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microorganisms Article Label-Free Quantitative Proteomics Analysis in Susceptible and Resistant Brassica napus Cultivars Infected with Xanthomonas campestris pv. campestris Md Tabibul Islam 1,2, Bok-Rye Lee 1,3 , Van Hien La 1, Dong-Won Bae 4, Woo-Jin Jung 5 and Tae-Hwan Kim 1,* 1 Department of Animal Science, Institute of Agricultural Science and Technology, College of Agriculture & Life Science, Chonnam National University, Gwangju 61186, Korea; [email protected] (M.T.I.); [email protected] (B.-R.L.); [email protected] (V.H.L.) 2 Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA 3 Asian Pear Research Institute, Chonnam National University, Gwangju 61186, Korea 4 Central Instrument Facility, Gyeongsang National University, Jinju 52828, Korea; [email protected] 5 Division of Applied Bioscience and Biotechnology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-62-530-2126 Abstract: Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the main disease of cruciferous vegetables. To characterize the resistance mechanism in the Brassica napus–Xcc pathosys- tem, Xcc-responsive proteins in susceptible (cv. Mosa) and resistant (cv. Capitol) cultivars were investigated using gel-free quantitative proteomics and analysis of gene expression. This allowed us to identify 158 and 163 differentially expressed proteins following Xcc infection in cv. Mosa and cv. Citation: Islam, M.T.; Lee, B.-R.; Capitol, respectively, and to classify them into five major categories including antioxidative systems, La, V.H.; Bae, D.-W.; Jung, W.-J.; proteolysis, photosynthesis, redox, and innate immunity. -
PANNZER 2: Annotate a Complete Proteome in Minutes!
PANNZER 2: Annotate a complete proteome in minutes! Alan J Medlar#, Petri Törönen#, Elaine Zosa, Liisa Holm* Structural Genomics Group, Institute of Biotechnology PO Box 56, 00014 University of Helsinki, Finland #These authors contributed equally *To whom correspondence should be addressed: [email protected] 1. INTRODUCTION As high-throughput sequencing has become increasingly efficient, downstream analysis has become the main bottleneck in genome sequencing projects. For example, a critical and time-consuming step is the annotation of the organism’s proteome: assigning molecular functions, involvement in biological processes and the cellular localizations of all identified protein sequences. The process of protein annotation involves classifying each protein using the Gene Ontology (GO) and selecting suitable free text descriptions, which are required for submission into sequence databases. We refer to these as GO and DE predictions, respectively. Although servers are available that perform functional annotation, none perform both GO and DE predictions concurrently, they tend to be slow and are restricted in the number of queries that can be submitted. Finally, many of the existing methods do not return an estimate of the prediction accuracy. 2. METHODS AND RESULTS The above shortcomings are remedied by PANNZER 2, an interactive web server and standalone program for protein function prediction. It is, to our knowledge, the only tool that performs both DE and GO prediction. It uses SANS-parallel [1], a high-throughput sequence search program that is thousands of times faster than BLAST, to identify homologous sequences. It is, therefore, capable of analyzing tens of thousands of proteins interactively. Results are displayed as an HTML table summarizing both DE and GO predictions, including a statistical estimate for the reliability of each prediction. -
Pan-Genome-Wide Analysis of Pantoea Ananatis Identified Genes Linked to Pathogenicity In
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.24.219337; this version posted July 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Pan-genome-wide analysis of Pantoea ananatis identified genes linked to pathogenicity in onion Gaurav Agarwal1*, Divya Choudhary1, Shaun P. Stice2, Brendon K. Myers1, Ronald D. Gitaitis1, Stephanus N. Venter3, Brian H. Kvitko2, Bhabesh Dutta1* 1Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, Georgia, USA 2Department of Plant Pathology, University of Georgia, Athens, Georgia, USA 3Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa *Corresponding authors: [email protected] (BD); [email protected] (GA) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.24.219337; this version posted July 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Pantoea ananatis is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally), for a phosphonate secondary metabolite, and the onion- virulence regions, OVR (localized on a megaplasmid), for onion pathogenicity and virulence, respectively. -
Workflows for Rapid Functional Annotation of Diverse
