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Labbé F, Abdeladhim M, Abrudan J, Araki AS, Araujo RN, Arensburger P, Benoit JB, Brazil RP, Bruno RV, Bueno da Silva Rivas G, Carvalho de Abreu V, Charamis J, Coutinho-Abreu IV, da Costa-Latgé SG, Darby A, Dillon VM, Emrich SJ, Fernandez-Medina D, Figueiredo Gontijo N, Flanley CM, Gatherer D, Genta FA, Gesing S, Giraldo-Calderón GI, Gomes B, Aguiar ERGR, Hamilton JGC, Hamarsheh O, Hawksworth M, Hendershot JM, Hickner PV, Imler JL, Ioannidis P, Jennings EC, Kamhawi S, Karageorgiou C, Kennedy RC, Krueger A, Latorre-Estivalis JM, Ligoxygakis P, Meireles-Filho ACA, Minx P, Miranda JC, Montague MJ, Nowling RJ, Oliveira F, Ortigão-Farias J, Pavan MG, Horacio Pereira M, Nobrega Pitaluga A, Proveti Olmo R, Ramalho-Ortigao M, Ribeiro JMC, Rosendale AJ, Sant’Anna MRV, Scherer SE, Secundino NFC, Shoue DA, da Silva Moraes C, Gesto JSM, Souza NA, Syed Z, Tadros S, Teles-de-Freitas R, Telleria EL, Tomlinson C, Traub-Csekö YM, Marques JT, Tu Z, Unger MF, Valenzuela J, Ferreira FV, de Oliveira KPV, Vigoder FM, Vontas J, Wang L, Weedall GD, Zhioua E, Richards S, Warren WC, Waterhouse RM, Dillon RJ, McDowell MA. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World. PLoS Negl Trop Dis 2023; 17:e0010862. [PMID: 37043542 PMCID: PMC10138862 DOI: 10.1371/journal.pntd.0010862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 04/27/2023] [Accepted: 02/13/2023] [Indexed: 04/13/2023] Open
Abstract
Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.
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Affiliation(s)
- Frédéric Labbé
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Maha Abdeladhim
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jenica Abrudan
- Genomic Sciences & Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alejandra Saori Araki
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ricardo N. Araujo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona, California, United States of America
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | | | - Rafaela V. Bruno
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gustavo Bueno da Silva Rivas
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Vinicius Carvalho de Abreu
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jason Charamis
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Greece
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
| | - Iliano V. Coutinho-Abreu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, California, United States of America
| | | | - Alistair Darby
- Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom
| | - Viv M. Dillon
- Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom
| | - Scott J. Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | | | - Nelder Figueiredo Gontijo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Catherine M. Flanley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Fernando A. Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sandra Gesing
- Discovery Partners Institute, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Gloria I. Giraldo-Calderón
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
- Dept. Ciencias Biológicas & Dept. Ciencias Básicas Médicas, Universidad Icesi, Cali, Colombia
| | - Bruno Gomes
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - James G. C. Hamilton
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Omar Hamarsheh
- Department of Life Sciences, Faculty of Science and Technology, Al-Quds University, Jerusalem, Palestine
| | - Mallory Hawksworth
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Jacob M. Hendershot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Paul V. Hickner
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, Texas, United States of America
| | - Jean-Luc Imler
- CNRS-UPR9022 Institut de Biologie Moléculaire et Cellulaire and Faculté des Sciences de la Vie-Université de Strasbourg, Strasbourg, France
| | - Panagiotis Ioannidis
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
| | - Emily C. Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Charikleia Karageorgiou
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Genomics Group – Bioinformatics and Evolutionary Biology Lab, Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
| | - Ryan C. Kennedy
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Andreas Krueger
- Medical Entomology Branch, Dept. Microbiology, Bundeswehr Hospital, Hamburg, Germany
- Medical Zoology Branch, Dept. Microbiology, Central Bundeswehr Hospital, Koblenz, Germany
| | - José M. Latorre-Estivalis
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Petros Ligoxygakis
- Laboratory of Cell Biology, Development and Genetics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Patrick Minx
- Donald Danforth Plant Science Center, Olivette, Missouri, United States of America
| | - Jose Carlos Miranda
- Laboratório de Imunoparasitologia, CPqGM, Fundação Oswaldo Cruz, Bahia, Brazil
| | - Michael J. Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronald J. Nowling
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - Fabiano Oliveira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | | | - Marcio G. Pavan
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
- Laboratório de Transmissores de Hematozoários, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Marcos Horacio Pereira
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Andre Nobrega Pitaluga
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, Brazil
| | - Roenick Proveti Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcelo Ramalho-Ortigao
- F. Edward Hebert School of Medicine, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - José M. C. Ribeiro
