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BMC Genomics

Emilien Peltier, Vikas Sharma, Maria Martí Raga, Miguel Roncoroni, Margaux Bernard, Vladimir Jiranek, Yves Gibon, Philippe Marullo
BACKGROUND: The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasting response is caused by gene-by-environment interactions (GxE). Understanding GxE interactions is particularly important in agronomy, since selected breeds and varieties may have divergent phenotypes according to their growing environment...
November 9, 2018: BMC Genomics
Shinya Watanabe, Yoshifumi Aiba, Xin-Ee Tan, Feng-Yu Li, Tanit Boonsiri, Kanate Thitiananpakorn, Bintao Cui, Yusuke Sato'o, Kotaro Kiga, Teppei Sasahara, Longzhu Cui
BACKGROUND: Staphylococcus caprae is an animal-associated bacterium regarded as part of goats' microflora. Recently, S. caprae has been reported to cause human nosocomial infections such as bacteremia and bone and joint infections. However, the mechanisms responsible for the development of nosocomial infections remain largely unknown. Moreover, the complete genome sequence of S. caprae has not been determined. RESULTS: We determined the complete genome sequences of three methicillin-resistant S...
November 8, 2018: BMC Genomics
Amanda W Ernlund, Robert J Schneider, Kelly V Ruggles
BACKGROUND: Translatomics data, particularly genome-wide ribosome profiling and polysome profiling, provide multiple levels of gene regulatory information that can be used to assess general transcription and translation, as well translational efficiency. The increasing popularity of these techniques has resulted in multiple algorithms to detect translational regulation, typically distributed in the form of command line tools that require a basic level of programming ability. Additionally, due to the static nature of current software, dynamic transcriptional and translational comparative analysis cannot be adequately achieved...
November 8, 2018: BMC Genomics
Miyako Kodama, Henrik Brinch-Pedersen, Shrikant Sharma, Inger Bæksted Holme, Bjarne Joernsgaard, Tsaneta Dzhanfezova, Daniel Buchvaldt Amby, Filipe Garrett Vieira, Shanlin Liu, M Thomas P Gilbert
BACKGROUND: Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix-loop-helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD repeat (MBW) complexes, which activates the transcription of structural genes in the anthocyanin pathway. Although black cultivars of carrots (Daucus carota L.) can accumulate large quantities of anthocyanin in their storage roots, the regulatory genes responsible for their biosynthesis are not well characterized...
November 8, 2018: BMC Genomics
Vania Patrone, Andrea Minuti, Michela Lizier, Francesco Miragoli, Franco Lucchini, Erminio Trevisi, Filippo Rossi, Maria Luisa Callegari
BACKGROUND: Animal studies show that high fat (HF) diet-induced gut microbiota contributes to the development of obesity. Oil composition of high-fat diet affects metabolic inflammation differently with deleterious effects by saturated fat. The aim of the present study was to examine the diversity and metabolic capacity of the cecal bacterial community in C57BL/6 N mice administered two different diets, enriched respectively with coconut oil (HFC, high in saturated fat) or soy oil (HFS, high in polyunsaturated fat)...
November 7, 2018: BMC Genomics
Luyun Ning, Zhiwei Lin, Jianwei Gu, Lu Gan, Yonghong Li, Hao Wang, Liyun Miao, Libin Zhang, Baoshan Wang, Maoteng Li
BACKGROUND: Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecular mechanism. In the present report, a multi-omics integrative analysis, including of the proteomic, transcriptomic and miRNAs, combined with morphological and physiological analysis were conducted...
November 7, 2018: BMC Genomics
Qiming Cheng, Shiqie Bai, Gentu Ge, Ping Li, Liying Liu, Chengdong Zhang, Yushan Jia
BACKGROUND: Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of the molecular mechanism of alfalfa defoliation traits remains unclear. The transcriptome database created by RNA-Seq is used to identify critical genes related to defoliation traits. RESULTS: In this study, we sequenced the transcriptomes of the Zhungeer variety (with easy leaf abscission) and WL319HQ variety (without easy leaf abscission)...
November 7, 2018: BMC Genomics
Chao Hu, Hongxing Yang, Kai Jiang, Ling Wang, Boyun Yang, Tungyu Hsieh, Siren Lan, Weichang Huang
BACKGROUND: Calanthe masuca and C. sinica are two genetically closely related species in Orchidaceae. C. masuca is widely distributed in Asia, whereas C. sinica is restricted to Yunnan and Guangxi Provinces in southwest China. Both play important roles in horticulture and are under the pressure of population decline. Understanding their genetic background can greatly help us develop effective conservation strategies for these species. Simple sequence repeats (SSRs) are useful for genetic diversity analysis, presumably providing key information for the study and preservation of the wild populations of the two species we are interested in...
November 6, 2018: BMC Genomics
Si-Won Jin, Md Abdur Rahim, Khandker Shazia Afrin, Jong-In Park, Jong-Goo Kang, Ill-Sup Nou
BACKGROUND: Ornamental cabbage (Brassica oleracea var. acephala) is an attractive landscape plant that remains colorful at low temperatures during winter. Its key feature is its inner leaf coloration, which can include red, pink, lavender, blue, violet and white. Some ornamental cabbages exhibit variation in leaf color pattern linked to leaf developmental stage. However, little is known about the molecular mechanism underlying changes in leaf pigmentation pattern between developmental stages...
