Feb 19.

Department of Pharmacology and Molecular Sciences, School of Medicine, Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.

Background: Pain is a subjective experience derived from complex interactions among biological, environmental, and psychosocial pathways. Sex differences in pain sensitivity and chronic pain prevalence are well established. However, the molecular basis underlying these sex dimorphisms are poorly understood particularly with regard to the role of the peripheral nervous system. Read More

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http://dx.doi.org/10.1186/s12864-019-5512-9DOI Listing
February 2019

Comparative study on seasonal hair follicle cycling by analysis of the transcriptomes from cashmere and milk goats.

Genomics 2019 Feb 16. Epub 2019 Feb 16.

College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia Autonomous Region 010018, China; Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, Inner Mongolia Autonomous Region 010018, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, Inner Mongolia Autonomous Region 010018, China; Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, Inner Mongolia Autonomous Region 010018, China. Electronic address:

Guard hair and cashmere undercoat are developed from primary and secondary hair follicle, respectively. Little is known about the gene expression differences between primary and secondary hair follicle cycling. In this study, we obtained RNA-seq data from cashmere and milk goats grown at four different seasons. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.02.013DOI Listing
February 2019

iNR-2L: A two-level sequence-based predictor developed via Chou's 5-steps rule and general PseAAC for identifying nuclear receptors and their families.

Genomics 2019 Feb 16. Epub 2019 Feb 16.

Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan. Electronic address:

Nuclear receptor proteins (NRPs) perform a vital role in regulating gene expression. With the rapidity growth of NRPs in post-genomic era, it is highly recommendable to identify NRPs and their sub-families accurately from their primary sequences. Several conventional methods have been used for discrimination of NRPs and their sub-families, but did not achieve considerable results. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.02.006DOI Listing
February 2019

Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.

BMC Genomics 2019 Feb 18;20(1):146. Epub 2019 Feb 18.

Vancouver Prostate Centre, Vancouver, Canada.

Background: Prostate cancer (PCa) is the most common malignant neoplasm among men in many countries. Since most precancerous and cancerous tissues show signs of inflammation, chronic bacterial prostatitis has been hypothesized to be a possible etiology. However, establishing a causal relationship between microbial inflammation and PCa requires a comprehensive analysis of the prostate microbiome. Read More

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http://dx.doi.org/10.1186/s12864-019-5457-zDOI Listing
February 2019
1 Read

A unique insight into the MiRNA profile during genital chlamydial infection.

BMC Genomics 2019 Feb 18;20(1):143. Epub 2019 Feb 18.

Department of Microbiology, Biochemistry & Immunology, Morehouse School of Medicine, 720 Westview Drive, S.W, Atlanta, GA, 30310, USA.

Background: Genital C. trachomatis infection may cause pelvic inflammatory disease (PID) that can lead to tubal factor infertility (TFI). Understanding the pathogenesis of chlamydial complications including the pathophysiological processes within the female host genital tract is important in preventing adverse pathology. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5495-6DOI Listing
February 2019
1 Read

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions.

BMC Genomics 2019 Feb 18;20(1):145. Epub 2019 Feb 18.

Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, Western Cape, South Africa.

Background: In wine fermentation starter cultures, the blending of non-Saccharomyces yeast with Saccharomyces cerevisiae to improve the complexity of wine has become common practice, but data regarding the impact of co-cultivation on yeast physiology and on genetic and metabolic regulation remain limited. Here we describe a transcriptomic analysis of mixed fermentations of Saccharomyces cerevisiae and Lachancea thermotolerans. The fermentations were carried out in carefully controlled environmental conditions in a bioreactor to reduce transcriptomic responses that would be due to factors other than the presence of the second species. Read More

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http://dx.doi.org/10.1186/s12864-019-5511-xDOI Listing
February 2019

Involvement of jasmonic acid, ethylene and salicylic acid signaling pathways behind the systemic resistance induced by Trichoderma longibrachiatum H9 in cucumber.

BMC Genomics 2019 Feb 18;20(1):144. Epub 2019 Feb 18.

Biology Institute, Hebei Academy of Sciences, Shijiazhuang, 050081, People's Republic of China.

