Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious,
results in intense pruritus, and represents a major welfare and economic concern. Here,
we report the first draft genome assembly and gene prediction of P. ovis based on
PacBio de novo sequencing. The  63.2-Mb genome encodes 12,041 protein-coding
genes.http://genomea.asm.orgam2019Genetic

Bartley, Kathryn

Burgess, Stewart T.G.

Haldenby, Sam

Hughes, Margaret

Marr, Edward J.

Nisbet, Alasdair J.

Prickett, Jessica C.

Rombauts, Stephane

Thi Le, Phuong

Van de Peer, Yves

Van Leeuwen, Thomas

Weaver, Robert J.

Wright, Harry W.

UPSpace at the University of Pretoria

Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovisStewart T. G. Burgess,a Kathryn Bartley,a Edward J. Marr,a Harry W. Wright,a Robert J. Weaver,j Jessica C. Prickett,jMargaret Hughes,b Sam Haldenby,b Phuong Thi Le,c,d,e,f,g Stephane Rombauts,c,d,e Thomas Van Leeuwen,iYves Van de Peer,c,d,e,h Alasdair J. NisbetaaMoredun Research Institute (MRI), Edinburgh, United KingdombInstitute of Integrative Biology, University of Liverpool, Liverpool, United KingdomcDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, BelgiumdVIB Center for Plant Systems Biology, Ghent, BelgiumeBioinformatics Institute Ghent, Ghent University, Ghent, BelgiumfNutriomics: Nutrition and Obesity–Systemic Approaches, Hôpital la Pitié Salpêtrière, Paris, FrancegIntegromics, Hôpital la Pitié Salpêtrière, Paris, FrancehDepartment of Genetics, University of Pretoria, Pretoria, South AfricaiDepartment of Plants and Crops, Ghent University, Ghent, BelgiumjFera Science Ltd., York, United KingdomABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious,results in intense pruritus, and represents a major welfare and economic concern. Here,we report the first draft genome assembly and gene prediction of P. ovis based onPacBio de novo sequencing. The 63.2-Mb genome encodes 12,041 protein-codinggenes.Sheep scab, caused by the ectoparasitic mite Psoroptes ovis, is characterized bypruritus and skin irritation and is a major welfare and economic concern for thelivestock industry (1, 2). Control relies on injectable macrocyclic lactone-based endec-tocides and organophosphate dips, but concerns over residues, environmental con-tamination, and the development of resistance threaten the sustainability of thisapproach and have highlighted interest in developing alternative control methods (3).However, the development of novel vaccines and identification of potential chemo-therapeutic targets has been hampered by the lack of transcriptomic and genomicresources for P. ovis.Adult female P. ovis mites (3,200, Moredun isolate) were harvested, as previouslydescribed (4), from experimentally infested sheep. Ethical approval was obtained fromthe Moredun Research Institute’s local ethics committee (E03/17). Any contaminatinghost material was removed by extensive washing before mites were cleaned with 0.01%Triton X-100. Mites were ground under liquid nitrogen in a prechilled (80°C) pestleand mortar, and genomic DNA (gDNA) was extracted using the SDS-proteinase Kmethod (5). DNA integrity was assessed on an Agilent Bioanalyzer and quantified usinga Qubit double-stranded DNA (dsDNA) broad-range (BR) assay kit. PacBio sequencinglibraries were generated from high-molecular-weight gDNA using the PacBio SMRTbelltemplate prep kit version 1.0 according to the manufacturer’s instructions, and se-quencing was performed using 10 single-molecule real-time (SMRT) cells on the PacBioRS II platform. Genomic sequences were assembled using the Hierarchical GenomeAssembly Process version 3 (HGAP3) pipeline embedded in PacBio SMRT Portal version2.3.0.140936.p0 (6). Filtered subreads were aligned to contigs using BLASR (7), and thecorrected consensus reads were generated using Quiver (6). The contaminating se-quences were identified using BLASTx searches of the NCBI prokaryotic RefSeq data set,combined with tetramer frequencies and read coverage for emergent self-organizingReceived 28 February 2018 Accepted 17March 2018 Published 19 April 2018Citation Burgess STG, Bartley K, Marr EJ, WrightHW, Weaver RJ, Prickett JC, Hughes M,Haldenby S, Thi Le P, Rombauts S, VanLeeuwen T, Van de Peer Y, Nisbet AJ. 2018.Draft genome assembly of the sheep scabmite, Psoroptes ovis. Genome Announc 6:e00265-18. https://doi.org/10.1128/genomeA.00265-18.Copyright © 2018 Burgess et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Stewart T. G.Burgess, stewart.burgess@moredun.ac.uk.EUKARYOTEScrossmVolume 6 Issue 16 e00265-18 genomea.asm.org 1map (ESOM) clustering, and removed from the final polished assembly, which con-tained 93 contigs, with an N50 value of 2,279,290 bp and an L50 value of 8 contigs (8,9, 10). The largest scaffold was 5,538,194 bp and, as with other closely related mites, theGC content of the coding sequences was 33.6%. The total genome size was estimatedto be 63.2 Mb, and 14 Gb of PacBio data provided 220-fold coverage.Gene prediction was performed with EUGENE version 4.1 (11), which was pretrainedon Dermatophagoides farinae (BioProject number PRJNA379991). The extrinsic dataused to support the ab initio gene models were protein sets from Tetranychus urticae,RefSeq data (invertebrates), D. farinae predictions, and transcript data from P. ovis. Thepipeline identified 12,041 predicted protein-coding genes, with an average length1,928.21 bp, in agreement with the predicted average gene size (1,800 bp) for agenome of 63.2 Mb. The presence of core eukaryotic protein-coding genes wasassessed with BUSCO version 1.22 (arthropod set) (12) with 91% of arthropod single-copy orthologs present. Predicted genes were functionally annotated by combiningInterProScan (13) and reciprocal best BLAST hits, generating sensible gene functiondescriptions. Potential secretion signals, transmembrane helices, and other domainswere predicted in PHOBIUS (14). BLAST hits against the NCBI nonredundant (nr)database (July 2016) were identified for 9,964 genes, and gene ontology (GO) assess-ment was performed in Blast2GO (15), resulting in the assignment of GO terms for 7,957genes and functional annotation for 5,217 genes.Accession number(s). This whole-genome shotgun project has been deposited atDDBJ/ENA/GenBank under the accession number PQWQ00000000. The version de-scribed in this paper is the first version, PQWQ01000000.REFERENCES1. Kirkwood AC. 1986. History, biology and control of sheep scab. ParasitolToday 2:302–307. https://doi.org/10.1016/0169-4758(86)90124-9.2. Nieuwhof GJ, Bishop SC. 2005. Costs of the major endemic diseases ofsheep in Great Britain and the potential benefits of reduction in diseaseimpact. Anim Sci 81:23–29. https://doi.org/10.1079/ASC41010023.3. Nisbet AJ, Huntley JF. 2006. Progress and opportunities in the develop-ment of vaccines against mites, fleas and myiasis-causing flies of veter-inary importance. Parasite Immunol 28:165–172. https://doi.org/10.1111/j.1365-3024.2006.00803.x.4. Burgess ST, Frew D, Nunn F, Watkins CA, McNeilly TN, Nisbet AJ, HuntleyJF. 2010. Transcriptomic analysis of the temporal host response to skininfestation with the ectoparasitic mite Psoroptes ovis. BMC Genomics11:624. https://doi.org/10.1186/1471-2164-11-624.5. Sambrook J, Russell DW. 2001. Molecular cloning: a laboratorymanual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold SpringHarbor, NY.6. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A,Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhy-brid, finished microbial genome assemblies from long-read SMRT sequenc-ing data. Nat Methods 10:563–569. https://doi.org/10.1038/nmeth.2474.7. Chaisson MJ, Tesler G. 2012. Mapping single molecule sequencing readsusing basic local alignment with successive refinement (BLASR): appli-cation and theory. BMC Bioinformatics 13:238. https://doi.org/10.1186/1471-2105-13-238.8. Ultsch A, Moerchen F. 2005. ESOM-Maps: tools for clustering, visualiza-tion, and classification with Emergent SOM, technical report no. 46.Department of Mathematics and Computer Science, University of Mar-burg, Marburg, Germany.9. Dick GJ, Andersson A, Baker BJ, Simmons SS, Thomas BC, Yelton AP,Banfield JF. 2009. Community-wide analysis of microbial genome se-quence signatures. Genome Biol 10:R85. https://doi.org/10.1186/gb-2009-10-8-r85.10. Kang DD, Froula J, Egan R, Wang Z. 2015. MetaBAT, an efficient tool foraccurately reconstructing single genomes from complex microbial com-munities. PeerJ 3:e1165. https://doi.org/10.7717/peerj.1165.11. Foissac S, Gouzy J, Rombauts S, Mathe C, Amselem J, Sterck L, de PeerY, Rouze P, Schiex T. 2008. Genome annotation in plants and fungi:EuGene as a model platform. Curr Bioinform 3:87–97. https://doi.org/10.2174/157489308784340702.12. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.2015. BUSCO: assessing genome assembly and annotation complete-ness with single-copy orthologs. Bioinformatics 31:3210 –3212. https://doi.org/10.1093/bioinformatics/btv351.13. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H,Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A,Scheremetjew M, Yong SY, Lopez R, Hunter S. 2014. InterProScan 5:genome-scale protein function classification. Bioinformatics 30:1236–1240.https://doi.org/10.1093/bioinformatics/btu031.14. Käll L, Krogh A, Sonnhammer ELL. 2004. A combined transmembranetopology and signal peptide prediction method. J Mol Biol 338:1027–1036. https://doi.org/10.1016/j.jmb.2004.03.016.15. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. 2005.Blast2GO: a universal tool for annotation, visualization and analysis infunctional genomics research. Bioinformatics 21:3674 –3676. https://doi.org/10.1093/bioinformatics/bti610.Burgess et al.Volume 6 Issue 16 e00265-18 genomea.asm.org 2

Draft genome assembly of the sheep scab mite, Psoroptes ovis

https://repository.up.ac.za/bitstream/2263/71827/1/Burgess_Distribution_2018.pdf

Draft genome assembly of the sheep scab mite, Psoroptes ovis

Abstract

Similar works

Full text

Available Versions

UPSpace at the University of Pretoria