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BMC Genomics

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https://www.readbyqxmd.com/read/28934931/mitochondrial-genomes-of-african-pangolins-and-insights-into-evolutionary-patterns-and-phylogeny-of-the-family-manidae
#1
Zelda du Toit, Morné du Plessis, Desiré L Dalton, Raymond Jansen, J Paul Grobler, Antoinette Kotzé
BACKGROUND: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934930/xcavator-accurate-detection-and-genotyping-of-copy-number-variants-from-second-and-third-generation-whole-genome-sequencing-experiments
#2
Alberto Magi, Tommaso Pippucci, Carlo Sidore
BACKGROUND: We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS: By using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions. To demonstrate the power of our software we applied it to the analysis Illumina and Pacific Bioscencies data and we compared its performance to other ten state of the art tools...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934929/single-molecule-counting-and-assessment-of-random-molecular-tagging-errors-with-transposable-giga-scale-error-correcting-barcodes
#3
Billy T Lau, Hanlee P Ji
BACKGROUND: RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression measures by detecting amplification duplicates, but are susceptible to errors generated during PCR and sequencing. This results in false positive counts, leading to inaccurate transcriptome quantification especially at low input and single-cell RNA amounts where the total number of molecules present is minuscule...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934927/evolution-and-expression-analysis-reveal-the-potential-role-of-the-hd-zip-gene-family-in-regulation-of-embryo-abortion-in-grapes-vitis-vinifera-l
#4
Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
BACKGROUND: The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS: A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28931375/identification-of-fasciclin-like-arabinogalactan-proteins-in-textile-hemp-cannabis-sativa-l-in-silico-analyses-and-gene-expression-patterns-in-different-tissues
#5
Gea Guerriero, Lauralie Mangeot-Peter, Sylvain Legay, Marc Behr, Stanley Lutts, Khawar Sohail Siddiqui, Jean-Francois Hausman
BACKGROUND: The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to participate in plant growth, development, defense against abiotic stresses and, notably, cell wall biosynthesis. Although some studies are available on the characterization of FLA genes from different species, both woody and herbaceous, no detailed information is available on the FLA family of textile hemp (Cannabis sativa L...
September 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28927378/genome-wide-imaging-association-study-implicates-functional-activity-and-glial-homeostasis-of-the-caudate-in-smoking-addiction
#6
David C Qian, David L Molfese, Jennifer L Jin, Alexander J Titus, Yixuan He, Yafang Li, Maxime Vaissié, Humsini Viswanath, Philip R Baldwin, Ralf Krahe, Ramiro Salas, Christopher I Amos
BACKGROUND: Nearly 6 million deaths and over a half trillion dollars in healthcare costs worldwide are attributed to tobacco smoking each year. Extensive research efforts have been pursued to elucidate the molecular underpinnings of smoking addiction and facilitate cessation. In this study, we genotyped and obtained both resting state and task-based functional magnetic resonance imaging from 64 non-smokers and 42 smokers. Smokers were imaged after having smoked normally ("sated") and after having not smoked for at least 12 h ("abstinent")...
September 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923029/mitochondrial-genomes-reveal-recombination-in-the-presumed-asexual-fusarium-oxysporum-species-complex
#7
Balázs Brankovics, Peter van Dam, Martijn Rep, G Sybren de Hoog, Theo A J van der Lee, Cees Waalwijk, Anne D van Diepeningen
BACKGROUND: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. RESULTS: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923023/comparative-transcriptomics-of-female-and-male-gametocytes-in-plasmodium-berghei-and-the-evolution-of-sex-in-alveolates
#8
Lee M Yeoh, Christopher D Goodman, Vanessa Mollard, Geoffrey I McFadden, Stuart A Ralph
BACKGROUND: The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into sexual forms, termed gametocytes, which are ingested by a mosquito vector. Sexual differentiation produces either female or male gametocytes, and involves significant morphological and biochemical changes. These transformations prepare gametocytes for the rapid progression to gamete formation and fertilisation, which occur within 20 min of ingestion...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923019/evolutionary-history-and-functional-divergence-of-the-cytochrome-p450-gene-superfamily-between-arabidopsis-thaliana-and-brassica-species-uncover-effects-of-whole-genome-and-tandem-duplications
#9
Jingyin Yu, Sadia Tehrim, Linhai Wang, Komivi Dossa, Xiurong Zhang, Tao Ke, Boshou Liao
BACKGROUND: The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. RESULTS: Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923016/5-hydroxymethylcytosine-is-highly-dynamic-across-human-fetal-brain-development
#10
Helen Spiers, Eilis Hannon, Leonard C Schalkwyk, Nicholas J Bray, Jonathan Mill
BACKGROUND: Epigenetic processes play a key role in orchestrating transcriptional regulation during the development of the human central nervous system. We previously described dynamic changes in DNA methylation (5mC) occurring during human fetal brain development, but other epigenetic processes operating during this period have not been extensively explored. Of particular interest is DNA hydroxymethylation (5hmC), a modification that is enriched in the human brain and hypothesized to play an important role in neuronal function, learning and memory...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923009/apophysomyces-variabilis-draft-genome-sequence-and-comparison-of-predictive-virulence-determinants-with-other-medically-important-mucorales