Background: Trichoderma spp. are effective biocontrol agents for many plant pathogens, thus the mechanism of Trichoderma-induced plant resistance is not fully understood. In this study, a novel Trichoderma strain was identified, which could promote plant growth and reduce the disease index of gray mold caused by Botrytis cinerea in cucumber. Read More

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http://dx.doi.org/10.1186/s12864-019-5513-8DOI Listing
February 2019

The transcriptome landscapes of ovary and three oviduct segments during chicken (Gallus gallus) egg formation.

Genomics 2019 Feb 14. Epub 2019 Feb 14.

Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address:

The avian embryo develops within a specialized biological container (eggshell) that contains crucial nutritional compartments (albumen, yolk). We analyzed the transcriptome of ovary and three segments of oviduct, including magnum, isthmus and uterus in the chicken during egg formation. RNA-Seq libraries (42 in total) for ovary and three different parts of the oviduct were sequenced for two different phases of egg formation. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.02.003DOI Listing
February 2019

VGSC2: Second generation vector graph toolkit of genome synteny and collinearity.

Genomics 2019 Feb 14. Epub 2019 Feb 14.

School of Computer Science and Engineering, Southeast University, Nanjing, Jiangsu, China.

Synteny and collinearity analysis is a standard investigative strategy done in many comparative genomic studies to understand genomic conservation and evolution. Currently, most visualization toolkits of synteny and collinearity do not emphasize the graphical representation of the results, especially the lack of extensible format on vector graphics outputs. This limitation becomes more apparent as 3rd generation sequencing brings high-throughput data, requiring relatively higher resolution for the resulting images. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.02.007DOI Listing
February 2019

Alterations in tissue microRNA after heat stress in the conscious rat: potential biomarkers of organ-specific injury.

BMC Genomics 2019 Feb 15;20(1):141. Epub 2019 Feb 15.

U.S. Army Center for Environmental Health Research, Fort Detrick, Maryland, MD, 21702-5010, USA.

Background: Heat illness remains a significant cause of morbidity in susceptible populations. Recent research elucidating the cellular mechanism of heat stress leading to heat illness may provide information to develop better therapeutic interventions, risk assessment strategies, and early biomarkers of organ damage. microRNA (miRNA) are promising candidates for therapeutic targets and biomarkers for a variety of clinical conditions since there is the potential for high specificity for individual tissues and unique cellular functions. Read More

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http://dx.doi.org/10.1186/s12864-019-5515-6DOI Listing
February 2019
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Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide.

BMC Genomics 2019 Feb 15;20(1):142. Epub 2019 Feb 15.

State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000, China.

Background: Plant Trihelix transcription factors, specifically bind to GT elements and play important roles in plant physiology and development. Wheat is a main cereal crop. Brachypodium distachyon is a close relative of wheat and has been described as a new model species for studying of grass functional genomics. Read More

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http://dx.doi.org/10.1186/s12864-019-5494-7DOI Listing
February 2019
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Analyses of histological and transcriptome differences in the skin of short-hair and long-hair rabbits.

BMC Genomics 2019 Feb 15;20(1):140. Epub 2019 Feb 15.

Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People's Republic of China.

Background: Hair fibre length is an important economic trait of rabbits in fur production. However, molecular mechanisms regulating rabbit hair growth have remained elusive.

Results: Here we aimed to characterise the skin traits and gene expression profiles of short-hair and long-hair rabbits by histological and transcriptome analyses. Read More

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http://dx.doi.org/10.1186/s12864-019-5503-xDOI Listing
February 2019
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Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon.

BMC Genomics 2019 Feb 15;20(1):139. Epub 2019 Feb 15.

Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia Brisbane, 4067, Australia.

Background: A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts.

Results: We report genome wide association studies (GWAS) using fish measured for sexual maturation in freshwater or the marine environment. Read More

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http://dx.doi.org/10.1186/s12864-019-5525-4DOI Listing
February 2019

Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO.

BMC Genomics 2019 Feb 15;20(1):138. Epub 2019 Feb 15.

School of Biological Sciences, Washington State University, Pullman, WA, USA.

