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BMC Genomics

Zhuyi Xue, René L Warren, Ewan A Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A Ennis, Abigail Hahn, Sheila Reynolds, Inanc Birol
BACKGROUND: Alternative polyadenylation (APA) results in messenger RNA molecules with different 3' untranslated regions (3' UTRs), affecting the molecules' stability, localization, and translation. APA is pervasive and implicated in cancer. Earlier reports on APA focused on 3' UTR length modifications and commonly characterized APA events as 3' UTR shortening or lengthening. However, such characterization oversimplifies the processing of 3' ends of transcripts and fails to adequately describe the various scenarios we observe...
July 13, 2018: BMC Genomics
Hyeji Lee, Mai Phuong Nguyen, Yunhee Choi, Yong-Hak Kim
BACKGROUND: The Zika virus (ZIKV) can cause microcephaly and congenital abnormalities in the foetus. Recent studies have provided insights into the evolution of ZIKV from the current and previous outbreaks, but the types have not been determined. RESULTS: We analysed the insertions and deletions (InDels) in 212 ZIKV polyproteins and 5 Dengue virus (DENV) reference sequences. Spearman correlation tests for the minimum InDel (minInDel) patterns were used to assess the type of polyprotein...
July 13, 2018: BMC Genomics
Natalia Escobar, Ivan D Valdes, Esther M Keizer, Soledad R Ordonez, Robin A Ohm, Han A B Wösten, Hans de Cock
BACKGROUND: Aspergillus fumigatus is the main causative agent of aspergillosis. Infections rarely occur in immunocompetent individuals, indicating efficient clearance of conidia by pulmonary defense mechanisms. Other aspergilli like Aspergillus niger also cause infections but to a much lesser extent. Our previous studies showed that A. fumigatus and A. niger have different behavior in the presence of type II alveolar A549 epithelial cells. A. fumigatus conidia are more efficiently internalized by these cells and germination is delayed when compared to A...
July 13, 2018: BMC Genomics
Panagiotis Moulos, Alexandros Alexandratos, Ioannis Nellas, Skarlatos G Dedos
BACKGROUND: The prothoracic gland (PG), the principal steroidogenic organ of insects, has been proposed as a model for steroid hormone biosynthesis and regulation. RESULTS: To validate the robustness of the model, we present an analysis of accumulated transcriptomic data from PGs of two model species, Drosophila melanogaster and Bombyx mori. We identify that the common core components of the model in both species are encoded by nine genes. Five of these are Halloween genes whose expression differs substantially between the PGs of these species...
July 13, 2018: BMC Genomics
Sang-Yoon Shin, Jin Seo Jeong, Jae Yun Lim, Taewook Kim, June Hyun Park, Ju-Kon Kim, Chanseok Shin
BACKGROUND: Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism. RESULTS: Here, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches...
July 13, 2018: BMC Genomics
Romolo Caniglia, Elena Fabbri, Pavel Hulva, Barbora Černá Bolfíková, Milena Jindřichová, Astrid Vik Stronen, Ihor Dykyy, Alessio Camatta, Paolo Carnier, Ettore Randi, Marco Galaverni
BACKGROUND: Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe...
July 13, 2018: BMC Genomics
Robin Kosch, Julien Delarocque, Peter Claus, Stefanie C Becker, Klaus Jung
BACKGROUND: Infections with the West Nile virus (WNV) can attack neurological tissues in the host and alter gene expression levels therein. Several individual studies have analyzed these changes in the transcriptome based on measurements with DNA microarrays. Individual microarray studies produce a high-dimensional data structure with the number of studied genes exceeding the available sample size by far. Therefore, the level of scientific evidence of these studies is rather low and results can remain uncertain...
July 13, 2018: BMC Genomics
Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D Zamore, Zhiping Weng
BACKGROUND: RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules...
July 13, 2018: BMC Genomics
Justin B Greer, Michael C Schmale, Lynne A Fieber
BACKGROUND: Large-scale molecular changes occur during aging and have many downstream consequences on whole-organism function, such as motor function, learning, and memory. The marine mollusk Aplysia californica can be used to study transcriptional changes that occur with age in identified neurons of the brain, because its simplified nervous system allows for more direct correlations between molecular changes, physiological changes, and their phenotypic outcomes. Behavioral deficits in the tail-withdrawal reflex of aged animals have been correlated with reduced excitation in sensory neurons that control the reflex...
July 11, 2018: BMC Genomics
Lena M Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G Lausted, Gustavo Glusman
BACKGROUND: Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these strand asymmetries arise as a result of mutational biases and selective constraints, particularly for energy efficiency. Analysis of compositional skews in a diverse set of bacteria provides a comparative context in which mutational and selective environmental constraints can be studied...
July 11, 2018: BMC Genomics
Qiuwen He, Qiangchuan Hou, Yanjie Wang, Jing Li, Weicheng Li, Lai-Yu Kwok, Zhihong Sun, Heping Zhang, Zhi Zhong
BACKGROUND: Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins. RESULTS: Although no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes...