#11
Hariprasath Prakash, Shivaprakash Mandya Rudramurthy, Prasad S Gandham, Anup Kumar Ghosh, Milner M Kumar, Chandan Badapanda, Arunaloke Chakrabarti
BACKGROUND: Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923004/regulatory-networks-underlying-mycorrhizal-development-delineated-by-genome-wide-expression-profiling-and-functional-analysis-of-the-transcription-factor-repertoire-of-the-plant-symbiotic-fungus-laccaria-bicolor
#12
Y Daguerre, E Levati, J Ruytinx, E Tisserant, E Morin, A Kohler, B Montanini, S Ottonello, A Brun, C Veneault-Fourrey, F Martin
BACKGROUND: Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28923001/a-molecular-view-of-the-normal-human-thyroid-structure-and-function-reconstructed-from-its-reference-transcriptome-map
#13
Lorenza Vitale, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Maria Chiara Pelleri, Maria Caracausi
BACKGROUND: The thyroid is the earliest endocrine structure to appear during human development, and thyroid hormones are necessary for proper organism development, in particular for the nervous system and heart, normal growth and skeletal maturation. To date a quantitative, validated transcriptional atlas of the whole normal human thyroid does not exist and the availability of a detailed expression map might be an excellent occasion to investigate the many features of the thyroid transcriptome...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28915789/rapid-transcriptional-and-metabolic-regulation-of-the-deacclimation-process-in-cold-acclimated-arabidopsis-thaliana
#14
Majken Pagter, Jessica Alpers, Alexander Erban, Joachim Kopka, Ellen Zuther, Dirk K Hincha
BACKGROUND: During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. This is accompanied by dampened oscillations of circadian clock genes and disrupted oscillations of output genes and metabolites. During deacclimation in response to warm temperatures, cold acclimated plants lose freezing tolerance and resume growth and development. While considerable effort has been directed toward understanding the molecular and metabolic basis of cold acclimation, much less information is available about the regulation of deacclimation...
September 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28915794/genome-sequence-of-the-ectophytic-fungus-ramichloridium-luteum-reveals-unique-evolutionary-adaptations-to-plant-surface-niche
#15
Bo Wang, Xiaofei Liang, Mark L Gleason, Rong Zhang, Guangyu Sun
BACKGROUND: Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis. RESULTS: The R...
September 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28915793/the-cacao-criollo-genome-v2-0-an-improved-version-of-the-genome-for-genetic-and-functional-genomic-studies
#16
X Argout, G Martin, G Droc, O Fouet, K Labadie, E Rivals, J M Aury, C Lanaud
BACKGROUND: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. METHODS: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome...
September 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28903739/evolving-dna-methylation-and-gene-expression-markers-of-b-cell-chronic-lymphocytic-leukemia-are-present-in-pre-diagnostic-blood-samples-more-than-10%C3%A2-years-prior-to-diagnosis
#17
Panagiotis Georgiadis, Irene Liampa, Dennie G Hebels, Julian Krauskopf, Aristotelis Chatziioannou, Ioannis Valavanis, Theo M C M de Kok, Jos C S Kleinjans, Ingvar A Bergdahl, Beatrice Melin, Florentin Spaeth, Domenico Palli, R C H Vermeulen, J Vlaanderen, Marc Chadeau-Hyam, Paolo Vineis, Soterios A Kyrtopoulos
BACKGROUND: B-cell chronic lymphocytic leukemia (CLL) is a common type of adult leukemia. It often follows an indolent course and is preceded by monoclonal B-cell lymphocytosis, an asymptomatic condition, however it is not known what causes subjects with this condition to progress to CLL. Hence the discovery of prediagnostic markers has the potential to improve the identification of subjects likely to develop CLL and may also provide insights into the pathogenesis of the disease of potential clinical relevance...
September 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28903734/transcriptomic-profiling-of-genes-in-matured-dimorphic-seeds-of-euhalophyte-suaeda-salsa
#18
Yange Xu, Yuanqin Zhao, Huimin Duan, Na Sui, Fang Yuan, Jie Song
BACKGROUND: Suaeda salsa (S. salsa) is a euhalophyte with high economic value. S. salsa can produce dimorphic seeds. Brown seeds are more salt tolerant, can germinate quickly and maintain the fitness of the species under high saline conditions. Black seeds are less salt tolerant, may become part of the seed bank and germinate when soil salinity is reduced. Previous reports have mainly focused on the ecophysiological traits of seed germination and production under saline conditions in this species...
September 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28899413/evolution-and-genome-specialization-of-brucella-suis-biovar-2-iberian-lineages
#19
Ana Cristina Ferreira, Rogério Tenreiro, Maria Inácia Corrêa de Sá, Ricardo Dias
BACKGROUND: Swine brucellosis caused by B. suis biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infected wild boars (Sus scrofa). In Portugal and Spain, the majority of strains share specific molecular characteristics, which allowed establishing an Iberian clonal lineage. However, several strains isolated from wild boars in the North-East region of Spain are similar to strains isolated in different Central European countries...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28899360/biological-networks-in-parkinson-s-disease-an-insight-into-the-epigenetic-mechanisms-associated-with-this-disease
#20
Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
BACKGROUND: Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT: We have studied gene co-expression network obtained from a PD-specific microarray data. The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD...
September 12, 2017: BMC Genomics
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