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BMC Genomics

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https://www.readbyqxmd.com/read/28747151/comparative-analysis-of-targeted-long-read-sequencing-approaches-for-characterization-of-a-plant-s-immune-receptor-repertoire
#1
Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D G Jones, Matthew D Clark
BACKGROUND: The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified...
July 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28743243/the-malr-type-regulator-acrc-is-a-transcriptional-repressor-of-acarbose-biosynthetic-genes-in-actinoplanes-sp-se50-110
#2
Timo Wolf, Julian Droste, Tetiana Gren, Vera Ortseifen, Susanne Schneiker-Bekel, Till Zemke, Alfred Pühler, Jörn Kalinowski
BACKGROUND: Acarbose is used in the treatment of diabetes mellitus type II and is produced by Actinoplanes sp. SE50/110. Although the biosynthesis of acarbose has been intensively studied, profound knowledge about transcription factors involved in acarbose biosynthesis and their binding sites has been missing until now. In contrast to acarbose biosynthetic gene clusters in Streptomyces spp., the corresponding gene cluster of Actinoplanes sp. SE50/110 lacks genes for transcriptional regulators...
July 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28743233/erratum-to-conserved-gene-expression-in-sperm-reservoirs-between-birds-and-mammals-in-response-to-mating
#3
Mohammad Atikuzzaman, Manuel Alvarez-Rodriguez, Alejandro Vicente-Carrillo, Martin Johnsson, Dominic Wright, Heriberto Rodriguez-Martinez
No abstract text is available yet for this article.
July 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28738828/unraveling-multifaceted-contributions-of-small-regulatory-rnas-to-photomorphogenic-development-in-arabidopsis
#4
Meng-Chun Lin, Huang-Lung Tsai, Sim-Lin Lim, Shih-Tong Jeng, Shu-Hsing Wu
BACKGROUND: Post-transcriptional control of gene expression mediated by small regulatory RNAs (sRNAs) is vital for growth and development of diverse organisms. The biogenesis of sRNAs is regulated by both positive and negative regulators known to regulate photomorphogenic development. Two microRNAs (miRNAs), miR157 and miR319, also regulate photomorphogenesis. However, genome-wide profiling of sRNAs and their regulation of target genes during photomorphogenesis has been missing. We provide a comprehensive view of sRNA-controlled gene expression in this developmental process...
July 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28738815/transcription-through-the-eye-of-a-needle-daily-and-annual-cyclic-gene-expression-variation-in-douglas-fir-needles
#5
Richard Cronn, Peter C Dolan, Sanjuro Jogdeo, Jill L Wegrzyn, David B Neale, J Bradley St Clair, Dee R Denver
BACKGROUND: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales...
July 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28738802/histological-and-transcriptomic-effects-of-17%C3%AE-methyltestosterone-on-zebrafish-gonad-development
#6
Stephanie Ling Jie Lee, Julia A Horsfield, Michael A Black, Kim Rutherford, Amanda Fisher, Neil J Gemmell
BACKGROUND: Sex hormones play important roles in teleost ovarian and testicular development. In zebrafish, ovarian differentiation appears to be dictated by an oocyte-derived signal via Cyp19a1a aromatase-mediated estrogen production. Androgens and aromatase inhibitors can induce female-to-male sex reversal, however, the mechanisms underlying gonadal masculinisation are poorly understood. We used histological analyses together with RNA sequencing to characterise zebrafish gonadal transcriptomes and investigate the effects of 17α-methyltestosterone on gonadal differentiation...
July 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28738780/distinct-herpesvirus-resistances-and-immune-responses-of-three-gynogenetic-clones-of-gibel-carp-revealed-by-comprehensive-transcriptomes
#7
Fan-Xiang Gao, Yang Wang, Qi-Ya Zhang, Cheng-Yan Mou, Zhi Li, Yuan-Sheng Deng, Li Zhou, Jian-Fang Gui
BACKGROUND: Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown. RESULTS: To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A(+), candidate variety clone F and wild clone H...
July 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28738779/anion-selective-formate-nitrite-transporters-taxonomic-distribution-phylogenetic-analysis-and-subfamily-specific-conservation-pattern-in-prokaryotes
#8
Mishtu Mukherjee, Manu Vajpai, Ramasubbu Sankararamakrishnan
BACKGROUND: The monovalent anions formate, nitrite and hydrosulphide are main metabolites of bacterial respiration during anaerobic mixed-acid fermentation. When accumulated in the cytoplasm, these anions become cytotoxic. Membrane proteins that selectively transport these monovalent anions across the membrane have been identified and they belong to the family of Formate/Nitrite Transporters (FNTs). Individual members that selectively transport formate, nitrite and hydrosulphide have been investigated...
July 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732532/gate-an-efficient-procedure-in-study-of-pleiotropic-genetic-associations
#9
Wei Zhang, Liu Yang, Larry L Tang, Aiyi Liu, James L Mills, Yuanchang Sun, Qizhai Li
BACKGROUND: The association studies on human complex traits are admittedly propitious to identify deleterious genetic markers. Compared to single-trait analyses, multiple-trait analyses can arguably make better use of the information on both traits and markers, and thus improve statistical power of association tests prominently. Principal component analysis (PCA) is a well-known useful tool in multivariate analysis and can be applied to this task. Generally, PCA is first performed on all traits and then a certain number of top principal components (PCs) that explain most of the trait variations are selected to construct the test statistics...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732470/erratum-to-comparative-transcriptome-analyses-on-silk-glands-of-six-silkmoths-imply-the-genetic-basis-of-silk-structure-and-coloration
#10
Yang Dong, Fangying Dai, Yandong Ren, Hui Liu, Lei Chen, Pengcheng Yang, Yanqun Liu, Xin Li, Wen Wang, Hui Xiang
No abstract text is available yet for this article.
