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https://www.readbyqxmd.com/read/29774565/local-and-systemic-regulation-of-psii-efficiency-in-triticale-infected-by-the-hemibiotrophic-pathogen-microdochium-nivale
#1
Mateusz Dyda, Iwona Wąsek, Mirosław Tyrka, Maria Wędzony, Magdalena Szechyńska-Hebda
Microdochium nivale is a fungal pathogen that causes yield losses of cereals during winter. Cold hardening under light conditions induces genotype-dependent resistance of a plant to infection. We aim to show how photosystem II (PSII) regulation contributes to plant resistance. Using mapping population of triticale doubled haploid lines, three M. nivale strains and different infection assays, we demonstrate that plants that maintain a higher maximum quantum efficiency of PSII show less leaf damage upon infection...
May 17, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/29774017/identifying-group-specific-sequences-for-microbial-communities-using-long-k-mer-sequence-signatures
#2
Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun
Comparing metagenomic samples is crucial for understanding microbial communities. For different groups of microbial communities, such as human gut metagenomic samples from patients with a certain disease and healthy controls, identifying group-specific sequences offers essential information for potential biomarker discovery. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered " group-specific " in our study. Our main purpose is to discover group-specific sequence regions between control and case groups as disease-associated markers...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773620/draft-genome-sequence-of-a-fungus-fusarium-tricinctum-cultured-from-a-monoisolate-native-to-the-himalayas
#3
Narendra Meena, M Vasundhara, M Sudhakara Reddy, Prashanth Suravajhala, U S Raghavender, Krishna Mohan Medicherla
Here, we report the draft de novo genome sequence assembly of Fusarium tricinctum (strain T6), using IonTorrent sequencing chemistry and an Ion 530 chip ExT kit for sequencing. The genome assembly resulted in 42,732,204 bp from a total 6.62 Gb, with a median read length of 386 bp.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29771371/allele-phasing-greatly-improves-the-phylogenetic-utility-of-ultraconserved-elements
#4
Tobias Andermann, Alexandre M Fernandes, Urban Olsson, Mats Töpel, Bernard Pfeil, Bengt Oxelman, Alexandre Aleixo, Brant C Faircloth, Alexandre Antonelli
Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for non-model organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies...
May 15, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29767365/current-and-future-methods-for-mrna-analysis-a-drive-toward-single-molecule-sequencing
#5
Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, Jiannis Ragoussis
The transcriptome encompasses a range of species including messenger RNA, and other noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge role played by mRNA in development and disease, several methods have been developed to sequence and characterize mRNA, with RNA sequencing (RNA-Seq) emerging as the current method of choice particularly for large high-throughput studies. Short-read RNA-Seq which involves sequencing of short cDNA fragments and computationally assembling them to reconstruct the transcriptome, or aligning them to a reference is the most widely used approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767360/transcript-profiling-using-long-read-sequencing-technologies
#6
Anthony Bayega, Yu Chang Wang, Spyros Oikonomopoulos, Haig Djambazian, Somayyeh Fahiminiya, Jiannis Ragoussis
RNA sequencing using next-generation sequencing (NGS, RNA-Seq) technologies is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise short-read RNA-Seq (dominated by Illumina) and long-read RNA-Seq technologies provided by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Although short-read sequencing technologies are the most widely used, long-read technologies are increasingly becoming the standard approach for de novo transcriptome assembly and isoform expression quantification due to the complex nature of the transcriptome which consists of variable lengths of transcripts and multiple alternatively spliced isoforms for most genes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767357/a-guide-for-designing-and-analyzing-rna-seq-data
#7
Aniruddha Chatterjee, Antonio Ahn, Euan J Rodger, Peter A Stockwell, Michael R Eccles
The identity of a cell or an organism is at least in part defined by its gene expression and therefore analyzing gene expression remains one of the most frequently performed experimental techniques in molecular biology. The development of the RNA-Sequencing (RNA-Seq) method allows an unprecedented opportunity to analyze expression of protein-coding, noncoding RNA and also de novo transcript assembly of a new species or organism. However, the planning and design of RNA-Seq experiments has important implications for addressing the desired biological question and maximizing the value of the data obtained...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765069/de-novo-characterization-of-phenacoccus-solenopsis-transcriptome-and-analysis-of-gene-expression-profiling-during-development-and-hormone-biosynthesis
#8
Surjeet Kumar Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma
The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29764461/characterization-of-a-new-apple-luteovirus-identified-by-high-throughput-sequencing
#9
Huawei Liu, Liping Wu, Ekaterina Nikolaeva, Kari Peter, Zongrang Liu, Dimitre Mollov, Mengji Cao, Ruhui Li
BACKGROUND: 'Rapid Apple Decline' (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing. METHODS: Illumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees...
