Krasileva Lab Publications

Ksenia's Google Scholar profile: link

Krasileva lab members in bold

Pre-prints & pre-publication datasets

42. Sutherland, C., Stevens, D. M., Seong, K., Wei, W., & Krasileva, K. (2024). The Resistance Awakens: Natural diversity informs engineering of plant immune receptors at the DNA, RNA, and protein levels (1.0). Zenodo. https://doi.org/10.5281/zenodo.14207051

41. Kyungyong Seong, Wei Wei, Brandon Vega, Amanda Dee, Griselda Ramirez-Bernardino, Rakesh Kumar, Lorena Parra, Ksenia Krasileva "Engineering the plant intracellular immune receptor Sr50 to restore recognition of the AvrSr50 escape mutant" bioRxiv 2024.08.07.607039; doi: https://doi.org/10.1101/2024.08.07.607039

40. China Lunde, Kyungyong Seong, Rakesh Kumar, Andrew Deatker, Bhavit Chhabra, Meinan Wang, Shivreet Kaur, Sarah Song, Ann Palayur, Cole Davies, William Cumberlich, Upinder Gill, Nidhi Rawat, Xianming Chen, Meriem Aoun, Christopher Mundt, Ksenia V Krasileva "Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust" bioRxiv 2024.05.10.593581; doi: https://doi.org/10.1101/2024.05.10.593581

39. Seong K, Kumar R, Lunde C,  Krasileva K. (2023). Chromosome-level genome assembly of Triticum turgidum var 'Kronos' [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.10215402 Open Source Dataset (before pre-print)

38. Baggs EL, Stark FG, Tiersma MB, Krasileva KV "Pseudomonas isolates from ponds populated with duckweed prevent disease caused by pathogenic Pseudomonas species” bioRxiv 2022.12.09.519836; doi: https://doi.org/10.1101/2022.12.09.519836 Research article

37. Seong K, Lunde C, Seo E, Li M, Krasileva K, Staskawicz B "A draft genome assembly for the heterozygous wild tomato Solanum habrochaites highlights haplotypic structural variations of intracellular immune receptors" bioRxiv 2022.01.21.477156; doi: https://doi.org/10.1101/2022.01.21.477156 Research article

Journals

2024

36. Xu B, Cerbu A, Tralie CJ, Lim D, Krasileva K. Structure-aware annotation of leucine-rich repeat domains. PLoS Comput Biol. 2024 Nov 5;20(11):e1012526. doi: 10.1371/journal.pcbi.1012526. PMID: 39499733 Research article

35. Thynne E, Ali H, Seong K, Abukhalaf M, Guerreiro MA, Flores-Nunez VM, Hansen R, Bergues A, Salman MJ, Rudd JJ, Kanyuka K, Tholey A, Krasileva KV, Kettles GJ, Stukenbrock EH. An array of Zymoseptoria tritici effectors suppress plant immune responses. Mol Plant Pathol. 2024 Oct;25(10):e13500. doi: 10.1111/mpp.13500. PMID: 39394693 Research article

34. Prigozhin DM, Sutherland CA, Rangavajjhala S, Krasileva KV. "Majority of the highly variable NLRs in maize share genomic location and contain additional target-binding domains". Mol Plant Microbe Interact. 2024 Jul 16. doi: 10.1094/MPMI-05-24-0047-FI. Epub ahead of print. PMID: 39013614 Research article

33. Tang Y, Yang X, Huang A, Seong K, Ye M, Li M, Zhao Q, Krasileva K, Gu Y. "Proxiome assembly of the plant nuclear pore reveals an essential hub for gene expression regulation". Nat Plants. 2024 Jun;10(6):1005-1017. doi: 10.1038/s41477-024-01698-9. Epub 2024 May 21. PMID: 38773271.

32. Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. "High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features". EMBO Rep. 2024 Mar 25. doi: 10.1038/s44319-024-00122-9 Research article

31. Schuster M, Schweizer G, Reißmann S, Happel P, Aßmann D, Rössel N, Güldener U, Mannhaupt G, Ludwig N, Winterberg S, Pellegrin C, Tanaka S, Vincon V, Presti LL, Wang L, Bender L, Gonzalez C, Vranes M, Kämper J, Seong K, Krasileva K, Kahmann R. Novel Secreted Effectors Conserved Among Smut Fungi Contribute to the Virulence of Ustilago maydis. Mol Plant Microbe Interact. 2024 Mar;37(3):250-263. doi: 10.1094/MPMI-09-23-0139-FI. Epub 2024 Apr 3. PMID: 38416124.