insects Article Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes Surya Saha 1,2 , Amanda M. Cooksey 2,3, Anna K. Childers 4 , Monica F. Poelchau 5 and Fiona M. McCarthy 2,* 1 Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA; [email protected] 2 School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA; [email protected] 3 CyVerse, BioScience Research Laboratories, University of Arizona, 1230 N. Cherry Ave., Tucson, AZ 85721, USA 4 Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, 10300 Baltimore Ave., Beltsville, MD 20705, USA; [email protected] 5 National Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Ave., Beltsville, MD 20705, USA; [email protected] * Correspondence: fi[email protected] Simple Summary: Genomic technologies are accumulating information about genes faster than ever before, and sequencing initiatives, such as the Earth BioGenome Project, i5k, and Ag100Pest Initiative, are expected to increase this rate of acquisition. However, if genomic sequencing is to be used for the improvement of human health, agriculture, and our understanding of biological systems, it is necessary to identify genes and understand how they contribute to biological outcomes. While there are several well-established workflows for assembling genomic sequences and identifying genes, understanding gene function is essential to create actionable knowledge. Moreover, this functional annotation process must be easily accessible and provide information at a genomic scale to keep up Citation: Saha, S.; Cooksey, A.M.; with new sequence data. We report a well-defined workflow for rapid functional annotation of whole Childers, A.K.; Poelchau, M.F.; proteomes to produce Gene Ontology and pathways information. -
How the Energy Sensor, AMPK, Impact the Testicular Function Pascal Froment, Mélanie Faure, Edith Guibert, Jean-Pierre Brillard
How the energy sensor, AMPK, impact the testicular function Pascal Froment, Mélanie Faure, Edith Guibert, Jean-Pierre Brillard To cite this version: Pascal Froment, Mélanie Faure, Edith Guibert, Jean-Pierre Brillard. How the energy sensor, AMPK, impact the testicular function. 27. Conference of European Comparative Endocrinologists, Aug 2014, Rennes, France. 2014. hal-02742016 HAL Id: hal-02742016 https://hal.inrae.fr/hal-02742016 Submitted on 3 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright 27th Conference of European Comparative Endocrinologists CECE 2014 25-29 August 2014 Rennes, France 3 27th Conference of European Comparative Endocrinologists Organized with the generous support and help of our sponsors Université de Rennes 1 European Society for Comparative Endocrinology (Grants) European Union INTEREG TC2N Rennes Métropole European Society of Endocrinology (Grants) Institut National de la Recherche Agronomique Société de Neuroendocrinologie (Grants) Institut National de l'Environnement Industriel et des Risques !"#$%$&$'()'*)+,)*+,)'#&*'-.'#."$/ -
Gene Co-Expression Network Analysis Identifies Porcine Genes Associated
www.nature.com/scientificreports OPEN Gene co-expression network analysis identifies porcine genes associated with variation in Received: 16 September 2016 Accepted: 29 March 2017 metabolizing fenbendazole and Published: xx xx xxxx flunixin meglumine in the liver Jeremy T. Howard1, Melissa S. Ashwell1, Ronald E. Baynes2, James D. Brooks2, James L. Yeatts2 & Christian Maltecca1 Identifying individual genetic variation in drug metabolism pathways is of importance not only in livestock, but also in humans in order to provide the ultimate goal of giving the right drug at the right dose at the right time. Our objective was to identify individual genes and gene networks involved in metabolizing fenbendazole (FBZ) and flunixin meglumine (FLU) in swine liver. The population consisted of female and castrated male pigs that were sired by boars represented by 4 breeds. Progeny were randomly placed into groups: no drug (UNT), FLU or FBZ administered. Liver transcriptome profiles from 60 animals with extreme (i.e. fast or slow drug metabolism) pharmacokinetic (PK) profiles were generated from RNA sequencing. Multiple cytochrome P450 (CYP1A1, CYP2A19 and CYP2C36) genes displayed different transcript levels across treated versus UNT. Weighted gene co-expression network analysis identified 5 and 3 modules of genes correlated with PK parameters and a portion of these were enriched for biological processes relevant to drug metabolism for FBZ and FLU, respectively. Genes within identified modules were shown to have a higher transcript level relationship (i.e. connectivity) in treated versus UNT animals. Investigation into the identified genes would allow for greater insight into FBZ and FLU metabolism. Drug use and how it is currently regulated in livestock has received increased attention due to animal welfare concerns, food safety and the prevalence of antibiotic resistance1. -
Comparative Genomics of Two Jute Species and Insight Into Fibre
