Ahmadi H, Sheikh-Assadi M, Fatahi R et al (2023) Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis. Sci Rep 13:12415. https://doi.org/10.1038/s41598-023-39620-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aime MC, McTaggart AR, Mondo SJ, Duplessis S (2017) Chapter Seven - Phylogenetics and phylogenomics of rust fungi. In: Townsend JP, Wang ZBT-A in G (eds) Fungal phylogenetics and phylogenomics. Academic, pp 267–307

Ali S, Hodson D (2017) In: Periyannan S (ed) Wheat rust surveillance: field disease scoring and sample collection for phenotyping and molecular genotyping BT - Wheat rust diseases: methods and protocols. Springer New York, New York, NY, pp 3–11

Google Scholar 

Ali S, Sharma S, Leconte M et al (2018) Low pathotype diversity in a Recombinant Puccinia striiformis population through convergent selection at the Eastern Himalayan centre of diversity (Nepal). Plant Pathol 67:810–820. https://doi.org/10.1111/ppa.12796

Article  Google Scholar 

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Bai Q, Wang M, Xia C et al (2022) Identification of secreted protein gene-based SNP markers associated with virulence phenotypes of Puccinia striiformis F. Sp. tritici, the wheat Stripe rust pathogen. Int J Mol Sci 23. https://doi.org/10.3390/ijms23084114

Beddow JM, Pardey PG, Chai Y et al (2015) Research investment implications of shifts in the global geography of wheat Stripe rust. Nat Plants 1:15132. https://doi.org/10.1038/nplants.2015.132

Article  PubMed  Google Scholar 

Bhavani S, Singh PK, Qureshi N et al (2021) Globally important wheat diseases: status, challenges, breeding and genomic tools to enhance resistance durability. In: Kole C (ed) Genomic designing for biotic stress resistant cereal crops. Springer International Publishing, Cham, pp 59–128

Chapter  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bueno-Sancho V, Bunting DCE, Yanes LJ et al (2017a) Field pathogenomics: an advanced tool for wheat rust surveillance. In: Periyannan S (ed) Wheat rust diseases: methods and protocols. Springer New York, New York, NY, pp 13–28

Chapter  Google Scholar 

Bueno-Sancho V, Persoons A, Hubbard A et al (2017b) Pathogenomic analysis of wheat yellow rust lineages detects seasonal variation and host specificity. Genome Biol Evol 9:3282–3296. https://doi.org/10.1093/gbe/evx241

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carmona MA, Sautua FJ, Pérez-Hernández O et al (2019) Rapid emergency response to yellow rust epidemics caused by newly introduced lineages of Puccinia striiformis F. Sp. tritici in Argentina. Trop Plant Pathol 44:385–391. https://doi.org/10.1007/s40858-019-00295-y

Article  Google Scholar 

Cat A, Tekin M, Akan K et al (2023) Virulence characterization of the wheat Stripe rust pathogen, Puccinia striiformis F. Sp. tritici, in Turkey F.om 2018 to 2020. Can J Plant Pathol 45:158–167. https://doi.org/10.1080/07060661.2023.2166126

Article  CAS  Google Scholar 

Cerveau N, Jackson DJ (2016) Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms. BMC Bioinformatics 17:525. https://doi.org/10.1186/s12859-016-1406-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen X (2017) Stripe rust epidemiology. In: Chen X, Kang Z (eds) Stripe rust. Springer Netherlands, Dordrecht, pp 283–352

Chapter  Google Scholar 

Chen X (2020) Pathogens which threaten food security: Puccinia striiformis, the wheat Stripe rust pathogen. Food Secur 12:239–251. https://doi.org/10.1007/s12571-020-01016-z

Article  Google Scholar 

Chen W, Zhang Z, Ma X et al (2021) Phenotyping and genotyping analyses reveal the Sp.ead of Puccinia striiformis F. Sp. tritici aeciospores F.om susceptible barberry to wheat in Qinghai of China. Front Plant Sci 12. https://doi.org/10.3389/fpls.2021.764304

Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20:238. https://doi.org/10.1186/s13059-019-1832-y

Article  PubMed  PubMed Central  Google Scholar 

Figueroa M, Hammond-Kosack KE, Solomon PS (2018) A review of wheat diseases—a field perspective. Mol Plant Pathol 19:1523–1536. https://doi.org/10.1111/mpp.12618

