Coccidioides fungi are widely distributed in the American continents, with an expanding western range documented by a recently discovered cryptic population of Coccidioides immitis in Washington State. The assembled and annotated reference genome sequence of the soil-derived C. immitis strain WA_211 will support population and functional genomics studies

Barker, Bridget Marie

Stajich, Jason E

Teixeira, Marcus de Melo

English

de Melo Teixeira, Marcus

eScholarship - University of California

UC RiversideUC Riverside Previously Published WorksTitleImproved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington StatePermalinkhttps://escholarship.org/uc/item/1vk654xhJournalMicrobiology Resource Announcements, 8(33)ISSN2576-098XAuthorsde Melo Teixeira, MarcusBarker, Bridget MarieStajich, Jason EPublication Date2019-08-15DOI10.1128/mra.00149-19Copyright InformationThis work is made available under the terms of a Creative Commons Attribution License, available at https://creativecommons.org/licenses/by/4.0/ Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaImproved Reference Genome Sequence of Coccidioides immitisStrain WA_211, Isolated in Washington StateMarcus de Melo Teixeira,a,b Bridget Marie Barker,b Jason E. StajichcaFaculty of Medicine, University of Brasília, Brasília, Federal District, BrazilbThe Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USAcDepartment of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USAABSTRACT Coccidioides fungi are widely distributed in the American continents,with an expanding western range documented by a recently discovered cryptic pop-ulation of Coccidioides immitis in Washington State. The assembled and annotatedreference genome sequence of the soil-derived C. immitis strain WA_211 will supportpopulation and functional genomics studies.Coccidioides immitis and Coccidioides posadasii are fungal species found in desert-likeareas of the American continents (1) and are the causative agents of coccidioido-mycosis or “valley fever.” While C. posadasii is broadly distributed, C. immitis is restrictedto southern California and northern Mexico. Infections due to C. immitis in California areincreasing and reached alarming rates in 2017 (2). The disease range appears to beexpanding, with uncommon autochthonous infections reported in Washington State(3). Washington C. immitis isolates from the soil and clinic are reciprocally monophyleticwithin C. immitis (4, 5) and rarely hybridize with C. posadasii (6). As most assembledgenomes of C. immitis are patient-derived isolates, we annotated and assembled thegenome of the soil-derived strain WA_211, as it represents a unique emerging lineageof C. immitis, for comparative, population, and functional genomics research.The WA_211 strain was cultured from soil on yeast extract medium at 37°C for 5 days(5), and its DNA was isolated after growth on Sabouraud’s medium using the DNeasyblood and tissue kit (Qiagen, Hilden, Germany). The sequencing library was preparedwith a Kapa Biosystems (Woburn, MA) kit (catalog number kk8201) and sequenced withan Illumina MiSeq platform (2  300 bp) (4, 5). The 2.8 million read pairs (1.7 Gbp) wereobtained from the SRA and processed with shovill v.1.0.4 (https://github.com/tseemann/shovill) using “–minlen 500 –trim” and shovill defaults for downstream tools.The shovill pipeline trimmed reads for adaptors and low quality using Trimmomaticv.0.39 (7), corrected bases using Lighter v.1.1.2 (8), and merged overlapping read pairsusing FLASH v.1.2.11 (9) to produce 1.6 million merged reads and 1 million unmergedread pairs. Contigs were assembled with SPAdes v.3.10.1 (10), polished with one roundof Pilon v.1.22 (11), and cleaned of vector sequence and redundant contigs by AAFTFv.0.2.1 (12), using default parameters. The 297 contigs were scaffolded to the C. immitisRS genome (GenBank accession number AAEC00000000) (13) with RagOO v.1.1 (14),with default parameters, to produce a 27.4-Mb assembly of 62 scaffolds (N50, 3.79 Mb;longest scaffold length, 8.24 Mb; GC content, 46.4%). This scaffolding assumes thecolinearity of WA_211 and RS, but no breakpoints were observed within contigs in acomparison of a dotplot by D-GENIES (15).The genome contains 15% repetitive sequences masked by RepeatMasker v.open-4.0.7 using a Coccidioides repeat element library (16). Genes were predicted in themasked genome with Funannotate v.1.5.2 (17). Gene prediction parameters weregenerated by “funannotate train” using alignments of C. immitis spherule and hyphalCitation Teixeira MDM, Barker BM, Stajich JE.2019. Improved reference genome sequenceof Coccidioides immitis strain WA_211, isolatedin Washington State. Microbiol ResourAnnounc 8:e00149-19. https://doi.org/10.1128/MRA.00149-19.Editor Christina A. Cuomo, Broad InstituteCopyright © 2019 Teixeira et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Jason E. Stajich,jason.stajich@ucr.edu.Received 14 February 2019Accepted 18 July 2019Published 15 August 2019GENOME SEQUENCEScrossmVolume 8 Issue 33 