LETTERS PUBLISHED: 30 JANUARY 2017 | VOLUME: 3 | ARTICLE NUMBER: 16223 OPEN Comparative genomics of two jute species and insight into fibre biogenesis Md Shahidul Islam1,2,3*,JenniferA.Saito1,4, Emdadul Mannan Emdad1, Borhan Ahmed1,2,3, Mohammad Moinul Islam1,2,3, Abdul Halim1,2,3, Quazi Md Mosaddeque Hossen1,2,3, Md Zakir Hossain1,2,3, Rasel Ahmed1, Md Sabbir Hossain1, Shah Md Tamim Kabir1, Md Sarwar Alam Khan1, Md Mursalin Khan1, Rajnee Hasan1, Nasima Aktar1,UmmayHoni1, Rahin Islam1, Md Mamunur Rashid1,XuehuaWan1,4, Shaobin Hou1,4, Taslima Haque3, Muhammad Shafiul Azam3, Mahdi Muhammad Moosa3, Sabrina M. Elias3,A.M.MahediHasan3, Niaz Mahmood3, Md Shafiuddin3,SaimaShahid3, Nusrat Sharmeen Shommu3, Sharmin Jahan3, Saroj Roy3,5, Amlan Chowdhury3,5, Ashikul Islam Akhand3,5, Golam Morshad Nisho3,5, Khaled Salah Uddin3,5,TaposhiRabeya3,5,S.M.EkramulHoque3,5, Afsana Rahman Snigdha3,5, Sarowar Mortoza3,5, Syed Abdul Matin3,5,MdKamrulIslam3,5,M.Z.H.Lashkar3,5, Mahboob Zaman3,5, Anton Yuryev1,6, Md Kamal Uddin1,2, Md Sharifur Rahman1,7, Md Samiul Haque1,2,3, Md Monjurul Alam1,2,3, Haseena Khan3,8 and Maqsudul Alam1,3,4† Jute (Corchorus sp.) is one of the most important sources of We performed whole-genome shotgun (WGS) sequencing with natural fibre, covering ∼80% of global bast fibre production1. the Roche/454 platform (Supplementary Table 1) and assembled Only Corchorus olitorius and Corchorus capsularis are commer- the genomes using CABOG6. The resulting assemblies were cially cultivated, though there are more than 100 Corchorus 445 Mb (scaffold N50 length, 3.3 Mb; longest scaffold, 45.5 Mb) species2 in the Malvaceae family. -
Mechanistic Underpinnings of Dehydration Stress in the American Dog Tick Revealed Through RNA-Seq and Metabolomics Andrew J
© 2016. Published by The Company of Biologists Ltd | Journal of Experimental Biology (2016) 219, 1808-1819 doi:10.1242/jeb.137315 RESEARCH ARTICLE Mechanistic underpinnings of dehydration stress in the American dog tick revealed through RNA-Seq and metabolomics Andrew J. Rosendale1,*, Lindsey E. Romick-Rosendale2, Miki Watanabe2, Megan E. Dunlevy1 and Joshua B. Benoit1 ABSTRACT and Denlinger, 2010). Therefore, a species’ ability to establish itself Ticks are obligate blood feeders but spend the majority of their lifetime in a particular habitat depends in large part on its ability to survive off-host where they must contend with a multitude of environmental various environmental stresses, including maintenance of water stresses. Survival under desiccating conditions is a determinant for content under potentially desiccating conditions. habitats where ticks can become established, and water-balance Ticks are able to prevent dehydration through behavioral characteristics of ticks have been extensively studied. However, little mechanisms, physical and physiological adaptations for water is known about the underlying aspects associated with dehydration conservation, and the acquisition of exogenous water (Benoit and stress in ticks. In this study, we examined the response of male Denlinger, 2010; Needham and Teel, 1986; Sonenshine, 1991; American dog ticks, Dermacentor variabilis, to dehydration using a Sonenshine and Roe, 2013). Ticks can avoid desiccating conditions combined transcriptomics and metabolomics approach. During by restricting host seeking to periods of high relative humidity dehydration, 497 genes were differentially expressed, including an and retreating to sheltered microhabitats at other times (Crooks and up-regulation of stress-response and protein-catabolism genes and Randolph, 2006; Short et al., 1989). -
Pan-Genome Mirnomics in Brachypodium
plants Article Pan-Genome miRNomics in Brachypodium Tugdem Muslu 1 , Sezgi Biyiklioglu-Kaya 1 , Bala Ani Akpinar 2, Meral Yuce 3 and Hikmet Budak 2,* 1 Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; [email protected] (T.M.); [email protected] (S.B.-K.) 2 Montana BioAgriculture, Inc., Missoula, MT 59802, USA; [email protected] 3 Sabanci University SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey; [email protected] * Correspondence: [email protected] Abstract: Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some Citation: Muslu, T.; lineages. -
Comparative Genomics Analysis in Prunoideae to Identify Biologically Relevant Polymorphisms
