Thines M, Choi YJ. Evolution, diversity, and taxonomy of the Peronosporaceae, with focus on the genus Peronospora. Phytopathology. 2016;106(1):6–18.
Article
PubMed
Google Scholar
McCarthy CGP, Fitzpatrick DA. Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes. mSphere. 2017;2(2):e00095–17.
Article
PubMed
PubMed Central
Google Scholar
Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, et al. Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. BMC Genomics. 2015;16(1):741.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ye W, Wang Y, Shen D, Li D, Pu T, Jiang Z, Zhang Z, Zheng X, Tyler BM, Wang Y. Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics. Mol Plant-Microbe Interact. 2016;29(7):573–83.
Article
CAS
PubMed
Google Scholar
Correll JC, Bluhm BH, Feng C, Lamour K, du Toit LJ, Koike ST. Spinach: better management of downy mildew and white rust through genomics. Eur J Plant Pathol. 2011;129(2):193–205.
Article
Google Scholar
Byford W. Host specialization of Peronospora farinosa on Beta, Spinacia and Chenopodium. Trans Br Mycol Soc. 1967;50(4):603–7.
Article
Google Scholar
Klosterman SJ, Anchieta A, McRoberts N, Koike ST, Subbarao KV, Voglmayr H, Choi YJ, Thines M, Martin FN. Coupling spore traps and quantitative PCR assays for detection of the downy mildew pathogens of spinach (Peronospora effusa) and beet (P. schachtii). Phytopathology. 2014;104(12):1349–59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feng C, Correll JC, Kammeijer KE, Koike ST. Identification of new races and deviating strains of the spinach downy mildew pathogen Peronospora farinosa f. sp. spinaciae. Plant Dis. 2013;98(1):145–52.
Article
Google Scholar
Feng C, Saito K, Liu B, Manley A, Kammeijer K, Mauzey SJ, Koike S, Correll JC. New races and novel strains of the spinach downy mildew pathogen Peronospora effusa. Plant Dis. 2018;102(3):613–8.
Article
PubMed
Google Scholar
Van Asch MAJ, Frinking HD. Heterothallism in Peronospora farinosa f.sp. spinaciae. Trans Br Mycol Soc. 1988;91(4):692–3.
Article
Google Scholar
Choi YJ, Hong SB, Shin HD. Re-consideration of Peronospora farinosa infecting Spinacia oleracea as distinct species, Peronospora effusa. Mycol Res. 2007;111(Pt 4):381–91.
Article
CAS
PubMed
Google Scholar
Choi YJ, Klosterman SJ, Kummer V, Voglmayr H, Shin HD, Thines M. Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach. Mol Phylogenet Evol. 2015;86:24–34.
Article
PubMed
PubMed Central
Google Scholar
Choi Y-J, Thines M. (2288) Proposal to reject the name Botrytis farinosa (Peronospora farinosa) (Peronosporaceae: oomycetes). Taxon. 2014;63(3):675–6.
Article
Google Scholar
Minor T Bond J. Vegetables and Pulses Outlook. Washington DC: U.S. Department of Agriculture, Economic Research Service, Situation and Outlook, VGS-358. 2017. Retrieved from: http://usda.mannlib.cornell.edu/usda/ers/VGS//2010s/2017/VGS-04-28-2017.pdf. Accessed 8 Nov 2018.
Koike S, Cahn M, Cantwell M, Fennimore S, Lestrange M, Natwick E, Smith RF, Takele E. Spinach production in California. Univ Calif Agric Nat Resour Publ. 2011;7212. https://escholarship.org/uc/item/67w2p91c. Accessed 8 Nov 2018.
Xu C, Jiao C, Sun H, Cai X, Wang X, Ge C, Zheng Y, Liu W, Sun X, Xu Y, et al. Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nat Commun. 2017;8:15275.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brandenberger L, Correll J, Morelock T. Identification of and cultivar reactions to a new race (race 4) of Peronospora farinosa f. sp. spinaciae on spinach in the United States. Plant Dis. 1991;75(6):630–4.
Article
Google Scholar
Correll J. Denomination of Pfs: 17, a new race of downy mildew in spinach. In: ANR Blogs: University of California Cooperative Extension, Division of Agriculture and Natural Resources; 2018. https://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=26906. Accessed 8 Nov 2018.