July 11, 2018: BMC Genomics
S Pereyre, C Bénard, C Brès, C Le Roy, J P Mauxion, F Rideau, P Sirand-Pugnet, B Henrich, C Bébéar
BACKGROUND: Mycoplasma hominis is a human urogenital pathogen involved in gynaecological, neonatal and extra-genital infections. However, no versatile genetic tools are currently available to study the pathogenicity of this bacterium. Targeting-Induced Local Lesions IN Genomes (TILLING) is a reverse-genetic method that combines point mutations induced by chemical mutagenesis with a DNA screening technique. We used ethyl methanesulfonate (EMS) that introduces C-G to T-A transition mutations to generate a library of M...
July 9, 2018: BMC Genomics
Guillaume Carissimo, Adrien Pain, Eugeni Belda, Kenneth D Vernick
BACKGROUND: Anopheles mosquitoes are efficient vectors of human malaria, but it is unknown why they do not transmit viruses as well as Aedes and Culex mosquitoes. The only arbovirus known to be consistently transmitted by Anopheles mosquitoes is O'nyong nyong virus (ONNV, genus Alphavirus, family Togaviridae). The interaction of Anopheles mosquitoes with RNA viruses has been relatively unexamined. RESULTS: We transcriptionally profiled the African malaria vector, Anopheles coluzzii, infected with ONNV...
July 9, 2018: BMC Genomics
John Cologne, Lenora Loo, Yurii B Shvetsov, Munechika Misumi, Philip Lin, Christopher A Haiman, Lynne R Wilkens, Loïc Le Marchand
BACKGROUND: Common variants have explained less than the amount of heritability expected for complex diseases, which has led to interest in less-common variants and more powerful approaches to the analysis of whole-genome scans. Because of low frequency (low statistical power), less-common variants are best analyzed using SNP-set methods such as gene-set or pathway-based analyses. However, there is as yet no clear consensus regarding how to focus in on potential risk variants following set-based analyses...
July 9, 2018: BMC Genomics
Marine Mommert, Olivier Tabone, Guy Oriol, Elisabeth Cerrato, Audrey Guichard, Magali Naville, Paola Fournier, Jean-Nicolas Volff, Alexandre Pachot, Guillaume Monneret, Fabienne Venet, Karen Brengel-Pesce, Julien Textoris, François Mallet
BACKGROUND: Human Endogenous Retroviruses (HERVs) and Mammalian apparent LTR-retrotransposons (MaLRs) represent the 8% of our genome and are distributed among our 46 chromosomes. These LTR-retrotransposons are thought to be essentially silent except in cancer, autoimmunity and placental development. Their Long Terminal Repeats (LTRs) constitute putative promoter or polyA regulatory sequences. In this study, we used a recently described high-density microarray which can be used to study HERV/MaLR transcriptome including 353,994 HERV/MaLR loci and 1559 immunity-related genes...
July 5, 2018: BMC Genomics
Hongran Li, James D Harwood, Tongxian Liu, Dong Chu
BACKGROUND: It has become increasingly clear that symbionts have crucial evolutionary and ecological ramifications for their host arthropods. However, little is known whether these symbiont infections influence the proteome and lysine acetylome of their host arthropods. Here we performed experiments to investigate the proteomes and acetylomes of Cardinium-infected (C*+ ) and -uninfected (C- ) Bemisia tabaci Q with identical backgrounds, through the combination of affinity enrichment and high-resolution LC-MS/MS analysis...
July 5, 2018: BMC Genomics
Maarten P M Vanhove, Andrew G Briscoe, Michiel W P Jorissen, D Tim J Littlewood, Tine Huyse
BACKGROUND: Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers...
July 4, 2018: BMC Genomics
Adam Amara, Eriko Takano, Rainer Breitling
BACKGROUND: Streptomyces species produce a vast diversity of secondary metabolites of clinical and biotechnological importance, in particular antibiotics. Recent developments in metabolic engineering, synthetic and systems biology have opened new opportunities to exploit Streptomyces secondary metabolism, but achieving industry-level production without time-consuming optimization has remained challenging. Genome-scale metabolic modelling has been shown to be a powerful tool to guide metabolic engineering strategies for accelerated strain optimization, and several generations of models of Streptomyces metabolism have been developed for this purpose...
July 4, 2018: BMC Genomics
Ruidong Xiang, Ben J Hayes, Christy J Vander Jagt, Iona M MacLeod, Majid Khansefid, Phil J Bowman, Zehu Yuan, Claire P Prowse-Wilkins, Coralie M Reich, Brett A Mason, Josie B Garner, Leah C Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D Daetwyler, Amanda J Chamberlain, Michael E Goddard
BACKGROUND: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression quantitative trait loci (expression QTLs) that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, sQTLs were compare with other two types of expression QTLs, 1) variants associated with variations in gene expression, i...
July 4, 2018: BMC Genomics
Lixiao Du, Xincheng Zhao, Xiangzhi Liang, Xiwu Gao, Yang Liu, Guirong Wang
BACKGROUND: The oriental armyworm, Mythimna separata, is an economically important and common Lepidopteran pest of cereal crops. Chemoreception plays a key role in insect life, such as foraging, oviposition site selection, and mating partners. To better understand the chemosensory mechanisms in M. separata, transcriptomic analysis of antennae, labial palps, and proboscises were conducted using next-generation sequencing technology to identify members of the major chemosensory related genes...
July 4, 2018: BMC Genomics
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