May 15, 2018: Virology Journal
https://www.readbyqxmd.com/read/29764375/the-aquatic-animals-transcriptome-resource-for-comparative-functional-analysis
#10
Chih-Hung Chou, Hsi-Yuan Huang, Wei-Chih Huang, Sheng-Da Hsu, Chung-Der Hsiao, Chia-Yu Liu, Yu-Hung Chen, Yu-Chen Liu, Wei-Yun Huang, Meng-Lin Lee, Yi-Chang Chen, Hsien-Da Huang
BACKGROUND: Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29764366/phylogenetic-signal-from-rearrangements-in-18-anopheles-species-by-joint-scaffolding-extant-and-ancestral-genomes
#11
Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cedric Chauve, Sèverine Bérard
BACKGROUND: Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. RESULTS: We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29763750/genome-sequence-and-analysis-of-mycobacterium-tuberculosis-strain-swlpk
#12
Muhammad Ibrahim, Asma Muhammad Yar, Ghunva Zaman, Changhui Yan, Muhammad Khurshid, Habib Bokhari
OBJECTIVES: Multidrug resistant Mycobacterium tuberculosis poses a global threat, particularly in developing countries such as Pakistan. Genome sequencing, comparative genomic analysis, and drug resistance gene analysis, could be beneficial for understanding and monitoring M. tuberculosis disease severity in Pakistan by elucidating the biology of M. tuberculosis. METHODS: In this study, we sequenced, assembled, and annotated a draft genome of M. tuberculosis strain swlpk using the Illumina MiSeq 300PE throughput 2M system...
May 12, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29758520/probing-the-transcriptome-of-aconitum-carmichaelii-reveals-the-candidate-genes-associated-with-the-biosynthesis-of-the-toxic-aconitine-type-c-19-diterpenoid-alkaloids
#13
Dake Zhao, Yong Shen, Yana Shi, Xingqiao Shi, Qin Qiao, Shuhui Zi, Erqiang Zhao, Diqiu Yu, Edward J Kennelly
Aconitum carmichaelii has long been used as a traditional Chinese medicine, and its processed lateral roots are known commonly as fuzi. Aconitine-type C19 -diterpenoid alkaloids accumulating in the lateral roots are some of the main toxicants of this species, yet their biosynthesis remains largely unresolved. As a first step towards understanding the biosynthesis of aconitine-type C19 -diterpenoid alkaloids, we performed de novo transcriptome assembly and analysis of rootstocks and leaf tissues of Aconitum carmichaelii by next-generation sequencing...
May 11, 2018: Phytochemistry
https://www.readbyqxmd.com/read/29757382/de-novo-genome-assembly-of-the-red-silk-cotton-tree-bombax-ceiba
#14
Yong Gao, Haibo Wang, Chao Liu, Honglong Chu, Dongqin Dai, Shengnan Song, Long Yu, Lihong Han, Yi Fu, Bin Tian, Lizhou Tang
Background: Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia, and northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate the further utilization of this plant resource, we present here the draft genome sequence for B. ceiba. Findings: We assembled a relatively intact genome of B...
May 10, 2018: GigaScience
https://www.readbyqxmd.com/read/29754103/the-ascent-of-man-made-oxidoreductases
#15
REVIEW
Katie J Grayson, Jl Ross Anderson
Though established 40 years ago, the field of de novo protein design has recently come of age, with new designs exhibiting an unprecedented level of sophistication in structure and function. With respect to catalysis, de novo enzymes promise to revolutionise the industrial production of useful chemicals and materials, while providing new biomolecules as plug-and-play components in the metabolic pathways of living cells. To this end, there are now de novo metalloenzymes that are assembled in vivo, including the recently reported C45 maquette, which can catalyse a variety of substrate oxidations with efficiencies rivalling those of closely related natural enzymes...