Lyon R, Correll J, Feng C, Bluhm B, Shrestha S, Shi A, Lamour K. Population structure of Peronospora effusa in the southwestern United States. PLoS One. 2016;11(2):e0148385.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kunjeti SG, Anchieta A, Subbarao KV, Koike ST, Klosterman SJ. Plasmolysis and vital staining reveal viable oospores of Peronospora effusa in spinach seed lots. Plant Dis. 2015;100(1):59–65.
Article
CAS
PubMed
Google Scholar
Inaba T, Morinaka T. Heterothallism in Peronospora effusa. Phytopathology. 1984;74(2):214–6.
Article
Google Scholar
Voglmayr H, Greilhuber J. Genome size determination in peronosporales (Oomycota) by Feulgen image analysis. Fungal Genet Biol. 1998;25(3):181–95.
Article
CAS
PubMed
Google Scholar
Derevnina L, Chin-Wo-Reyes S, Martin F, Wood K, Froenicke L, Spring O, Michelmore R. Genome sequence and architecture of the tobacco downy mildew pathogen Peronospora tabacina. Mol Plant-Microbe Interact. 2015;28(11):1198–215.
Article
CAS
PubMed
Google Scholar
Dussert Y, Gouzy J, Richart-Cervera S, Mazet ID, Delière L, Couture C, Legrand L, Piron M-C, Mestre P, Delmotte F. Draft genome sequence of Plasmopara viticola, the grapevine downy mildew pathogen. Genome Announc. 2016;4(5):e00987–16.
Article
PubMed
PubMed Central
Google Scholar
Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep. 2017;7:46553.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2.
Article
CAS
PubMed
Google Scholar
Pryszcz LP, Gabaldon T. Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Res. 2016;44(12):e113.
Article
PubMed
PubMed Central
CAS
Google Scholar
Huang S, Kang M, Xu A. HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics. 2017;33:2577–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011;27(6):764–70.
Article
PubMed
PubMed Central
CAS
Google Scholar
Soderlund C, Nelson W, Shoemaker A, Paterson A. SyMAP: a system for discovering and viewing syntenic regions of FPC maps. Genome Res. 2006;16(9):1159–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smit A, Hubley R. RepeatModeler Open-1.0.; 2008-2015.
Google Scholar
Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004;5(1):59.
Article
PubMed
PubMed Central
Google Scholar
Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008;18(1):188–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42(D1):D222–30.
Article
CAS
PubMed
Google Scholar
Mapleson D, Garcia Accinelli G, Kettleborough G, Wright J, Clavijo BJ. KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies. Bioinformatics. 2017;33(4):574–6.
CAS
PubMed
Google Scholar
Grayburn WS, Hudspeth DS, Gane MK, Hudspeth ME. The mitochondrial genome of Saprolegnia ferax: organization, gene content and nucleotide sequence. Mycologia. 2004;96(5):981–9.
Article
CAS
PubMed
Google Scholar
Levesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 2010;11:R73.
Article
PubMed
PubMed Central
CAS
Google Scholar
Makkonen J, Vesterbacka A, Martin F, Jussila J, Diéguez-Uribeondo J, Kortet R, Kokko H. Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans. Sci Rep. 2016;6:36089.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martin FN, Bensasson D, Tyler BM, Boore JL. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Curr Genet. 2007;51(5):285–96.
Article
CAS
PubMed
Google Scholar
O'Brien MA, Misner I, Lane CE. Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata. J Eukaryot Microbiol. 2014;61(2):146–54.
Article
CAS
PubMed
Google Scholar
Yuan X, Feng C, Zhang Z, Zhang C. Complete mitochondrial genome of Phytophthora nicotianae and identification of molecular markers for the oomycetes. Front Microbiol. 2017;8:1484.
Article
PubMed
PubMed Central
Google Scholar
Bertier L, Leus L, D’hondt L, de Cock AWAM, Höfte M. Host adaptation and speciation through hybridization and polyploidy in Phytophthora. PLoS One. 2013;8(12):e85385.
Article
PubMed
PubMed Central
CAS
Google Scholar
Whittaker SL, Shattock RC, Shaw DS. Variation in DNA content of nuclei of Phytophthora infestans as measured by a microfluorimetric method using the fluorochrome DAPI. Mycol Res. 1991;95(5):602–10.
Article
Google Scholar
Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W. Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science (New York, NY). 2010;330:1549–51.