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Andrew J. Rosendale
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Mauricio R. V. Sant’Anna
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Steven E. Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | | | | | - Nataly Araujo Souza
- Laboratory Interdisciplinar em Vigilancia Entomologia em Diptera e Hemiptera, Fiocruz, Rio de Janeiro, Brazil
| | - Zainulabueddin Syed
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Samuel Tadros
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | | | - Erich L. Telleria
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | | | - João Trindade Marques
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Zhijian Tu
- Fralin Life Science Institute and Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Maria F. Unger
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jesus Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Flávia V. Ferreira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Karla P. V. de Oliveira
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Felipe M. Vigoder
- Universidade Federal do Rio de Janeiro, Instituto de Biologia. Rio de Janeiro, Brazil
| | - John Vontas
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Pesticide Science Lab, Department of Crop Science, Agricultural University of Athens, Athens Greece
| | - Lihui Wang
- Donald Danforth Plant Science Center, Olivette, Missouri, United States of America
| | - Gareth D. Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine (LSTM), Liverpool, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Elyes Zhioua
- Vector Ecology Unit, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wesley C. Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
| | - Robert M. Waterhouse
- Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Rod J. Dillon
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Mary Ann McDowell
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
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Uzoechi SC, Rosa BA, Singh KS, Choi YJ, Bracken BK, Brindley PJ, Townsend RR, Sprung R, Zhan B, Bottazzi ME, Hawdon JM, Wong Y, Loukas A, Djuranovic S, Mitreva M. Excretory/Secretory Proteome of Females and Males of the Hookworm Ancylostoma ceylanicum. Pathogens 2023; 12:95. [PMID: 36678443 PMCID: PMC9865600 DOI: 10.3390/pathogens12010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
The dynamic host-parasite mechanisms underlying hookworm infection establishment and maintenance in mammalian hosts remain poorly understood but are primarily mediated by hookworm's excretory/secretory products (ESPs), which have a wide spectrum of biological functions. We used ultra-high performance mass spectrometry to comprehensively profile and compare female and male ESPs from the zoonotic human hookworm Ancylostoma ceylanicum, which is a natural parasite of dogs, cats, and humans. We improved the genome annotation, decreasing the number of protein-coding genes by 49% while improving completeness from 92 to 96%. Compared to the previous genome annotation, we detected 11% and 10% more spectra in female and male ESPs, respectively, using this improved version, identifying a total of 795 ESPs (70% in both sexes, with the remaining sex-specific). Using functional databases (KEGG, GO and Interpro), common and sex-specific enriched functions were identified. Comparisons with the exclusively human-infective hookworm Necator americanus identified species-specific and conserved ESPs. This is the first study identifying ESPs from female and male A. ceylanicum. The findings provide a deeper understanding of hookworm protein functions that assure long-term host survival and facilitate future engineering of transgenic hookworms and analysis of regulatory elements mediating the high-level expression of ESPs. Furthermore, the findings expand the list of potential vaccine and diagnostic targets and identify biologics that can be explored for anti-inflammatory potential.
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Affiliation(s)
- Samuel C. Uzoechi
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bruce A. Rosa
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kumar Sachin Singh
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Young-Jun Choi
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - R. Reid Townsend
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Sprung
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bin Zhan
- Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria-Elena Bottazzi
- Department of Pediatric Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M. Hawdon
- Department of Microbiology, Immunology & Tropical Medicine, Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Yide Wong
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4878, Australia
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
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Yi X, Liu J, Chen S, Wu H, Liu M, Xu Q, Lei L, Lee S, Zhang B, Kudrna D, Fan W, Wing RA, Wang X, Zhang M, Zhang J, Yang C, Chen N. Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics. G3 (BETHESDA, MD.) 2022; 12:jkac017. [PMID: 35188189 PMCID: PMC8982393 DOI: 10.1093/g3journal/jkac017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/11/2022] [Indexed: 12/30/2022]
Abstract
Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromosome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with 3 published soybeans (WM82, ZH13, and W05), which identified 5 large inversions and 2 large translocations specific to JD17, 20,984-46,912 presence-absence variations spanning 13.1-46.9 Mb in size. A total of 1,695,741-3,664,629 SNPs and 446,689-800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.