Background: Carbonic anhydrase (CA) catalyzes the hydration of CO in the first biochemical step of C photosynthesis, and has been considered a potentially rate-limiting step when CO availability within a leaf is low. Previous work in Zea mays (maize) with a double knockout of the two highest-expressed β-CA genes, CA1 and CA2, reduced total leaf CA activity to less than 3% of wild-type. Surprisingly, this did not limit photosynthesis in maize at ambient or higher COconcentrations. Read More

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http://dx.doi.org/10.1186/s12864-019-5522-7DOI Listing
February 2019

Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setariaitalica L.).

BMC Genomics 2019 Feb 15;20(1):136. Epub 2019 Feb 15.

National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.

Background: Potassium (K) is essential to plant growth and development. Foxtail millet (Setaria italic L.) is an important fodder grain crop in arid and semi-arid regions of Asia and Africa because of its strong tolerance to drought and barren stresses. Read More

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http://dx.doi.org/10.1186/s12864-019-5519-2DOI Listing
February 2019

PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities.

BMC Genomics 2019 Feb 15;20(1):137. Epub 2019 Feb 15.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.

Background: Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, most lncRNAs remain uncharacterized due to a shortage of predictive tools available to guide functional experiments. Read More

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http://dx.doi.org/10.1186/s12864-019-5497-4DOI Listing
February 2019

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development.

BMC Genomics 2019 Feb 14;20(1):135. Epub 2019 Feb 14.

The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.

Background: Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.

Results: By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. Read More

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http://dx.doi.org/10.1186/s12864-019-5521-8DOI Listing
February 2019

PmiRDiscVali: an integrated pipeline for plant microRNA discovery and validation.

BMC Genomics 2019 Feb 13;20(1):133. Epub 2019 Feb 13.

College of Life and Environmental Sciences, Hangzhou Normal University, Xuelin Street 16#, Xiasha, Hangzhou, 310036, People's Republic of China.

Background: MicroRNAs (miRNAs) constitute a well-known small RNA (sRNA) species with important regulatory roles. To date, several bioinformatics tools have been developed for large-scale prediction of miRNAs based on high-throughput sequencing data. However, some of these tools become invalid without reference genomes, while some tools cannot supply user-friendly outputs. Read More

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http://dx.doi.org/10.1186/s12864-019-5478-7DOI Listing
February 2019

The plastid and mitochondrial genomes of Eucalyptus grandis.

BMC Genomics 2019 Feb 13;20(1):132. Epub 2019 Feb 13.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.

Background: Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes.

Results: In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. Read More

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http://dx.doi.org/10.1186/s12864-019-5444-4DOI Listing
February 2019

Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes.

BMC Genomics 2019 Feb 13;20(1):134. Epub 2019 Feb 13.

Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, Fujian, China.

Background: The amount of RNA per cell, namely the transcriptome size, may vary under many biological conditions including tumor. If the transcriptome size of two cells is different, direct comparison of the expression measurements on the same amount of total RNA for two samples can only identify genes with changes in the relative mRNA abundances, i.e. Read More

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http://dx.doi.org/10.1186/s12864-019-5502-yDOI Listing
February 2019

A comparative transcriptome analysis of the novel obligate methanotroph Methylomonas sp. DH-1 reveals key differences in transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol.

BMC Genomics 2019 Feb 12;20(1):130. Epub 2019 Feb 12.

Department of Chemical Engineering, Kyung Hee University, Yongin, 17104, Republic of Korea.

Background: Methanotrophs play an important role in biotechnological applications, with their ability to utilize single carbon (C1) feedstock such as methane and methanol to produce a range of high-value compounds. A newly isolated obligate methanotroph strain, Methylomonas sp. DH-1, became a platform strain for biotechnological applications because it has proven capable of producing chemicals, fuels, and secondary metabolites from methane and methanol. Read More

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http://dx.doi.org/10.1186/s12864-019-5487-6DOI Listing
February 2019

Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data.

BMC Genomics 2019 Feb 12;20(1):131. Epub 2019 Feb 12.

Laboratorio de Transducción de Señales y Cáncer. Departamento de Bioquímica y Biología Molecular. Facultad Cs. Biológicas, Universidad de Concepción, Concepción, Chile.