30. Joubert PM, Krasileva KV. Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae. Genetics. 2024 Apr 3;226(4):iyae012. doi: 10.1093/genetics/iyae012 Research article

2023

29. Nakamoto AA, Joubert PM, Krasileva KV "Evolutionary dynamics of transposable elements in Magnaporthe oryzaereveal evidence of genomic transfer and key differences between rice and wheat blast pathotypes" Genome Biology and Evolution, Volume 15, Issue 12, December 2023, evad206, https://doi.org/10.1093/gbe/evad206  Research article

28. Tamborski J, Seong K, Liu F, Staskawicz B, Krasileva K.V "Engineering of Sr33 and Sr50 plant immune receptors to alter recognition specificity and autoactivity" Mol Plant Microbe Interact. 2023 Mar 3. doi: 10.1094/MPMI-07-22-0154-R. Research article

27. Arora S, Steed A, Goddard R, Gaurav K, O’Hara T, Schoen A, Rawat N, Elkot AF, Chinoy C, Nicholson MH, Asuke S, Steuernagel B, Yu G, Awal R, Forner-Martínez M, Wingen L, Baggs E, Clarke J, Krasileva KV, Tosa Y, Jones JDG, Tiwari VK, Wulff BBH, Nicholson P “A wheat kinase and immune receptor form the host-specificity barrier against the blast fungus” Nature Plants 2023; https://doi.org/10.1101/2022.01.27.477927 Research article

26. Seong K, Krasileva KV. "Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses". Nat Microbiol. 2023 Jan;8(1):174-187. doi: https://doi.org/10.1038/s41564-022-01287-6. Research article

2022

25. Joubert PM, Krasileva KV. "The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors." BMC Biol 20, 260 (2022). https://doi.org/10.1186/s12915-022-01457-2 Research article

24. Johanndrees O*, Baggs EL*, Uhlmann C, Locci F, Läßle HL, Melkonian K, Käufer K, Dongus JA, Nakagami H, Krasileva KV#, Parker JE#, Lapin D# "Variation in plant Toll/Interleukin-1 receptor domain protein dependence on ENHANCED DISEASE SUSCEPTIBILITY 1" Plant Physiology, 2022; kiac480, https://doi.org/10.1093/plphys/kiac480 Research article
*equal first authorship #corresponding

23. Baggs EL, Tiersma MB, Abramson B.W, Michael T.P, Krasileva KV "Characterization of defense responses against bacterial pathogens in duckweeds lacking EDS1" New Phytologist. Sept 2nd, https://doi.org/10.1111/nph.18453 Epub ahead of print. Research article

2021

22. Gaurav K, Arora S, Silva P, Sanchez-Martin J, Horsnell R et al (Open Wild Wheat Consortium) "Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement" Nat Biotechnol 2021 (bioRxiv Feb 2021). https://doi.org/10.1038/s41587-021-01058-4 Research article (PDF)

21. Seong K, Krasileva KV "Computational structural genomics unravels common folds and predicted functions in the secretome of fungal phytopathogen Magnaporthe oryzae" Mol Plant Microbe Interact. 2021 Aug 19. (bioRxiv Jan 2021) https://doi.org/10.1094/MPMI-03-21-0071-R. Research article (PDF)

  • The top MPMI Graduate Student Paper Award for 2021
  • Dataset for "Computational structural genomics unravels common folds and predicted functions in the secretome of fungal phytopathogen Magnaporthe oryzae" Zenodo DOI: 10.5281/zenodo.4456015

20. Prigozhin DM and Krasileva KV "Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites" The Plant Cell Jan 2021 (bioRxiv v1 July 2020 v1) https://doi.org/10.1093/plcell/koab013 Research article (PDF)

  • Code for identification of hvNLRs is available on GitHub (link).
  • Dataset for "Intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites" Zenodo DOI 10.5281/zenodo.3951780

19. Hufford MB, Seetharam A, Woodhouse M, Chougule K, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Coletta RD, Tittes S, Hudson AI, Marand A, Wei S, Lu Z, Wang B, Wang N, Kim D, Zeng Y, Piri R, O’Connor C, Li X, Gilbert A, Baggs E, Krasileva KV, Portwood J, Cannon E, Andorf C, Manchanda N, Snodgrass S, Hufnagel D, Jiang Q, Pedersen S, Syring M, Kudrna DA,  McGaugh S, Schmitz RJ, Llaca V, Fengler K, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK "De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes" Science. 2021 Aug 6;373(6555):655-662. (bioRxiv Jan 2021) https://doi.org/10.1126/science.abg5289. Research article (PDF)

2020

18. Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martienssen RA, Lam E "Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth Genome Research, Dec 2020 (bioRxiv April 2020) doi:10.1101/gr.266429.120 Research article (PDF)

17. Walkowiak et al "Multiple wheat genomes reveal global variation in modern breeding" Nature, Nov 2020 Research article (PDF)

16. Schwessinger B and Krasileva KV "Editorial overview: Biotic interactions — from single molecules to complex ecosystems"  Current Opinion in Plant Biology, v56 Aug 2020 Editorial. (PDF)

15. Baggs EL, Monroe JG, Thanki AS, O'Grady R, Schudoma C, Haerty W, Krasileva KV "Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Co-evolved Components of Plant Immunity and Drought Response." The Plant Cell (2020). https://doi.org/10.1105/tpc.19.00903  (bioRxiv March, Nov 2019: v1, v2) Research article (PDF)