May 10, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29752761/spatial-analysis-of-lipid-metabolites-and-expressed-genes-reveals-tissue-specific-heterogeneity-of-lipid-metabolism-in-high-and-low-oil-brassica-napus-l-seeds
#16
Shaoping Lu, Drew Sturtevant, Mina Aziz, Cheng Jin, Qing Li, Kent D Chapman, Liang Guo
Despite the importance of oilseeds to worldwide human nutrition, and more recently to the production of bio-based diesel fuels, the detailed mechanisms regulating seed oil biosynthesis remain partly understood, especially from a tissue-specific perspective. Here, we investigated the spatial distributions of lipid metabolites and transcripts involved in oil biosynthesis from seeds of two low-erucic acid genotypes of Brassica napus with high and low seed oil content. Integrated results from matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) of lipids in situ, lipidome profiling of extracts from seed tissues, and tissue-specific transcriptome analysis revealed complex spatial distribution patterns of lipids and transcripts...
May 11, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29751568/cyanogenesis-in-arthropods-from-chemical-warfare-to-nuptial-gifts
#17
REVIEW
Mika Zagrobelny, Érika Cristina Pinheiro de Castro, Birger Lindberg Møller, Søren Bak
Chemical defences are key components in insect⁻plant interactions, as insects continuously learn to overcome plant defence systems by, e.g., detoxification, excretion or sequestration. Cyanogenic glucosides are natural products widespread in the plant kingdom, and also known to be present in arthropods. They are stabilised by a glucoside linkage, which is hydrolysed by the action of β-glucosidase enzymes, resulting in the release of toxic hydrogen cyanide and deterrent aldehydes or ketones. Such a binary system of components that are chemically inert when spatially separated provides an immediate defence against predators that cause tissue damage...
May 3, 2018: Insects
https://www.readbyqxmd.com/read/29751013/the-properties-of-amyloid-%C3%AE-fibrils-are-determined-by-their-path-of-formation
#18
Kristoffer Brännström, Tohidul Islam, Anna L Gharibyan, Irina Iakovleva, Lina Nilsson, Cheng Choo Lee, Linda Sandblad, Annelie Pamrén, Anders Olofsson
Fibril formation of the amyloid-β peptide (Aβ) follows a nucleation-dependent polymerization process and is associated with Alzheimer's disease. Several different lengths of Aβ are observed in vivo, but Aβ1-40 and Aβ1-42 are the dominant forms. The fibril architectures of Aβ1-40 and Aβ1-42 differ and Aβ1-42 assemblies are generally considered more pathogenic. We show here that monomeric Aβ1-42 can be cross-templated and incorporated into the ends of Aβ1-40 fibrils, while incorporation of Aβ1-40 monomers into Aβ1-42 fibrils is very poor...
May 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29748765/de-novo-assembly-of-mitochondrial-genomes-provides-insights-into-genetic-diversity-and-molecular-evolution-in-wild-boars-and-domestic-pigs
#19
Pan Ni, Ali Akbar Bhuiyan, Jian-Hai Chen, Jingjin Li, Cheng Zhang, Shuhong Zhao, Xiaoyong Du, Hua Li, Hui Yu, Xiangdong Liu, Kui Li
Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression...
May 10, 2018: Genetica
https://www.readbyqxmd.com/read/29747012/comparative-transcriptome-analysis-reveals-the-gene-expression-profiling-in-bighead-carp-aristichthys-nobilis-in-response-to-acute-nitrite-toxicity
#20
Ling-Hong Miao, Yan Lin, Wen-Jing Pan, Xin Huang, Xian-Ping Ge, Qun-Lan Zhou, Bo Liu, Ming-Chun Ren, Wu-Xiao Zhang, Hua-Liang Liang, Han Yu, Ke Ji
OBJECTIVE: Nitrite exposure induces growth inhibition, metabolic disturbance, oxidative stress, organic damage, and infection-mediated mortality of aquatic organism. This study aimed to investigate the mechanism in responses to acute nitrite toxicity in bighead carp (Aristichthys nobilis, A. nobilis) by RNA-seq analysis. METHODS: Bighead carps were exposed to water with high nitrite content (48.63 mg/L) for 72 h, and fish livers and gills were separated for RNA-seq analysis...
May 7, 2018: Fish & Shellfish Immunology
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