Background: Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Historically, gene targeting was first done in embryonic stem cells (ESCs) derived from the 129 family of inbred strains, leading to a mixed background or congenic mice when crossed with C57BL/6 mice. Depending on the number of backcrosses and breeding strategies, genomic segments from 129-derived ESCs can be introgressed into the C57BL/6 genome, establishing a unique genetic makeup that needs characterization in order to obtain valid conclusions from experiments using GEM lines. Read More

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http://dx.doi.org/10.1186/s12864-019-5504-9DOI Listing
February 2019

Genome analysis identifies a spontaneous nonsense mutation in ppsD leading to attenuation of virulence in laboratory-manipulated Mycobacterium tuberculosis.

BMC Genomics 2019 Feb 12;20(1):129. Epub 2019 Feb 12.

Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.

Background: A previous laboratory study involving wild type, mutant and devR/dosR complemented strains of Mycobacterium tuberculosis reported the attenuation phenotype of complemented strain, Comp1. This phenotype was intriguing since the parental strain H37Rv, devR mutant (Mut1) and additional complemented strains, Comp9 and Comp11, were virulent in the guinea pig model.

Results: Towards deciphering the mechanism underlying the attenuation of Comp1, a whole genome sequencing approach was undertaken. Read More

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http://dx.doi.org/10.1186/s12864-019-5482-yDOI Listing
February 2019

Genome-wide transcriptome analysis reveals the molecular mechanism of high temperature-induced floral abortion in Litchi chinensis.

BMC Genomics 2019 Feb 11;20(1):127. Epub 2019 Feb 11.

Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.

Background: Warm winter and hot spring attributed to global warming affected floral development and may induce floral abortion, resulted in poor flowering in litchi. To identify genes potentially involved in litchi floral abortion, six RNA-sequencing (RNA-Seq) libraries of the developing panicles (DPs) under low temperature (LT) conditions and the shrinking panicles (SPs) under high temperature (HT) conditions were constructed.

Results: 3. Read More

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http://dx.doi.org/10.1186/s12864-019-5493-8DOI Listing
February 2019

Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition.

BMC Genomics 2019 Feb 11;20(1):126. Epub 2019 Feb 11.

Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China.

Background: Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting D. Read More

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http://dx.doi.org/10.1186/s12864-019-5461-3DOI Listing
February 2019

Genome changes due to artificial selection in U.S. Holstein cattle.

BMC Genomics 2019 Feb 11;20(1):128. Epub 2019 Feb 11.

Department of Animal Science, University of Minnesota, Saint Paul, MN, USA.

Background: The availability of a unique unselected Holstein line since 1964 provided a direct comparison between selected and unselected Holstein genomes whereas large Holstein samples provided unprecedented statistical power for identifying high-confidence SNP effects. Utilizing these unique resources, we aimed to identify genome changes affected by selection since 1964.

Results: Direct comparison of genome-wide SNP markers between a Holstein line unselected since 1964 and contemporary Holsteins showed that the 40 years of artificial selection since 1964 resulted in genome landscape changes. Read More

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http://dx.doi.org/10.1186/s12864-019-5459-xDOI Listing
February 2019

Transcriptomic profiling of the flower scent biosynthesis pathway of Cymbidium faberi Rolfe and functional characterization of its jasmonic acid carboxyl methyltransferase gene.

BMC Genomics 2019 Feb 11;20(1):125. Epub 2019 Feb 11.

Center of Applied Biotechnology, Wuhan University of Bioengineering, Wuhan, 430415, People's Republic of China.

Background: Cymbidium faberi, one of the most famous oriental orchids, has a distinct flower scent, which increases its economic value. However, the molecular mechanism of the flower scent biosynthesis was unclear prior to this study. Methyl jasmonate (MeJA) is one of the main volatile organic compounds (VOC) produced by the flowers of C. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5501-zDOI Listing
February 2019
2 Reads

Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis.

BMC Genomics 2019 Feb 11;20(1):124. Epub 2019 Feb 11.

Department of Population and Quantitative Health Science, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.

Background: Rheumatoid arthritis (RA) is the most common autoimmune disease and affects about 1% of the population. The cause of RA remains largely unknown and could result from a complex interaction between genes and environment factors. Recent studies suggested that gut microbiota and their collective metabolic outputs exert profound effects on the host immune system and are implicated in RA. Read More

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http://dx.doi.org/10.1186/s12864-019-5510-yDOI Listing
February 2019
1 Read

CodSeqGen: A tool for generating synonymous coding sequences with desired GC-contents.