  • The Plant Cell in Brief on "Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Co-evolved Components of Plant Immunity and Drought Response." (link)
  • First author profile: Erin Louise Baggs (link)
  • Short summary of "Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Co-evolved Components of Plant Immunity and Drought Response."  in garnet research round-up (link)
  • Code for orthogroups and identification of missing pathways is available on GitHub (link)

14. Steuernagel B, Witek K, Krattinger SG, Ramirez-Gonzalez RH, Schoonbeek HJ, Yu G, Baggs E, Witek A, Yadav I, Krasileva KV, Jones JD, Uauy C, Keller B, Ridout CJ, Wulff BB "The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire." Plant Physiology 2020 Mar 17.  https://doi.org/10.1104/pp.19.01273 Research article (PDF)

13. Tamborski J and Krasileva KV “Evolution of Plant NLRs: From Natural History to Precise Modifications”  Annu Rev Plant Biol. 2020 Feb 24. Review (PDF)  

2019

12. Krasileva KV "The role of transposable elements and DNA damage repair mechanisms in gene amplification and protein domain shuffling in plant genomes"  Current Opinion in Plant Biology. Volume 48, April 2019, Pages 18-25 (first on PeerJ preprint) Review (PDF)

2018

11. From plant immunity to food security: an interview with Ksenia Krasileva BMC Biology 2018 16:123 Interview https://doi.org/10.1186/s12915-018-0597-1 (PDF)

10. Bailey PC, Schudoma C, Jackson W, Baggs E, Dagdas G, Haerty W, Moscou M, Krasileva KV "Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions" Genome Biology 2018 19:23 (first at bioRxiv) Research article (PDF)

  • Code for identification of tandem NLRs is available on GitHub (link)

2017

9. Krasileva KV "Secrets of a hardy crop: New genomic resources for pearl millet are revealing how crops stand up to challenging environments" Nature Biotechnology, 35(10) Oct 2017 News and Views (PDF)

8. Baggs E, Dagdas G, Krasileva KV "NLR diversity, helpers and integrated domains: making sense of the NLR IDentity" Curr
Opinion in Plant Biology, 2017 38:59-67. Review (PDF)

7. Bevan MW, Uauy C, Wulff BBH, Zhou1 J, Krasileva KV, and Clark M "Genomic Innovation for Crop Improvement" Nature, Mar 15;543(7645):346-354. Review (PDF)

6. Krasileva KV, Vasquez-Gross H, Bailey P, Paraiso F, Clissold L, Howell T, Ramirez-Gonzalez R, Wang X, Ayling S, Fosker C,
Phillips A, Uauy C, Dubcovsky "Uncovering hidden variation in polyploid wheat." Proceeding of National Academy of Sciences U S A, 2017 Feb 7;114(6):E913-E921 Research article (PDF)

  • A publicly available resource of >10,000,000 alleles in wheat genes: www.wheat-tilling.com (UK), WHEAT TILLING (US).
  • Update 2020: The resource has been updated to RefSeq v1.1 and incorporated into Ensembl Plants and Grain Genes.

5. Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, Wright J, Borrill P, Kettleborough G, Heavens D, Chapman H, Lipscombe J, Barker T, Lu FH, McKenzie N, Raats D, Ramirez-Gonzalez RH, Coince A, Peel N, Percival-Alwyn L, Duncan O, Trösch J, Yu G, Bolser DM, Namaati G, Kerhornou A, Spannagl M, Gundlach H, Haberer G, Davey RP, Fosker C, Palma FD, Phillips AL, Millar AH, Kersey PJ, Uauy C, Krasileva KV, Swarbreck D, Bevan MW, Clark MD "An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations." Genome Research 2017 May;27(5):885-896 (first on BioRxiv) Research article (PDF)

2016

4. Sarris PF, Cevik V, Dagdas G, Jones JD, Krasileva KV "Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens" BMC Biology, 2016 14(1):8. Research article (PDF)

  • Commentary by J Ellis "Integrated decoys and effector traps: how to catch a plant pathogen" (link)
  • Code for NLR-ID detection is available on GitHub (link)

3. Petre B, Saunders DG, Sklenar J, Lorrain C, Krasileva KV, Win J, Duplessis S, Kamoun S. "Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies" PLoS One 2016 11(2):e0149035. (first on BioRxiv) Research article (PDF)

2015

2. Schwessinger B, Bart R, Krasileva KV and Coaker G. "Focus issue on plant immunity: from model systems to crop species." Front Plant Sci. 2015 6:195. Editorial (PDF)

1. Wu CH, Krasileva KV, Banfield MJ, Terauchi R, Kamoun S. "The "sensor domains" of plant NLR proteins: more than decoys?" Front Plant Sci. 2015 6:134. Perspective (PDF)