e00149-19 mra.asm.org 1 on August 26, 2019 at UNIV OF CALIFORNIA RIVERSIDEhttp://mra.asm.org/Downloaded from RNA sequencing (RNA-seq) (18). Gene prediction (“funannotate predict”) was per-formed running ab initio predictors Augustus (19), SNAP v.2013-11-29 (20), Coding-Quarry v.2.0 (21), and GeneMark-ES v.4.33 (22) using exon hints from spliced alignmentsof transcripts, Onygenales proteins (13, 23, 24), and the Swiss-Prot database (25).Consensus gene models were generated by Funannotate running EVidenceModelerv.1.1.1 (26). Funannotate assigned putative gene products by searches to the Swiss-Prot, InterPro (27), eggNOG (28), MEROPS (29), and dbCAN (30) databases, using defaultparameters. A total of 7,815 protein-coding gene models were predicted, of which5,477 had InterPro domains. Twenty-one secondary metabolite clusters were predictedby antiSMASH 4.0 (31), comprising 8 polyketide synthases (PKS), 4 nonribosomalpeptide synthetases (NRPS), 2 hybrid PKS-NRPS, 1 indole-NRPS, 3 terpene, and 4 “other”type clusters. The annotation and assembly pipeline steps, full parameters, and log filesare archived in the GitHub repository (32).Data availability. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number RHJW00000000. The version described in thispaper is version RHJW02000000. The genomic sequence reads used in this assemblywere previously deposited under SRA project accession number SRR1292227, and theRNA-seq reads used had been deposited under BioProject number PRJNA169242 andSRA accession number SRP013923.ACKNOWLEDGMENTSGenome annotation was performed on the UC Riverside High-Performance Com-putational Cluster supported by NSF grant DBI-1429826 and NIH grant S10-OD016290.B.M.B. was supported by NIH grant R21AI28536. J.E.S. was supported by funds from theUniversity of California Multicampus Research Programs and Initiatives “Center forValley Fever Research” and the U.S. Department of Agriculture, National Institute ofFood and Agriculture Hatch project CA-R-PPA-5062-H.REFERENCES1. Lewis ERG, Bowers JR, Barker BM. 2015. Dust devil: the life and times ofthe fungus that causes valley fever. PLoS Pathog 11:e1004762. https://doi.org/10.1371/journal.ppat.1004762.2. California Department of Public Health. 2019. Epidemiologic summary ofcoccidioidomycosis in California, 2017. Infectious Diseases Branch, Divi-sion of Communicable Disease Control, Center for Infectious Diseases,California Department of Public Health, Sacramento, CA. https://www.cdph.ca.gov/Programs/CID/DCDC/CDPH%20Document%20Library/CocciEpiSummary2017.pdf.3. James AE, Pastenkos G, Bradway D, Baszler T. 2019. Autochthonoustransmission of Coccidioides in animals, Washington, USA. Emerg InfectDis J 25:123. https://doi.org/10.3201/eid2501.180411.4. Engelthaler DM, Roe CC, Hepp CM, Teixeira M, Driebe EM, Schupp JM,Gade L, Waddell V, Komatsu K, Arathoon E, Logemann H, Thompson GR,III, Chiller T, Barker B, Keim P, Litvintseva AP. 2016. Local populationstructure and patterns of Western Hemisphere dispersal for Coccidioidesspp., the fungal cause of valley fever. mBio 7:e00550-16. https://doi.org/10.1128/mBio.00550-16.5. Litvintseva AP, Marsden-Haug N, Hurst S, Hill H, Gade L, Driebe EM,Ralston C, Roe C, Barker BM, Goldoft M, Keim P, Wohrle R, Thompson GR,III, Engelthaler DM, Brandt ME, Chiller T. 2015. Valley fever: finding newplaces for an old disease: Coccidioides immitis found in Washington Statesoil associated with recent human infection. Clin Infect Dis 60:e1– e3.https://doi.org/10.1093/cid/ciu681.6. Maxwell CS, Mattox K, Turissini DA, Teixeira MM, Barker BM, Matute DR.2019. Gene exchange between two divergent species of the fungalhuman pathogen, Coccidioides. Evolution 73:42–58. https://doi.org/10.1111/evo.13643.7. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer forIllumina sequence data. Bioinformatics 30:2114 –2120. https://doi.org/10.1093/bioinformatics/btu170.8. Song L, Florea L, Langmead B. 2014. Lighter: fast and memory-efficientsequencing error correction without counting. Genome Biol 15:509.https://doi.org/10.1186/s13059-014-0509-9.9. Magoc T, Salzberg SL. 2011. FLASH: fast length adjustment of short readsto improve genome assemblies. Bioinformatics 27:2957–2963. https://doi.org/10.1093/bioinformatics/btr507.10. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV,Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell sequenc-ing. J Comput Biol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021.11. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, CuomoCA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integratedtool for comprehensive microbial variant detection and genome assem-bly improvement. PLoS One 9:e112963. https://doi.org/10.1371/journal.pone.0112963.12. Stajich JE, Palmer J. 2018. AAFTF: Automated Assembly for the Fungi,v0.2.1. https://doi.org/10.5281/zenodo.1658103.13. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS,Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Musze-wska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN,Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. 