Genomics 2019 Feb 6. Epub 2019 Feb 6.

Department of Computer Science, College of Computer & Information Sciences, King Saud University, Riyadh 11543, Saudi Arabia. Electronic address:

Identification of regulatory elements is essential for understanding the mechanism behind regulating gene expression. These regulatory elements-located in or near gene-bind to proteins called transcription factors to initiate the transcription process. Their occurrences are influenced by the GC-content or nucleotide composition. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.02.002DOI Listing
February 2019
2 Reads

Developmental characteristics of pearl oyster Pinctada fucata martensii: insight into key molecular events related to shell formation, settlement and metamorphosis.

BMC Genomics 2019 Feb 8;20(1):122. Epub 2019 Feb 8.

Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China.

Background: Marine bivalves undergo complex development processes, such as shell morphology conversion and changes of anatomy and life habits. In this study, the transcriptomes of pearl oyster Pinctada fucata martensii and Pacific oyster Crassostrea gigas at different development stages were analyzed to determine the key molecular events related to shell formation, settlement and metamorphosis.

Result: According to the shell matrix proteome, biomineralization-related genes exhibited a consensus expression model with the critical stages of shell formation. Read More

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http://dx.doi.org/10.1186/s12864-019-5505-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368781PMC
February 2019

Virulence factor landscape of a Staphylococcus aureus sequence type 45 strain, MCRF184.

BMC Genomics 2019 Feb 8;20(1):123. Epub 2019 Feb 8.

Center for Human Genetics, 1000 North Oak Avenue # MLR, Marshfield, WI, 54449, USA.

Background: We describe the virulence factors of a methicillin-sensitive Staphylococcus aureus sequence type (ST) 45 strain, MCRF184, (spa type t917), that caused severe necrotizing fasciitis in a 72-year-old diabetic male. The genome of MCRF184 possesses three genomic islands: a relatively large type III νSaα with 42 open reading frames (ORFs) that includes superantigen- and lipoprotein-like genes, a truncated νSaβ that consists mostly of the enterotoxin gene cluster (egc), and a νSaγ island with 18 ORFs including α-toxin. Additionally, the genome has two phage-related regions: phage φSa3 with three genes of the immune evasion cluster (IEC), and an incomplete phage that is distinct from other S. Read More

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http://dx.doi.org/10.1186/s12864-018-5394-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368776PMC
February 2019
1 Read

Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes.

BMC Genomics 2019 Feb 8;20(1):121. Epub 2019 Feb 8.

Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea.

Background: Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. Read More

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http://dx.doi.org/10.1186/s12864-019-5509-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368761PMC
February 2019

Gene co-expression network approach for predicting prognostic microRNA biomarkers in different subtypes of breast cancer.

Genomics 2019 Feb 5. Epub 2019 Feb 5.

Food Hygiene and Public Health Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran. Electronic address:

New diagnostic miRNA biomarkers for different types of cancer have been studied extensively, particularly for breast cancer (BC), which is a leading cause of death among women and has many different subtypes. In the present study, a systems biology approach was used to find remarkable and novel miRNA biomarkers for five molecular subtypes of BC: luminal A, luminal B, ERBB2, basal-like and normal-like. The mRNA expression data from the five BC subtypes was used to reconstruct co-expression networks. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.01.010DOI Listing
February 2019
2 Reads

Should 'Omics' education be a part of allied health profession curricula?

Genomics 2019 Feb 5. Epub 2019 Feb 5.

Department of Nutrition and Food Sciences, Texas Woman's University, Denton, TX, USA; Section of Endocrinology, Department of Medicine, LSU Health Sciences Center, New Orleans, LA, USA. Electronic address:

Sequencing of human genome followed by monumental progress in omics sciences within last two decades has made personalized nutrition for better health is a reality for near future. The complexity of underlying science in making personalized nutrition recommendation has led to the need for training of health care providers. The International Society of Nutrigenetics/Nutrigenomics (ISNN) has mission to increase the understanding among both professionals and the general public of the role of genetic variation and nutrients in gene expression. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.01.009DOI Listing
February 2019

MicroRNA-related markers associated with corpus luteum tropism in buffalo (Bubalus bubalis).

Genomics 2019 Feb 5. Epub 2019 Feb 5.

ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana 125001, India.

The study was undertaken to decipher the microRNA (miRNA) related markers associated with corpus luteum (CL) tropism in buffalo. The data obtained from deep sequencing of CL tissue from different physiological stages was mined in silico for the identification of miRNA-related markers (SSR & SNP). From the present study, 5 annotated and 176 unannotated miRNA were deduced while comparing with Bos taurus genome. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.01.018DOI Listing
February 2019
1 Read

The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.

BMC Genomics 2019 Feb 7;20(1):119. Epub 2019 Feb 7.

Department of Plant Pathology, Iowa State University, Ames, IA, USA.

Background: Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. Read More

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http://dx.doi.org/10.1186/s12864-019-5485-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367775PMC
February 2019
1 Read

In silico characterization of multiple genes encoding the GP63 virulence protein from Leishmania braziliensis: identification of sources of variation and putative roles in immune evasion.

BMC Genomics 2019 Feb 7;20(1):118. Epub 2019 Feb 7.

Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (Fiocruz-Pernambuco), Recife, Pernambuco, Brazil.

Background: The leishmaniasis are parasitic diseases caused by protozoans of the genus Leishmania, highly divergent eukaryotes, characterized by unique biological features. To survive in both the mammalian hosts and insect vectors, these pathogens make use of a number of mechanisms, many of which are associated with parasite specific proteases. The metalloprotease GP63, the major Leishmania surface antigen, has been found to have multiple functions required for the parasite's survival. Read More

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http://dx.doi.org/10.1186/s12864-019-5465-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367770PMC
February 2019

Molecular characterization of carbendazim resistance of Fusarium species complex that causes sugarcane pokkah boeng disease.

BMC Genomics 2019 Feb 7;20(1):115. Epub 2019 Feb 7.

State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, Nanning, 530005, China.

Background: Pokkah boeng is one of the most serious and devastating diseases of sugarcane and causes significant loss in cane yield and sugar content. Although carbendazim is widely used to prevent fungal diseases, the molecular basis of Fusarium species complex (FSC) resistance to carbendazim remains unknown.

Results: The EC (fungicide concentration that inhibits 50% of mycelial growth) values of carbendazim for 35 FSC isolates collected in cane growing regions of China were ranged from 0. Read More

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http://dx.doi.org/10.1186/s12864-019-5479-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367828PMC
February 2019
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Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters.

BMC Genomics 2019 Feb 7;20(1):116. Epub 2019 Feb 7.

Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.

Background: Cytochrome P450 (P450) is a functionally diverse and multifamily class of enzymes which catalyses vast variety of biochemical reactions. P450 genes play regulatory role in growth, development and secondary metabolite biosynthesis. Solanum lycopersicum L. Read More

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http://dx.doi.org/10.1186/s12864-019-5483-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367802PMC
February 2019

Methylome and transcriptome analyses of apple fruit somatic mutations reveal the difference of red phenotype.

BMC Genomics 2019 Feb 7;20(1):117. Epub 2019 Feb 7.

College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.

Background: Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect the phenotype of mutation, there are large unknown of difference of the DNA methylation in plant and its mutants. Read More

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http://dx.doi.org/10.1186/s12864-019-5499-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367808PMC
February 2019
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Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum.

BMC Genomics 2019 Feb 7;20(1):120. Epub 2019 Feb 7.

Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA.

Background: Genes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse. Even strains of the same species may exhibit differences in metabolite production, a finding that has important implications for drug discovery. Unlike in other eukaryotes, genes producing SMs are often clustered and co-expressed in fungal genomes, but the genetic mechanisms involved in the creation and maintenance of these secondary metabolite biosynthetic gene clusters (SMBGCs) remains poorly understood. Read More

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http://dx.doi.org/10.1186/s12864-018-5399-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367777PMC
February 2019
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A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes.

BMC Genomics 2019 Feb 6;20(1):114. Epub 2019 Feb 6.

Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.

Background: Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation, since the amounts of miRNAs in cells also vary upon irradiation. To address this possibility, we designed experiments using cancer-derived cell lines transfected with luciferase reporter gene containing sequences targeted by different miRNA species in its 3'- untranslated region. Read More

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http://dx.doi.org/10.1186/s12864-019-5464-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366035PMC
February 2019

Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera.