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Affiliation(s)
- Xinxin Yi
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jing Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Shengcai Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Hao Wu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Min Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qing Xu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lingshan Lei
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Seunghee Lee
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Bao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Dave Kudrna
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Wei Fan
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Rod A Wing
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, Henan, China
| | - Mengchen Zhang
- Institute of Food and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050031, Hebei, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Chunyan Yang
- Institute of Food and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050031, Hebei, China
| | - Nansheng Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Wang L, Guo S, Zeng B, Wang S, Chen Y, Cheng S, Liu B, Wang C, Wang Y, Meng Q. Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation. MYCOBIOLOGY 2022; 50:69-81. [PMID: 35291590 PMCID: PMC8890563 DOI: 10.1080/12298093.2022.2038844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.
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Affiliation(s)
- Laiyou Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shuxian Guo
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Bo Zeng
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shanshan Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Yan Chen
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shuang Cheng
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Bingbing Liu
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Chunyan Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Yu Wang
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Qingshan Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Bertazzoni S, Jones DAB, Phan HT, Tan KC, Hane JK. Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome. BMC Genomics 2021; 22:382. [PMID: 34034667 PMCID: PMC8146201 DOI: 10.1186/s12864-021-07699-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Background The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised – ToxA, Tox1 and Tox3. Results A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions. Conclusions We present an updated series of genomic resources for P. nodorum Sn15 – an important reference isolate and model necrotroph – with a comprehensive survey of its predicted pathogenicity content. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07699-8.
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Affiliation(s)
| | - Darcy A B Jones
- Centre for Crop & Disease Management, Curtin University, Perth, Australia
| | - Huyen T Phan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - James K Hane
- Centre for Crop & Disease Management, Curtin University, Perth, Australia. .,Curtin Institute for Computation, Curtin University, Perth, Australia.
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Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. PLoS Negl Trop Dis 2020; 14:e0008869. [PMID: 33196647 PMCID: PMC7704054 DOI: 10.1371/journal.pntd.0008869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/30/2020] [Accepted: 10/09/2020] [Indexed: 01/01/2023] Open
Abstract
Filarial parasitic nematodes (Filarioidea) cause substantial disease burden to humans and animals around the world. Recently there has been a coordinated global effort to generate, annotate, and curate genomic data from nematode species of medical and veterinary importance. This has resulted in two chromosome-level assemblies (Brugia malayi and Onchocerca volvulus) and 11 additional draft genomes from Filarioidea. These reference assemblies facilitate comparative genomics to explore basic helminth biology and prioritize new drug and vaccine targets. While the continual improvement of genome contiguity and completeness advances these goals, experimental functional annotation of genes is often hindered by poor gene models. Short-read RNA sequencing data and expressed sequence tags, in cooperation with ab initio prediction algorithms, are employed for gene prediction, but these can result in missing clade-specific genes, fragmented models, imperfect mapping of gene ends, and lack of isoform resolution. Long-read RNA sequencing can overcome these drawbacks and greatly improve gene model quality. Here, we present Iso-Seq data for B. malayi and Dirofilaria immitis, etiological agents of lymphatic filariasis and canine heartworm disease, respectively. These data cover approximately half of the known coding genomes and substantially improve gene models by extending untranslated regions, cataloging novel splice junctions from novel isoforms, and correcting mispredicted junctions. Furthermore, we validated computationally predicted operons, manually curated new operons, and merged fragmented gene models. We carried out analyses of poly(A) tails in both species, leading to the identification of non-canonical poly(A) signals. Finally, we prioritized and assessed known and putative anthelmintic targets, correcting or validating gene models for molecular cloning and target-based anthelmintic screening efforts. Overall, these data significantly improve the catalog of gene models for two important parasites, and they demonstrate how long-read RNA sequencing should be prioritized for ongoing improvement of parasitic nematode genome assemblies. Filarial parasitic nematodes are vector-borne parasites that infect humans and animals. Brugia malayi and Dirofilaria immitis are transmitted by mosquitoes and cause human lymphatic filariasis and canine heartworm disease, respectively. Recent years have seen a dramatic increase in genomic and transcriptomic data sets and the concomitant increase in innovative strategies for drug target identification, validation, and screening. However, while the completeness of genome assemblies of filarial parasitic nematodes has seen steady improvements, the reliability of gene models has not kept pace, hindering cloning efforts. Long-read RNA sequencing technologies are uniquely able to improve gene models, but have not been widely used for the causative agents of neglected tropical diseases. Here, we report the improvement of gene models in both B. malayi and D. immitis by long-read RNA sequencing. We identified novel operons, deprecated false positive operons, identified dozens of novel genes, and described the parameters of polyadenylation. We also focused on putative anthelmintic targets, identifying novel isoforms and correcting gene models. These data substantially increase the trustworthiness of gene models in these two species and demonstrate how long-read sequencing approaches should be prioritized in the continued improvement of genome assemblies and their gene annotations.