Article  PubMed  Google Scholar 

Fonseca NR, Ibarra Caballero J, Kim M-S et al (2019) Transcriptome analysis of a powdery mildew pathogen (Podosphaera pannosa) infecting Eucalyptus urophylla: de Novo assembly, expression profiling and secretome prediction. Pathol 49:e12508. https://doi.org/10.1111/efp.12508

Article  Google Scholar 

Gangwar OP, Kumar S, SC Bhardwaj et al (2017) Detection of new Yr1- virulences in Puccinia striiformis F. Sp. tritici population and its sources of resistance N advance wheat lines and released cultivars. Indian Phytopathol 70:307–314. https://doi.org/10.24838/ip.2017.v70.i3.74238

Gangwar OP, Kumar S, Chander Bhardwaj S et al (2021) Virulence and molecular diversity among Puccinia striiformis F. Sp. tritici pathotypes identified in India between 2015 and 2019. Crop Prot 148:105717. https://doi.org/10.1016/j.cropro.2021.105717

Article  CAS  Google Scholar 

Gangwar OP, Prasad P, Lata C, Kumar S, Manjul AS (2024) Mehtaensis: Six-monthly newsletter. ICAR-Indian Institute of Wheat and Barley Research, Regional Station 14:12–13

Ghanbarnia K, Gourlie R, Amundsen E, Aboukhaddour R (2021) The changing virulence of Stripe rust in Canada from 1984 to 2017. Phytopathology 111:1840–1850. https://doi.org/10.1094/PHYTO-10-20-0469-R

Article  CAS  PubMed  Google Scholar 

Haider MW, Kaur J, Bala R et al (2023) Stripe rust resistance gene(s) postulation in wheat germplasm with the help of differentials and tagged molecular markers. Sci Rep 13:9007. https://doi.org/10.1038/s41598-023-36197-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hawkesford MJ, Araus J-L, Park R et al (2013) Prospects of doubling global wheat yields. Food Energy Secur 2:34–48. https://doi.org/10.1002/fes3.15

Article  Google Scholar 

Hovmøller MS, Walter S, Bayles RA et al (2016) Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region. Plant Pathol 65:402–411. https://doi.org/10.1111/ppa.12433

Article  Google Scholar 

Hubbard A, Lewis CM, Yoshida K et al (2015) Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biol 16:23. https://doi.org/10.1186/s13059-015-0590-8

Article  PubMed  PubMed Central  Google Scholar 

ICAR-IIWBR (2024) Director’s report of AICRP on wheat and barley 2022-23. GP Singh, vol 21. ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India

Google Scholar 

Jin Y, Szabo LJ, Carson M (2010) Century-old mystery of Puccinia striiformis life history solved with the identification of Berberis as an alternate host. Phytopathology 100:432–435. https://doi.org/10.1094/PHYTO-100-5-0432

Article  PubMed  Google Scholar 

Jindal MM, Sharma I, Bains NS (2012) Losses due to Stripe rust caused by Puccinia striiformis in different varieties of wheat. J Wheat Res 4:33–36

Google Scholar 

Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. https://doi.org/10.1093/molbev/mst010

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kiran K, Rawal HC, Dubey H et al (2017) Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing. Sci Rep 7:42419. https://doi.org/10.1038/srep42419

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kulik T, Molcan T, Fiedorowicz G et al (2022) Whole-genome single nucleotide polymorphism analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto. Front Microbiol 13. https://doi.org/10.3389/fmicb.2022.885978

Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and samtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352

Article  CAS  PubMed  PubMed Central  Google Scholar 

Libro P, Chiocchio A, De Rysky E et al (2023) De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage. Sci Data 10:330. https://doi.org/10.1038/s41597-023-02217-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma J, Awais M, Chen L et al (2023) Identification of Puccinia striiformis races from the spring wheat crop in Xinjiang, China. Front Plant Sci 14. https://doi.org/10.3389/fpls.2023.1273306

Mahmood K, Orabi J, Kristensen PS et al (2020) De novo transcriptome assembly, functional annotation, and expression profiling of Rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea). Sci Rep 10:13475. https://doi.org/10.1038/s41598-020-70406-2