Krasileva Lab Publications

Krasileva lab members in bold

2021

22. Gaurav K, Arora S, Silva P, Sanchez-Martin J, Horsnell R et al (Open Wild Wheat Consortium) "Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii" bioRxiv Feb 2021 https://doi.org/10.1101/2021.01.31.428788 Research article

21. 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 v1https://doi.org/10.1093/plcell/koab013 Research article

  • 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

20. Seong K, Krasileva KV "Computational structural genomics unravels common folds and predicted functions in the secretome of fungal phytopathogen Magnaporthe oryzae" bioRxiv Jan 2021 https://doi.org/10.1101/2021.01.25.427855 Research article

  • 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

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" bioRxiv Jan 2021 https://doi.org/10.1101/2021.01.14.426684 Research article

2020

18. Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs ELSree KS, Appenroth KJ, Fuchs J, Jupe, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JRMartienssen 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

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

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.

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

  • 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

13. Tamborski J and Krasileva KVEvolution of Plant NLRs: From Natural History to Precise Modifications”  Annu Rev Plant Biol. 2020 Feb 24. Review   

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 BiologyVolume 48, April 2019, Pages 18-25 (first on PeerJ preprint) Review

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

10. Bailey PCSchudoma C, Jackson W, Baggs EDagdas 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

  • 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

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

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

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

  • 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

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

  • 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

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

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

Ksenia's full publication list, including those prior to establishing the lab (PhD and postdoctoral training) is here (link)