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Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, Rollinson D, Brindley PJ, Gasser RB, Young ND. High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Gigascience 2019; 8:giz108. [PMID: 31494670 PMCID: PMC6736295 DOI: 10.1093/gigascience/giz108] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/25/2019] [Accepted: 08/10/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation. FINDINGS Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available. CONCLUSIONS We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.
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Affiliation(s)
- Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Teik Min Chong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Yan Lue Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Bonnie Webster
- Parasites and Vectors Division, The Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - David Rollinson
- Parasites and Vectors Division, The Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - Paul J Brindley
- School of Medicine & Health Sciences, Department of Microbiology, Immunology & Tropical Medicine, George Washington University, 2300 Eye Street, NW, Suite 502, Washington, DC 20037, USA
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
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Hoang NV, Furtado A, Perlo V, Botha FC, Henry RJ. The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome. Front Genet 2019; 10:654. [PMID: 31396260 PMCID: PMC6664245 DOI: 10.3389/fgene.2019.00654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. Here, we analyzed the transcriptome of sugarcane, a highly polyploidy plant genome, by PacBio isoform sequencing (Iso-Seq) of two different cDNA library preparations, with and without a normalization step. The results demonstrated that, while the two libraries included many of the same transcripts, many longer transcripts were removed, and many new generally shorter transcripts were detected by normalization. For the same input cDNA and data yield, the normalized library recovered more total transcript isoforms and number of predicted gene families and orthologous groups, resulting in a higher representation for the sugarcane transcriptome, compared to the non-normalized library. The non-normalized library, on the other hand, included a wider transcript length range with more longer transcripts above ∼1.25 kb and more transcript isoforms per gene family and gene ontology terms per transcript. A large proportion of the unique transcripts comprising ∼52% of the normalized library were expressed at a lower level than the unique transcripts from the non-normalized library, across three tissue types tested including leaf, stalk, and root. About 83% of the total 5,348 predicted long noncoding transcripts was derived from the normalized library, of which ∼80% was derived from the lowly expressed fraction. Functional annotation of the unique transcripts suggested that each library enriched different functional transcript fractions. This demonstrated the complementation of the two approaches in obtaining a complete transcriptome of a complex genome at the sequencing depth used in this study.
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Affiliation(s)
- Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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Cooke I, Mead O, Whalen C, Boote C, Moya A, Ying H, Robbins S, Strugnell JM, Darling A, Miller D, Voolstra CR, Adamska M. Molecular techniques and their limitations shape our view of the holobiont. ZOOLOGY 2019; 137:125695. [PMID: 31759226 DOI: 10.1016/j.zool.2019.125695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 11/26/2022]
Abstract
It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.
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Affiliation(s)
- Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia.
| | - Oliver Mead
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, 2601, Australia; Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Casey Whalen
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Chloë Boote
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Aurelie Moya
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Steven Robbins
- Australian Center for Ecogenomics, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jan M Strugnell
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre of Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, 4810, QLD, Australia; Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, 3083, Australia
| | - Aaron Darling
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | | | - Maja Adamska
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, 2601, Australia; Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
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10
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Jex AR, Gasser RB, Schwarz EM. Transcriptomic Resources for Parasitic Nematodes of Veterinary Importance. Trends Parasitol 2018; 35:72-84. [PMID: 30529253 DOI: 10.1016/j.pt.2018.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/17/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022]
Abstract
Parasitic nematodes are important pathogens of animals, causing diseases that impact on agricultural production worldwide. Research on these worms has been constrained by a lack of genetic and genomic tools. Nonetheless, over the past decade this field has made substantial advances, many of which have been led by transcriptomic sequencing. The present review summarises major transcriptomic studies of veterinary parasitic nematodes in recent years, and comments on overarching themes stemming from this work that inform our understanding of parasitism. Finally, we comment on current, state-of-the-art informatic tools for the analysis of complex worm transcriptomes to extract maximum the molecular information from them.
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Affiliation(s)
- Aaron R Jex
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Erich M Schwarz
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Cornell University, Ithaca, NY 14850, USA
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