Black lives matter
231 Koshland Hall, Berkeley CA 94720 kseniak [at] berkeley.edu.
Upcoming science presentations at conferences and symposia
Main Presenter - Title - Conference information
Daniil Prigozhin - "A limited subset of plant immune receptors undergoes extensive within-species diversification" - ASPB, July 19-23, talk
Pierre Joubert - "Extrachromosomal circular DNAs and their role in fungal plant pathogen adaptation to stress" - IS-MPMI Congress: eSymposia Series, Pathogen-Host Co-evolution, Sept 15-16, 2021 poster
Who we are and what we do
Krasileva lab an inter-disciplinary group of people who combine new technologies, basic and translational research. Our common goal is to understand innate immunity, a system that maintains plant health. We focus on evolution and function of immune genes, as well as the mechanisms that regulate genetic diversity in plants and fungi.
The lab is located in Koshland Hall, we are part of Department of Plant and Microbial Biology as well as the Innovative Genomics Institute and The Center for Computational Biology at the University of California Berkeley.
If you are interested in joining the lab, here is how you can approach us:
- undergraduate research: reach out to us directly before the semester begins or look for projects at URAP and SPUR.
- graduate students: please, see description of our graduate programs in Microbiology and Plant Biology. We are also part of Center for Computational Biology rotation program. To discuss a rotation, please reach out at least a few weeks in advance.
- postdocs: please send Ksenia the postdoc fellowship you would like to apply for and your CV.
- staff: occassionally, positions become available. Please, watch this space or send us a note.
My aspiration is to build the lab based on honesty and transparency, to ensure open communication and to maintain the highest quality of research and strongest work ethic without sacrificing our health or wellbeing of our families. Our lab culture is summarized in the Krasileva Lab Charter
If you have any questions about Krasileva Lab, do not hesitate to contact me.
July 2021 - Wow Grace!
Congratulations to Frances (Grace) Stark for winning a highly prestigious Graduate Level Scholarship at the Sonoma County Mycological Association. Grace, a molecular mycologist and PhD candidate in our lab, will give an invited lecture in January at the SOMA camp alongside biggest mycology experts (check here for updates).
Grace defended her QE on fungal-bacterial interactions in April*, a project she brought to Krasileva laboratory and is developing very rapidly into a fantastic study. She is open, collaborative, and you can find her project description (Do fungi also have innate immune responses?) here
You can also follow Grace into the world of all things fungi and more on Instagram @the_molecular_mycologist
*we gathered to celebrate Grace's quals in April at the UC Berkeley Botanical Gardens - the first time we saw each other in person since the lockdown
June 2021 - Congrats to Boyan Xu for passing his QE
Boyan Xu successfully defended Qualification Exams in the areas of Biological Sequence Analysis, Machine Learning and Topology. Congrats to our newest PhD candidate!
May 2021 - Welcome to two new graduate students and a farewell to Mark
We welcome two graduate students who joined the lab this May after completing their rotation year. Kyungyong Seong joins us as a Microbiology student with Designated Emphasis in Genomics and Computational biology. Chandler Sutherland joins us as a Plant Biology student, also with a deep interest in genomics and genome evolution.
We are also saying farewell to Mark Tiersma, who is graduating with BA degree in Molecular and Cell Biology with an emphasis in genetics. After spending two year doing research with us, Mark will be now joining Prof Maya Kasowski lab at Stanford as a predoctoral laboratory technician working on single cell genomics.
January 2021 - starting the year strong with preprints and publications
It is exciting to start the new year with several publications.
We are opening the year with new age of computational structural genomics, led by Kyungyong Seong and accomplished during his rotation. In his preprint, Kyungyong shows the power of latest machine learning algorithms and high throughput structure predictions to cluster virulence factors that are highly divergent in their sequences and to uncover new patterns of their evolution.
- 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
A paper started last year on phylogenomics and using information theory plus structural analyses to identify highly variable NLRs and predict their rapidly evolving ligand binding sites, is now published (and includes 2.5 new figures that were not in the original preprint):
- 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
Erin Baggs' analyses of immune receptors in maize are included in this latest preprint:
- 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
December 2020 - The plant that lost its NLRs
Congratulations to Erin Baggs on collaborative work on a duckweed Wolffia! Wolffia is one of the plant species that has fewest NLRs (only 1 left), yet it is resistant to pathogens.
- 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 , , , , , , , , , , , , , , , , ,
November, 2020 - Welcome Lorena, Kyungyang, Boyan and Dean
Lorena Parra joined us this month as a postdoc on a grant funded by Foundation for Food and Agriculture Research, 2Blades Foundation and Innovative Genome Institute to improve disease resistance in wheat. Dr Parra obtained her PhD in University of California, Davis, working with Prof Richard Michelmore. In her project with us, she will establish high throughput assays for engineering new NLR binding specificities.
We are hosting graduate students for rotations this year despite all obstacles. Kyungyong Seong, Boyan Xu and Dean Pettinga join for the second rotation. They come from different programs: Microbiology, Plant Biology and Math, respectively, yet all are computational biologists - this is the power of cross cutting research. Welcome to the virtual reality of our lab today, and we hope for safe interactions in person in 2021!
October, 2020 - Ksenia joins UC Berkeley Center for Computational Biology
UC Berkeley Center for Computational Biology (https://ccb.berkeley.edu) is a unique interdisciplinary hub of faculty and students from over 12 departments that are united by common research interest and hold events, seminar and retreats together. The center offers a Computational Biology PhD program (link) as well as an opportunity for graduate students from any UC Berkeley department to join the Center through the Designated Emphasis in Computational Biology (DE link). Pierre Joubert in our lab is part of the DE program. It's exiting to join this rich community!