Plant Biotechnology Journal (2013), pp. 1–11 doi: 10.1111/pbi.12081 Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms Tyson Koepke1,2,†, Scott Schaeffer1,2,†, Artemus Harper1, Federico Dicenta3, Mark Edwards4, Robert J. Henry5, Birger L. Møller6, Lee Meisel7, Nnadozie Oraguzie8, Herman Silva9, Raquel Sanchez-P erez 3,6,* and Amit Dhingra1,2,* 1Department of Horticulture, Washington State University, Pullman, WA, USA 2Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA 3Department of Plant Breeding, CEBAS-CSIC, Murcia, Spain 4Southern Cross University, Lismore, NSW, Australia 5Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Qld, Australia 6Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark 7INTA-Universidad de Chile, Santiago, Chile 8IAREC, Department of Horticulture, Washington State University, Prosser, WA, USA 9Laboratorio de Genomica Funcional & Bioinformatica, Departamento de Produccion Agrıcola, Facultad de Ciencias Agronomicas, Universidad de Chile, La Pintana Santiago, Chile Received 12 December 2012; Summary revised 27 March 2013; Prunus is an economically important genus with a wide range of physiological and biological accepted 8 April 2013. variability. Using the peach genome as a reference, sequencing reads from four almond *Correspondence (fax 509 335 8690; accessions and one sweet cherry cultivar were used for comparative analysis of these three email [email protected]; [email protected]) Prunus species. Reference mapping enabled the identification of many biological relevant †The authors wish it to be known that the polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall first two authors would like to be regarded as co-first authors. -
Functional Genomics Analysis of Newly Sequenced
Functional Genomics Analysis of Newly Sequenced Species with Blast2GO Carlos Menor, David Seide, Robert Nica, Mariana Monteiro, Alejandro Rocamonde, Francisco Salavert, Stefan Götz BioBam Bioinformatics S.L., Valencia, Spain Abstract Toolbox features RNA-seq Features: Functional genomics attempts to describe functions of genes and Quality assessment, trimming, assembly, quantification, pair- proteins by making use of data derived from genomic and filtering and adapter removal of wise and time-course transcriptomic experiments. raw sequence data differential expressions analysis Blast2GO is a bioinformatics platform which offers an integrated solution for functional genomics analysis of novel genomes. It allows biologists to get from raw NGS data through all steps up to the Eukaryotic and prokaryotic High-throughput functional generation of biological insights for a species without any previous genome characterization annotation prediction genome resources. supported by RNA-seq data This poster provides an overview of the different analysis strategies, details about new features as well as describes the bioinformatic Rich Visualization: Functional enrichment and pipeline of a de-novo transcriptomics analysis - from read-assembly up Track-based genome browser for pathway analysis to the functional analysis and generation of biological insights. GFF, VCF, BAM and FASTA files 1. Quality check and pre-processing Complete Transcriptome 3. Expression quantification and raw sequence data Analysis Workflow differential expression analysis A good quality control check and preprocessing Blast2GO provides a fast and easy way to of raw sequence data coming from high quantify transcript expression levels from RNA- throughput sequencing pipelines is fundamental Seq data and to perform differential expression for optimal downstream analysis. Blast2GO analysis to detect significantly expressed provides summary evaluations that guide the transcripts. -
Sociogenomics of Maternal Care and Parent-Offspring Coadaptation in the European Earwigs (Forficula Auricularia)
Sociogenomics of maternal care and parent-offspring coadaptation in the European earwigs (Forficula auricularia) Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Min Wu aus China Zürich, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Fakultätsverantwortlicher: Prof. Dr. Dieter Ebert, Professor, Universität Basel Dissertationsleiter: Dr. Mathias Kölliker, Universität Basel Dr. Jean-Claude Walser, ETH, Zürich Korreferent: Prof. Dr. Michel Chapuisat, Universität Lausanne Basel, den 15.11.2016 Prof. Dr. Jörg Schibler, Dekan 2 ACKNOWLEDGEMENTS I would like to thank all the people involved in my PhD work in one way or another. First, great thanks to Mathias Kölliker and Jean-Claude Walser for the opportunity studying such a super exciting project as well their patient supervision and strengthful support to conquer all the challenges throughout my PhD. Special thank to Dieter Ebert for taking me into the daphnia group during the last year of my PhD, and all the support and advice he gave to finish my original project and for future plans on academic career. Thanks to Michel Chapuisat for being the external referee of my defense all the way from Lausanne. And thanks for his detailed comments and corrections of my thesis. I thank Anne Roulin for all the collaboration in the first chapter, sharing first co-authorship in the publication and her advice regarding bioinformatic analysis in the second chapter. Thanks to Roberto Arbore for showing me how to extract RNA firsthand, Simone Kühn-Bühlmann for showing me how to dissect the tiny delicate earwig brain.