AlmagroArmenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotech. 2019;37(4):420–3.

Article  CAS  Google Scholar 

Alonge M, Lebeigle L, Kirsche M, Jenike K, Ou S, Aganezov S, Wang X, Lippman ZB, Schatz MC, Soyk S. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022;23(1):1–19.

Article  Google Scholar 

Andrews S (2010). FastQC: a quality control tool for high throughput sequence data. In: Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom.

Armenteros JJA, Salvatore M, Emanuelsson O, Winther O, Von Heijne G, Elofsson A, Nielsen H. Detecting sequence signals in targeting peptides using deep learning. Life Sci Alliance. 2019. https://doi.org/10.26508/lsa.201900429.

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. 2010;330(6010):1549–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bharathi LK, Behera TK, Sureja AK, John KJ, Wehner TC. Snake gourd and pointed gourd: botany and horticulture. Hortic Rev. 2013;41:457–96.

Google Scholar 

Brouwer H, Coutinho PM, Henrissat B, de Vries RP. Carbohydrate-related enzymes of important Phytophthora plant pathogens. Fungal Genet Biol. 2014;72:192–200. https://doi.org/10.1016/j.fgb.2014.08.011.

Article  CAS  PubMed  Google Scholar 

Brůna T, Hoff KJ, Lomsadze A, Stanke M, Borodovsky M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics Bioinform. 2021;3(1):1qaa108.

Article  Google Scholar 

Brůna T, Lomsadze A, Borodovsky M. GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genomics Bioinform. 2020;2(2):1qaa026.

Article  Google Scholar 

Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60.

Article  CAS  PubMed  Google Scholar 

Bushnell B (2023) BBTools software package. 2014. Available online: http:/sourceforge. net/projects/bbmap Accessed 11 June 2021.

Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38(12):5825–9. https://doi.org/10.1093/molbev/msab293.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen Q, Li B, Liu P, Lan C, Zhan Z, Weng Q. Development and evaluation of specific PCR and LAMP assays for the rapid detection of Phytophthora melonis. Eur J Plant Pathol. 2013;137:597–607.

Article  CAS  Google Scholar 

Chepsergon J, Motaung TE, Moleleki LN. “Core” RxLR effectors in phytopathogenic oomycetes: a promising way to breeding for durable resistance in plants? Virulence. 2021;12(1):1921–35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cooke D, Drenth A, Duncan J, Wagels G, Brasier C. A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet Biol. 2000;30(1):17–32.

Article  CAS  PubMed  Google Scholar 

Cox MP, Guo Y, Winter DJ, Sen D, Cauldron NC, Shiller J, Bradley EL, Ganley AR, Gerth ML, Lacey RF. Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families. Front Microbiol. 2022;13:1038444.

Article  PubMed  PubMed Central  Google Scholar 

Derevnina L, Dagdas YF, De la Concepcion JC, Bialas A, Kellner R, Petre B, Domazakis E, Du J, Wu CH, Lin X. Nine things to know about elicitins. New Phytol. 2016;212(4):888–95.

Article  CAS  PubMed  Google Scholar 

Dey T, Saville A, Myers K, Tewari S, Cooke DE, Tripathy S, Fry WE, Ristaino JB, Guha Roy S. Large sub-clonal variation in Phytophthora infestans from recent severe late blight epidemics in India. Sci Rep. 2018;8(1):4429.

Article  PubMed  PubMed Central  Google Scholar 

Dhali R, Dey T, Tewari S, Roy SG. A survey of Phytophthora spp. in Eastern Indian nurseries and their sensitivity to six oomycete-targeted commercial fungicides. Plant Dis. 2024;108(2):486–501.

Article  CAS  PubMed  Google Scholar 

Elliott M, Yuzon J, Tripathy S, Bui M, Chastagner GA, Coats K, Rizzo DM, Garbelotto M, Kasuga T. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts. BMC Genomics. 2018;19:1–19.

Article  Google Scholar 

Fang Y, Coelho MA, Shu H, Schotanus K, Thimmappa BC, Yadav V, Chen H, Malc EP, Wang J, Mieczkowski PA. Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages. PLoS Genet. 2020;16(3):e1008646.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Finn R D, Clements J, & Eddy S R (2011) HMMER web server: interactive sequence similarity searching. Nucleic acids research, 39(suppl_2), W29-W37. https://doi.org/10.1093/nar/gkr367

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci. 2020;117(17):9451–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gabriel L, Hoff KJ, Brůna T, Borodovsky M, Stanke M. TSEBRA: transcript selector for BRAKER. BMC Bioinform. 2021;22(1):1–12.

Article  Google Scholar 

Gallegly, M. E., & Hong ChuanXue, H. C. (2008). Phytophthora: Identifying species by morphology and DNA fingerprints.

Gotoh O. A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic Acids Res. 2008;36(8):2630–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guha Roy S, Bhattacharyya S, Mukherjee SK, Khatua DC. Molecular identification of Phytophthora spp. affecting some economically important crops in Eastern India through ITS-RFLP and sequencing of the ITS region. J Phytopathol. 2009;157(11–12):666–74.

Article  Google Scholar 

Guharoy S, Bhattacharyya S, Mukherjee S, Mandal N, Khatua D. Phytophthora melonis associated with fruit and vine rot disease of pointed gourd in India as revealed by RFLP and sequencing of ITS region. J Phytopathol. 2006;154(10):612–5.

Article  CAS  Google Scholar 

Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 2009;461(7262):393–8.

Article  CAS  PubMed  Google Scholar 

Ho H-H. Taiwan Phytophthora. Bot Bull Acad Sinica. 1990;31:89–106.

Google Scholar 

Ho H. Phytophthora melonis and P. sinensis synonymous with P. drechsleri. Mycologia. 1986;78(6):907–12.

Article  Google Scholar 

Ho H, Gallegly M, Hong C. Redescription of Phytophthora melonis. Mycotaxon. 2007;102:339.

Google Scholar 

Hoff K, Lomsadze A, Borodovsky M, & Stanke M (2019) Whole-genome annotation with BRAKER. In gene prediction: methods and protocols, M. Kollmar, ed. In: New York, NY: Springer New York.

Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics. 2016;32(5):767–9.

Article  CAS  PubMed  Google Scholar 

Iwata H, Gotoh O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res. 2012;40(20):e161–e161.

Article  CAS  PubMed  PubMed Central  Google Scholar