2009.Comparative genomic analyses of the human fungal pathogens Coccid-ioides and their relatives. Genome Res 19:1722–1731. https://doi.org/10.1101/gr.087551.108.14. Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ,Lippman ZB, Schatz MC. 2019. Fast and accurate reference-guided scaf-folding of draft genomes. bioRxiv. https://doi.org/10.1101/519637.15. Cabanettes F, Klopp C. 2018. D-GENIES: dot plot large genomes in aninteractive, efficient and simple way. PeerJ 6:e4958. https://doi.org/10.7717/peerj.4958.16. Kirkland TN, Muszewska A, Stajich JE. 2018. Analysis of transposableelements in Coccidioides species. J Fungi 4:13. https://doi.org/10.3390/jof4010013.17. Palmer JM, Stajich JE. 2018. Funannotate: eukaryotic genome anno-tation pipeline. http://funannotate.readthedocs.io.18. Whiston E, Zhang Wise H, Sharpton TJ, Jui G, Cole GT, Taylor JW. 2012.Teixeira et al.Volume 8 Issue 33 e00149-19 mra.asm.org 2 on August 26, 2019 at UNIV OF CALIFORNIA RIVERSIDEhttp://mra.asm.org/Downloaded from Comparative transcriptomics of the saprobic and parasitic growthphases in Coccidioides spp. PLoS One 7:e41034. https://doi.org/10.1371/journal.pone.0041034.19. Stanke M, Waack S. 2003. Gene prediction with a hidden Markov modeland a new intron submodel. Bioinformatics 19:ii215–ii225. https://doi.org/10.1093/bioinformatics/btg1080.20. Korf I. 2004. Gene finding in novel genomes. BMC Bioinformatics 5:59.https://doi.org/10.1186/1471-2105-5-59.21. Testa AC, Hane JK, Ellwood SR, Oliver RP. 2015. CodingQuarry: highlyaccurate hidden Markov model gene prediction in fungal genomesusing RNA-seq transcripts. BMC Genomics 16:170. https://doi.org/10.1186/s12864-015-1344-4.22. Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. 2008.Gene prediction in novel fungal genomes using an ab initio algorithmwith unsupervised training. Genome Res 18:1979 –1990. https://doi.org/10.1101/gr.081612.108.23. Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, HungCY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, AbouelleilA, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP,Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, HennMR, Taylor JW, Rounsley SD. 2010. Population genomic sequencing ofCoccidioides fungi reveals recent hybridization and transposon control.Genome Res 20:938 –946. https://doi.org/10.1101/gr.103911.109.24. Mitchell NM, Sherrard AL, Dasari S, Magee DM, Grys TE, Lake DF. 2018.Proteogenomic re-annotation of Coccidioides posadasii strain Silveira.Proteomics 18:1700173. https://doi.org/10.1002/pmic.201700173.25. Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S,Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F,Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, vanNimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V,Appel RD. 2014. Fifteen years SIB Swiss Institute of Bioinformatics: lifescience databases, tools and support. Nucleic Acids Res 42:W436 –W441.https://doi.org/10.1093/nar/gku380.26. Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, BuellCR, Wortman JR. 2008. Automated eukaryotic gene structure annotationusing EVidenceModeler and the Program to Assemble Spliced Align-ments. Genome Biol 9:R7. https://doi.org/10.1186/gb-2008-9-1-r7.27. 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/btu031.28. Huerta-Cepas J, Szklarczyk D, Heller D, Hernandez-Plaza A, ForslundSK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C,Bork P. 2019. eggNOG 5.0: a hierarchical, functionally and phyloge-netically annotated orthology resource based on 5090 organisms and2502 viruses. Nucleic Acids Res 47:D309 –D314. https://doi.org/10.1093/nar/gky1085.29. Rawlings ND, Waller M, Barrett AJ, Bateman A. 2014. MEROPS: thedatabase of proteolytic enzymes, their substrates and inhibitors. NucleicAcids Res 42:D503–D509. https://doi.org/10.1093/nar/gkt953.30. Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. 2012. dbCAN: a Web resourcefor automated carbohydrate-active enzyme annotation. Nucleic AcidsRes 40:W445–W451. https://doi.org/10.1093/nar/gks479.31. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY,Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, MedemaMH. 2015. antiSMASH 3.0 —a comprehensive resource for the genomemining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243.https://doi.org/10.1093/nar/gkv437.32. Stajich JE. 2019. stajichlab/Coccidioides_immitis_211: Coccidioidesimmitis 211 annotation for MRA. https://zenodo.org/record/3300712#.XTemWB1Ki1s.Microbiology Resource AnnouncementVolume 8 Issue 33 e00149-19 mra.asm.org 3 on August 26, 2019 at UNIV OF CALIFORNIA RIVERSIDEhttp://mra.asm.org/Downloaded from 

Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State

Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State.

https://escholarship.org/uc/item/1vk654xh

Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State.

Abstract

Similar works

Full text

Available Versions

eScholarship - University of California

eScholarship - University of California