September, 2020 - Welcome Anne Nakamoto and Yiling Fang (and welcome back Mark and Daniel)
As the pandemic affects all aspects of our lives, we strive to provide the training to undergraduates that we can. Anne Nakamoto, an undergraduate student in MCB with minor in Computer Science and a URAP student joins Pierre Joubert on a computational project. Anne will be working on genomics of a devastating (and fascinating) fungal pathogen of wheat, Magnaporthe oryzae. Mark Tiersma and DanielChoAhn come back also as URAP students to work with Erin Baggs on duckweed.
Yiling Fang, 1st year graduate student in Plant Biology, joins the lab for a 10 week rotation to work on NLR designs with Janina Tamborski.
July, 2020 - Collaborative preprint on NLR phylogenomics and binding sites prediction
A new preprint from the lab (link). We applied phylogeny-based clustering and information theory to examine the evolution of plant NLR immune receptors. The question we sought to answer was: how can plants with only innate immune receptors develop new recognition specificities? We found that a subset of plant NLRs are highly variable and this variation mostly clusters on the surfaces of their C-terminal LRR and post-LRR domains. We also made a key observation that recognition of plant's own molecules adapted for indirect recognition of pathogen activity on the cell evolved as a functional byproduct of direct recognition of any molecules (mostly used to catch pathogen-derived proteins). This unifies a previously proposed 'Birth and Death' theory of plant immunity evolution (Michelmore and Meyers, 1998) with current understanding of how these receptors function inside the cell.
This study is a product of long-term discussions with Daniil Prigozhin who has been trained in mathematics, molecular and cellular biology and structural biology and is currently a project scientist at LBNL (and for full COI disclosure, Ksenia's husband).
June, 2020 - Lab statement against racism
In Krasileva Lab, we condemn any racist actions, opinions and behavior. We aim to be proactively anti-racist and help to introduce structural and societal change.
If you do not have time, this is the essence: "If you read no further, understand this: Black Lives Matter = if anyone kills a Black person, their punishment should be the same as if they killed someone from any other race."
June, 2020 - A new paper led by Erin comes out in The Plant Cell
We have a new publication from the lab (link). Conceptualized and led by a graduate student Erin L Baggs, our new study provides a comparative analysis of plant immune receptors and signaling pathways across plants. Erin discovered that at least five plant species that belong to different lineages, including duckweed and asparagus, convergently lost most of NLR immune receptors as well as a key EDS1/PAD4 signaling pathway. Erin took this analysis further to look for other genes convergently lost in these species and predicted other possible components of plant immunity. She also uncovered an intriguing link between immunity and drought response that connects these genes on a transcriptional level.
Baggs et al Plant Cell "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 (link)
Recognizing Plant Cell authors: Erin Baggs (link)
Plantae IN BRIEF: ASTREL Projection: Comparative Phylogenomics Uncovers Novel Genes Co-eliminated with the EDS1 Immune Pathway (link)
May, 2020 - New PhD student joins the lab
A very warm welcome to Frances (Grace) Stark who joins the lab this year. Grace got her BSc in University of Texas at Austin. She is "a mycologist fascinated by plant/fungal symbioses and the molecular mechanisms driving their relationships!" Whoo hoo!
April, 2020 - A collaborative pre-print: Wolffia genome has only 1 NLR left
March, 2020 - Collaborative paper describes NLR in wheat
This paper describes a new tool, NLR-Annotator developed by Dr that can mine for NLR motifs in unannotated genomes. We have used NLR-Annotator on a number of genomes in our studies, and find it very useful and complementary to other approaches, such as domain-based searches implemented in plant_rgenes. We now routinely use NLR-Annotator as a quality check of NLR annotations in proteomes.
Secondly, this paper carefully catalogs NLRs in hexaploid wheat and provides an annotated phylogeny which is openly available in interactive mode (link).
February, 2020 - New review article from our lab
January, 2020 - Welcome China Lunde Shaw, our new lab manager!
Joseph Brodsky once said "A school is a factory is a poem is a prison is academia is boredom, with flashes of panic" (J. Brodsky, Less than One, 1976). We are excited for China to join our lab, she will keep down our flashes of panic when it comes to lab organization, ordering and running the lab while enjoying the bits of poetry that is research.
The Gordon and Betty Moore Innovator 2019 Fellowship
We are thrilled to have our first grant at UC Berkeley. Ksenia and our lab were selected as one of only 5 recipients of the grant this year. The grant is focused on sustainable agriculture and boosting plant health through new protein engineering approaches (akin to antibody therapy for us humans) that will be able to recognize invading pathogens. This project stems directly from our discovery of plant immune receptors naturally prone to new protein fusions that can function as 'baits' for the pathogen.
Pierre awarded Grace Kase Fellowship
Congratulations Pierre on receiving Grace Kase Graduate Fellowship Award 2019-2020 to investigate evolution of 'Genomes under stress'.
New preprint: What genomics can tell us about aquatic vs terrestrial plant lifestyle
Erin Baggs has her new paper out on bioarxiv preprint: "Convergent gene loss in aquatic plants predicts new components of plant immunity and drought response"
Welcome our first rotation students at Berkeley!
Two new students, Pierre Joubert (microbiology) and Lorenzo Washington (plant) start their 3rd rotation with us today. Welcome to the Lab.