December 2021 – Congratulations Erin on new preprint and completing PhD!

Congratulations to Erin Baggs for completion her outstanding dissertation this month. Dr Baggs is the 1st PhD graduate from the lab! Two of her chapters have been published or pre-printed, and two more will come to the preprint server near you in the next few months.

To read some of Erin’s work, see our latest collaborative preprint with the Parker lab, in which we describe evolution and function of plant Toll-Interleukine like (TIR) proteins.

• Johanndrees O*, Baggs EL*, Uhlmann C, Locci F, Läßle HL, Melkonian K, Käufer K, Dongus JA, Nakagami H, Krasileva KV, Parker JE, Lapin D “Differential EDS1 requirement for cell death activities of plant TIR-domain proteins” bioRxiv 2021.11.29.470438; https://doi.org/10.1101/2021.11.29.470438 *equal authorship

October 2021 – NIH Director’s New Innovator Award & new preprint from the lab

Ksenia has been awarded NIH Director’s New Innovator Award (read the announcement here) which will provide $1.5 million to the lab to fund high-risk high-reward research program “Cross kingdom health: evolution of immune receptors and their targets” for the next 5 years. Thank you NIH and congratulations to all award recipients.In our latest preprint, Pierre Joubert describes extra chromosomal circular DNA (eccDNA) from a filamentous fungus, plant pathogen extraordinaire –  Magnaporthe oryzae.

• Joubert PM and Krasileva KV “The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors”bioRxiv 2021.10.12.464130; doi: https://doi.org/10.1101/2021.10.12.464130

September 2021 – New grant from USDA-NIFA and welcome Ryan

We are lucky with our funding! Diversity of projects led by lab members is being matched by good funding. This month, we got awarded a 3 year grant by USDA-NIFA (joint initiative with NSF) to study “Genes and pathways that boost wheat resistance to stripe rust” using our wheat mutant lines with enhanced disease resistance. The project is currently led by an experienced geneticist China Lunde. Interested to know more and work with us? Send Ksenia an email at kseniak@berkeley.edu.

Ryan Kenneally joins the lab for his first PhD rotation to work on #project-wheat. Welcome Ryan!

July 2021 – Chandler is awarded Grace Kase-Tsujimoto Graduate Fellowship

Congratulations to Chandler Sutherland for being awarded the 2021-22 Grace Kase-Tsujimoto Graduate Fellowship for her exceptional academic and rotation performance during first year as a graduate student. Chandler joined our lab to study evolution and diversity generation mechanisms in plant immune receptors.

The Grace Kase-Tsujimoto Fellowship celebrates Mr. Harry Tsujimoto’s (Grace Kase’s husband) long and productive affiliation with and career at UC Berkeley. After graduating from Cornell, Mr. Tsujimoto received a Master of Science degree with the late Professor Daniel Arnon and continued working closely with him in the then Cell Physiology department for over 30 years. After his retirement, Mr. Tsujimoto and his wife, Grace Kase, established the K/T Foundation that set up an endowment in our department to provide ongoing support for the Grace Kase fellowship and the annual Tsujimoto and Buchanan Lectures.

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 Research article