November 6, 2018: BMC Genomics
Sven Warris, Elio Schijlen, Henri van de Geest, Rahulsimham Vegesna, Thamara Hesselink, Bas Te Lintel Hekkert, Gabino Sanchez Perez, Paul Medvedev, Kateryna D Makova, Dick de Ridder
BACKGROUND: Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long sequencing reads. RESULTS: Here, we present Pacasus, a tool for correcting such errors. Two datasets show that it markedly improves read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA...
November 6, 2018: BMC Genomics
Yue-Ting Tang, Yi-Yao Huang, Jing-Huan Li, Si-Hua Qin, Yong Xu, Tai-Xue An, Chun-Chen Liu, Qian Wang, Lei Zheng
BACKGROUND: Epithelial-mesenchymal transition (EMT) is regarded as a critical event during tumor metastasis. Recent studies have revealed changes and the contributions of proteins in/on exosomes during EMT. Besides proteins, microRNA (miRNA) is another important functional component of exosomes. We hypothesized that the miRNA profile of exosomes may change following EMT and these exosomal miRNAs may in return promote EMT, migration and invasion of cancer cells. RESULTS: The small RNA profile of exosomes was altered following EMT...
November 6, 2018: BMC Genomics
Yan Chen, Xue Li, Liyao Su, Xu Chen, Shuting Zhang, Xiaoping Xu, Zihao Zhang, Yukun Chen, Xu XuHan, Yuling Lin, Zhongxiong Lai
BACKGROUND: Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development. RESULTS: In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed...
November 6, 2018: BMC Genomics
M Senthil Kumar, Eric V Slud, Kwame Okrah, Stephanie C Hicks, Sridhar Hannenhalli, Héctor Corrada Bravo
BACKGROUND: Count data derived from high-throughput deoxy-ribonucliec acid (DNA) sequencing is frequently used in quantitative molecular assays. Due to properties inherent to the sequencing process, unnormalized count data is compositional, measuring relative and not absolute abundances of the assayed features. This compositional bias confounds inference of absolute abundances. Commonly used count data normalization approaches like library size scaling/rarefaction/subsampling cannot correct for compositional or any other relevant technical bias that is uncorrelated with library size...
November 6, 2018: BMC Genomics
Yves Moné, Sandra Nhim, Sylvie Gimenez, Fabrice Legeai, Imène Seninet, Hugues Parrinello, Nicolas Nègre, Emmanuelle d'Alençon
BACKGROUND: A change in the environment may impair development or survival of living organisms leading them to adapt to the change. The resulting adaptation trait may reverse, or become fixed in the population leading to evolution of species. Deciphering the molecular basis of adaptive traits can thus give evolutionary clues. In phytophagous insects, a change in host-plant range can lead to emergence of new species. Among them, Spodoptera frugiperda is a major agricultural lepidopteran pest consisting of two host-plant strains having diverged 3 MA, based on mitochondrial markers...
November 6, 2018: BMC Genomics
Suchawan Pornsukarom, Arnoud H M van Vliet, Siddhartha Thakur
BACKGROUND: Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states. RESULTS: WGS data of 200 S...
November 6, 2018: BMC Genomics
Rui Hu, Jie Xiao, Ting Gu, Xiaofen Yu, Yang Zhang, Junli Chang, Guangxiao Yang, Guangyuan He
BACKGROUND: WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modification, transcription regulation, and signal transduction. WD40 proteins are regarded as crucial regulators of plant development processes. However, the systematic identification and analysis of WD40 proteins have yet to be reported in wheat. RESULTS: In this study, a total of 743 WD40 proteins were identified in wheat, and they were grouped into 5 clusters and 11 subfamilies...
November 6, 2018: BMC Genomics
Albert Caballero-Solares, Xi Xue, Christopher C Parrish, Maryam Beheshti Foroutani, Richard G Taylor, Matthew L Rise
BACKGROUND: Dependence on marine natural resources threatens the sustainability of Atlantic salmon aquaculture. In the present study, Atlantic salmon fed for 14 weeks with an experimental diet based on animal by-products and vegetable oil (ABP) exhibited reduced growth performance compared with others fed a fish meal/fish oil based experimental diet (MAR) and a plant protein/vegetable oil-based experimental diet (VEG). To characterize the molecular changes underlying the differences in growth performance, we conducted a 44 K microarray study of the liver transcriptome of the three dietary groups...
November 3, 2018: BMC Genomics
Stacey E Wahl, Brent H Wyatt, Stephen D Turner, Amanda J G Dickinson
BACKGROUND: Development of the face and mouth is orchestrated by a large number of transcription factors, signaling pathways and epigenetic regulators. While we know many of these regulators, our understanding of how they interact with each other and implement changes in gene expression during orofacial development is still in its infancy. Therefore, this study focuses on uncovering potential cooperation between transcriptional regulators and one important signaling pathway, retinoic acid, during development of the midface...
November 3, 2018: BMC Genomics
Majid Khansefid, Jennie E Pryce, Sunduimijid Bolormaa, Yizhou Chen, Catriona A Millen, Amanda J Chamberlain, Christy J Vander Jagt, Michael E Goddard
BACKGROUND: The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple individuals (eQTL mapping), or by comparing the expression of the alleles in a heterozygous individual (allele specific expression or ASE analysis). The aims of the study were to find and compare ASE and local eQTL in 4 bovine RNA-sequencing (RNA-Seq) datasets, validate them in an independent ASE study and investigate if they are associated with complex trait variation...
November 3, 2018: BMC Genomics
Juan Carlos Higareda-Almaraz, Michael Karbiener, Maude Giroud, Florian M Pauler, Teresa Gerhalter, Stephan Herzig, Marcel Scheideler
BACKGROUND: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. RESULTS: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation...
November 3, 2018: BMC Genomics
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