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732469/microsatellite-marker-development-by-partial-sequencing-of-the-sour-passion-fruit-genome-passiflora-edulis-sims
#11
Susan Araya, Alexandre M Martins, Nilton T V Junqueira, Ana Maria Costa, Fábio G Faleiro, Márcio E Ferreira
BACKGROUND: The Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. edulis, the most important commercial Passiflora species, are still incipient. In spite of many recognized applications of microsatellite markers in genetics and breeding, their availability for passion fruit research remains restricted. Microsatellite markers in P. edulis are usually limited in number, show reduced polymorphism, and are mostly based on compound or imperfect repeats...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732465/genome-wide-signals-of-positive-selection-in-strongylocentrotid-sea-urchins
#12
Kord M Kober, Grant H Pogson
BACKGROUND: Comparative genomics studies investigating the signals of positive selection among groups of closely related species are still rare and limited in taxonomic breadth. Such studies show great promise in advancing our knowledge about the proportion and the identity of genes experiencing diversifying selection. However, methodological challenges have led to high levels of false positives in past studies. Here, we use the well-annotated genome of the purple sea urchin, Strongylocentrotus purpuratus, as a reference to investigate the signals of positive selection at 6520 single-copy orthologs from nine sea urchin species belonging to the family Strongylocentrotidae paying careful attention to minimizing false positives...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#13
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28732460/novel-efficient-genome-wide-snp-panels-for-the-conservation-of-the-highly-endangered-iberian-lynx
#14
Daniel Kleinman-Ruiz, Begoña Martínez-Cruz, Laura Soriano, Maria Lucena-Perez, Fernando Cruz, Beatriz Villanueva, Jesús Fernández, José A Godoy
BACKGROUND: The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STRs, but their limited variability and the more complex situation of current populations demand more efficient molecular markers. The recent characterization of the Iberian lynx genome identified more than 1...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28728593/high-throughput-sequencing-of-small-rnas-reveals-dynamic-micrornas-expression-of-lipid-metabolism-during-camellia-oleifera-and-c-meiocarpa-seed-natural-drying
#15
Jin-Ling Feng, Zhi-Jian Yang, Shi-Pin Chen, Yousry A El-Kassaby, Hui Chen
BACKGROUND: Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted...
July 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28728575/genome-wide-association-study-identifies-a-major-gene-for-beech-bark-disease-resistance-in-american-beech-fagus-grandifolia-ehrh
#16
Irina Ćalić, Jennifer Koch, David Carey, Charles Addo-Quaye, John E Carlson, David B Neale
BACKGROUND: The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees. METHODS: In this case-control genome-wide association study (GWAS), we tested 16 K high quality SNPs using the Affymetrix Axiom 1...
July 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724410/identification-and-characterization-of-long-non-coding-rnas-in-subcutaneous-adipose-tissue-from-castrated-and-intact-full-sib-pair-huainan-male-pigs
#17
Jing Wang, Liushuai Hua, Junfeng Chen, Jiaqing Zhang, Xianxiao Bai, Binwen Gao, Congjun Li, Zhihai Shi, Weidong Sheng, Yuan Gao, Baosong Xing
BACKGROUND: Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular systems and metabolic features. RESULTS: We identified lncRNAs in subcutaneous adipose tissue by deep RNA-sequencing using the intact and castrated Huainan male pigs...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724409/hybrid-assembly-with-long-and-short-reads-improves-discovery-of-gene-family-expansions
#18
Jason R Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P Walenz, Junqi Liu, Robert M Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G Maron, Susan R McCouch, W Richard McCombie, Michael C Schatz, Peter Tiffin, Nevin D Young, Kevin A T Silverstein
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724407/characterization-of-the-cytochrome-p450-monooxygenase-genes-p450ome-from-the-carotenogenic-yeast-xanthophyllomyces-dendrorhous
#19
Pamela Córdova, Ana-María Gonzalez, David R Nelson, María-Soledad Gutiérrez, Marcelo Baeza, Víctor Cifuentes, Jennifer Alcaíno
BACKGROUND: The cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases involved in the oxidative metabolism of an enormous diversity of substrates. These enzymes require electrons for their activity, and the electrons are supplied by NAD(P)H through a P450 electron donor system, which is generally a cytochrome P450 reductase (CPR). The yeast Xanthophyllomyces dendrorhous has evolved an exclusive P450-CPR system that specializes in the synthesis of astaxanthin, a carotenoid with commercial potential...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724357/genome-analysis-of-e-coli-isolated-from-crohn-s-disease-patients
#20
Daria V Rakitina, Alexander I Manolov, Alexandra V Kanygina, Sofya K Garushyants, Julia P Baikova, Dmitry G Alexeev, Valentina G Ladygina, Elena S Kostryukova, Andrei K Larin, Tatiana A Semashko, Irina Y Karpova, Vladislav V Babenko, Ruzilya K Ismagilova, Sergei Y Malanin, Mikhail S Gelfand, Elena N Ilina, Roman B Gorodnichev, Eugenia S Lisitsyna, Gennady I Aleshkin, Petr L Scherbakov, Igor L Khalif, Marina V Shapina, Igor V Maev, Dmitry N Andreev, Vadim M Govorun
BACKGROUND: Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS: We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains...
July 19, 2017: BMC Genomics
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