Article
CAS
Google Scholar
Kasuga T, Bui M, Bernhardt E, Swiecki T, Aram K, Cano LM, Webber J, Brasier C, Press C, Grünwald NJ, et al. Host-induced aneuploidy and phenotypic diversification in the sudden oak death pathogen Phytophthora ramorum. BMC Genomics. 2016;17(1):385.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li Y, Shen H, Zhou Q, Qian K, van der Lee T, Huang S. Changing ploidy as a strategy: the Irish potato famine pathogen shifts ploidy in relation to its sexuality. Mol Plant-Microbe Interact. 2016;30(1):45–52.
Article
Google Scholar
Spring O, Zipper R. Evidence for asexual genetic recombination in sunflower downy mildew, Plasmopara halstedii. Mycol Res. 2006;110(6):657–63.
Article
CAS
PubMed
Google Scholar
Spring O, Zipper R. Asexual recombinants of Plasmopara halstedii Pathotypes from dual infection of sunflower. PLoS One. 2016;11(12):e0167015.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife. 2013;2:e00731.
Article
PubMed
PubMed Central
Google Scholar
Jiao W-B, Schneeberger K. The impact of third generation genomic technologies on plant genome assembly. Curr Opin Plant Biol. 2017;36:64–70.
Article
CAS
PubMed
Google Scholar
Cabral A, Stassen JHM, Seidl MF, Bautor J, Parker JE, Van den Ackerveken G. Identification of Hyaloperonospora arabidopsidis transcript sequences expressed during infection reveals isolate-specific effectors. PLoS One. 2011;6(5):e19328.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stassen JH, Boer E, Vergeer PW, Andel A, Ellendorff U, Pelgrom K, Pel M, Schut J, Zonneveld O, Jeuken MJ. Specific in planta recognition of two GKLR proteins of the downy mildew Bremia lactucae revealed in a large effector screen in lettuce. Mol Plant-Microbe Interact. 2013;26(11):1259–70.
Article
CAS
PubMed
Google Scholar
Sun J, Gao Z, Zhang X, Zou X, Cao L, Wang J. Transcriptome analysis of Phytophthora litchii reveals pathogenicity arsenals and confirms taxonomic status. PLoS One. 2017;12(6):e0178245.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ah-Fong AMV, Kim KS, Judelson HS. RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development. BMC Genomics. 2017;18(1):198.
Article
PubMed
PubMed Central
CAS
Google Scholar
Judelson HS. Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution. Eukaryot Cell. 2012;11(11):1304–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee S-J, Rose JKC. Mediation of the transition from biotrophy to necrotrophy in hemibiotrophic plant pathogens by secreted effector proteins. Plant Signal Behav. 2010;5(6):769–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Catal M, King L, Tumbalam P, Wiriyajitsomboon P, Kirk WW, Adams GC. Heterokaryotic nuclear conditions and a heterogeneous nuclear population are observed by flow cytometry in Phytophthora infestans. Cytometry A. 2010;77(8):769–75.
Article
PubMed
CAS
Google Scholar
Hudspeth ME, Shumard DS, Bradford CJ, Grossman LI. Organization of Achlya mtDNA: a population with two orientations and a large inverted repeat containing the rRNA genes. Proc Natl Acad Sci U S A. 1983;80(1):142–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
McNabb SA, Boyd DA, Belkhiri A, Dick MW, Klassen GR. An inverted repeat comprises more than three-quarters of the mitochondrial genome in two species of Pythiumm. Curr Genet. 1987;12(3):205–8.
Article
CAS
Google Scholar
Martin FN. Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum. Curr Genet. 2008;54(1):23–34.
Article
CAS
PubMed
Google Scholar
Bennett MD, Leitch IJ, Price HJ, Johnston JS. Comparisons with Caenorhabditis (∼100 Mb) and drosophila (∼175 Mb) using flow cytometry show genome size in Arabidopsis to be ∼157 Mb and thus ∼25% larger than the Arabidopsis genome initiative estimate of ∼125 Mb. Ann Bot. 2003;91(5):547–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bushnell B. BBMap short read aligner. Berkeley: University of California; 2016. https://sourceforge.net/projects/bbmap. Accessed 8 Nov 2018.
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM: arXiv preprint arXiv:1303.3997; 2013.
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29(21):2669–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res. 2016;44(19):e147.
PubMed
PubMed Central
Google Scholar
Smit A, Hubley R, Green P. RepeatMasker open-4.0.; 2013-2015.
Google Scholar
Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res. 1999;27(11):2369–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 2013;14(5):R47.
Article
PubMed
PubMed Central
Google Scholar
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience. 2013;2(1):10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16(1):157.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30(9):1236–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004;340(4):783–95.