BMC Genomics 2019 Feb 6;20(1):111. Epub 2019 Feb 6.

Ifremer, UMR 241 Ecosystèmes Insulaires Océaniens (EIO), Labex Corail, Centre Ifremer du Pacifique, BP 49, 98719, Tahiti, French Polynesia.

Background: Cultured pearls are unique gems produced by living organisms, mainly molluscs of the Pinctada genus, through the biomineralization properties of pearl sac tissue. Improvement of P. margaritifera pearl quality is one of the biggest challenges that Polynesian research has faced to date. Read More

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http://dx.doi.org/10.1186/s12864-019-5443-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366105PMC
February 2019

Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model.

BMC Genomics 2019 Feb 6;20(1):106. Epub 2019 Feb 6.

Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

Background: Theory predicts that dependency within host-endosymbiont interactions results in endosymbiont genome size reduction. Unexpectedly, the largest Wolbachia genome was found in the obligate, parthenogenesis-associated wFol. In this study, we investigate possible processes underlying this genome expansion by comparing a re-annotated wFol genome to other Wolbachia genomes. Read More

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http://dx.doi.org/10.1186/s12864-019-5492-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364476PMC
February 2019
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De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development.

BMC Genomics 2019 Feb 6;20(1):108. Epub 2019 Feb 6.

Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Avenida República 330, 8370035, Santiago, RM, Chile.

Background: Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. Read More

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http://dx.doi.org/10.1186/s12864-019-5486-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364401PMC
February 2019
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Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics.

BMC Genomics 2019 Feb 6;20(1):109. Epub 2019 Feb 6.

Sorbonne Université, CNRS, Lab. Adaptation et Diversité en Milieu Marin, Team ABICE, Station Biologique de Roscoff, 29680, Roscoff, France.

Background: Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. Read More

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http://dx.doi.org/10.1186/s12864-019-5456-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364412PMC
February 2019

Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding.

BMC Genomics 2019 Feb 6;20(1):107. Epub 2019 Feb 6.

Department of Microbiology and Immunology, UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA, 94143, USA.

Background: While pooled loss- and gain-of-function CRISPR screening approaches have become increasingly popular to systematically investigate mammalian gene function, the large majority of them have thus far not investigated the influence of cellular heterogeneity on screen results. Instead most screens are analyzed by averaging the abundance of perturbed cells from a bulk population of cells.

Results: Here we developed multi-level barcoded sgRNA libraries to trace multiple clonal Cas9 cell lines exposed to the same environment. Read More

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http://dx.doi.org/10.1186/s12864-019-5480-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364396PMC
February 2019

Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum).

BMC Genomics 2019 Feb 6;20(1):113. Epub 2019 Feb 6.

College of Life Science, Sichuan Agricultural University, Ya'an, China.

Background: The NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, there is no comprehensive study on the NAC genes of Tartary buckwheat (Fagopyrum tataricum), a large group of extensively cultivated medicinal and edible plants. The recently published Tartary buckwheat genome permits us to explore all the FtNAC genes on a genome-wide basis. Read More

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http://dx.doi.org/10.1186/s12864-019-5500-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366116PMC
February 2019

Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq.

BMC Genomics 2019 Feb 6;20(1):110. Epub 2019 Feb 6.

Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, 45662-900, Brazil.

Background: Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available for citrus propagation, 'Rangpur' lime is known to confer enhanced tolerance to drought as compared to other citrus rootstocks. The objective of this study was to investigate the poorly understood molecular responses underlying the rootstock-induced drought tolerance in sweet orange. Read More

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http://dx.doi.org/10.1186/s12864-019-5481-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364419PMC
February 2019

Genetic and transcriptomic dissection of the fiber length trait from a cotton (Gossypium hirsutum L.) MAGIC population.

BMC Genomics 2019 Feb 6;20(1):112. Epub 2019 Feb 6.

Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA.

Background: Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic diversity of modern cotton cultivars and negative correlations between fiber quality and yield traits. A multi-parent advanced generation inter-cross (MAGIC) population developed through random mating provides an excellent genetic resource that allows quantitative trait loci (QTL) and causal genes to be identified. Read More

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http://dx.doi.org/10.1186/s12864-019-5427-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366115PMC
February 2019