Article
PubMed
CAS
Google Scholar
Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8(10):785–6.
Article
CAS
PubMed
Google Scholar
Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 2000;300(4):1005–16.
Article
CAS
PubMed
Google Scholar
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(Web Server issue):W29–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boutemy LS, King SRF, Win J, Hughes RK, Clarke TA, Blumenschein TMA, Kamoun S, Banfield MJ. Structures of RXLR Effector Proteins. J Biol Chem. 2011;286(41):35834–842.
Article
CAS
PubMed
PubMed Central
Google Scholar
Win J, Krasileva KV, Kamoun S, Shirasu K, Staskawicz BJ, Banfield MJ. Sequence divergent RXLR effectors share a structural fold conserved across plant pathogenic oomycete species. PLoS Pathog. 2012;8(1):e1002400.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fawke S, Doumane M, Schornack S. Oomycete interactions with plants: infection strategies and resistance principles. Microbiol Mol Biol Rev. 2015;79(3):263–80.
Article
PubMed
PubMed Central
Google Scholar
Mestre P, Carrere S, Gouzy J, Piron MC, Tourvieille de Labrouhe D, Vincourt P, Delmotte F, Godiard L. Comparative analysis of expressed CRN and RXLR effectors from two Plasmopara species causing grapevine and sunflower downy mildew. Plant Pathol. 2016;65(5):767–81.
Article
CAS
Google Scholar
Stassen JHM. Identification and functional analysis of downy mildew effectors in lettuce and Arabidopsis; 2012.
Google Scholar
Tian M, Win J, Savory E, Burkhardt A, Held M, Brandizzi F, Day B. 454 genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif. Mol Plant-Microbe Interact. 2011;24(5):543–53.
Article
CAS
PubMed
Google Scholar
Quinlan AR. BEDTools: the Swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11.12.11–34 editoral board, Andreas D Baxevanis [et al].
Article
Google Scholar
Burkhardt A, Buchanan A, Cumbie JS, Savory EA, Chang JH, Day B. Alternative splicing in the obligate biotrophic oomycete pathogen Pseudoperonospora cubensis. Mol Plant-Microbe Interact. 2015;28(3):298–309.
Article
CAS
PubMed
Google Scholar
Savory EA, Zou C, Adhikari BN, Hamilton JP, Buell CR, Shiu S-H, Day B. Alternative splicing of a multi-drug transporter from Pseudoperonospora cubensis generates an RXLR effector protein that elicits a rapid cell death. PLoS One. 2012;7(4):e34701.
Article
CAS
PubMed
PubMed Central
Google Scholar
The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45(D1):D158–69.
Article
CAS
Google Scholar
GAG: the Genome Annotation Generator (Version 1.0) [Software] [http://genomeannotation.github.io/GAG]. Accessed 8 Nov 2018.
Annie: the ANNotation Information Extractor (Version 1.0) [Software] [http://genomeannotation.github.io/annie]. Accessed 8 Nov 2018.
Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S, Kahn D. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 2005;33(Database issue):D212–5.
Article
CAS
PubMed
Google Scholar
Kasuya A, Thornton JM. Three-dimensional structure analysis of PROSITE patterns. J Mol Biol. 1999;286(5):1673–91.
Article
CAS
PubMed
Google Scholar
Lees J, Yeats C, Perkins J, Sillitoe I, Rentzsch R, Dessailly BH, Orengo C. Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucleic Acids Res. 2012;40(Database issue):D465–71.
Article
CAS
PubMed
Google Scholar
Letunic I, Bork P. "20 years of the SMART protein domain annotation resource." Nucleic Acids Res. 2017;46(D1):D493-6.
Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017;45(Database issue):D200–3.
Article
CAS
PubMed
Google Scholar
Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003;31(1):334–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Conway JR, Lex A, Gehlenborg N. "UpSetR: an R package for the visualization of intersecting sets and their properties." Bioinformatics. 2017;33(18):2938–40.
R Development Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2012.
Google Scholar
R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2013.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nayaka, S. Chandra, et al. Draft genome sequence of Sclerospora graminicola, the pearl millet downy mildew pathogen. Biotechnology reports. 2017;16:18-20.
Article
PubMed
PubMed Central
Google Scholar
Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 2009;461(7262):393–8.
Article
CAS
PubMed
Google Scholar
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (New York, NY). 2006;313:1261–6.
Article
CAS
Google Scholar