Publications

2025

1. Pangenomic context reveals the extent of intraspecific plant NLR evolution

   Luisa C Teasdale , Kevin D Murray , Max Collenberg , Adrian Contreras-Garrido , Theresa Schlegel , Leon Ess , Justina Jüttner , Christa Lanz , Oliver Deusch , Joffrey Fitz , Regina Mencia , Rosanne Velthoven , Hajk-Georg Drost , Detlef Weigel , and Gautam Shirsekar

   Cell Host & Microbe, Aug 2025

   Abs PDF

   Nucleotide-binding leucine-rich repeat (NLR) proteins are major components of the plant immune system, recognizing pathogen effectors and triggering defense responses. Because of the diversity of pathogen effector repertoires, NLRs have extraordinary sequence, structural, and regulatory variability. Although processes contributing to NLR diversity have been identified, the precise evolution of NLRs in their genomic context and along the multiple axes of diversity has been difficult to trace. We integrate genome-specific full-length transcript, homology, and transposable element information to annotate 3,789 NLRs in 17 diverse Arabidopsis thaliana accessions. We define 121 pangenomic NLR neighborhoods, which vary greatly in size, content, and complexity. NLRs are diverse across many axes, and multiple metrics are required to fully capture NLR variation. Based on these findings, we propose that diversity in diversity generation is fundamental to maintaining a functionally "adaptive" immune system in plants and that mechanistic studies should consider multiple axes of immune system diversity.

2024

1. Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response

   Regina Mencia , Agustı́n L Arce , Candela Houriet , Wenfei Xian , Adrián Contreras , Gautam Shirsekar , Detlef Weigel , and Pablo A Manavella

   Nature structural & molecular biology, Aug 2024
2. Atlas of telomeric repeat diversity in Arabidopsis thaliana

   Yueqi Tao , Wenfei Xian , Zhigui Bao , Fernando A Rabanal , Andrea Movilli , Christa Lanz , Gautam Shirsekar , and Detlef Weigel

   Genome Biology, Aug 2024
3. Pangenomic context reveals the extent of intraspecific plant NLR evolution

   Luisa C Teasdale , Kevin D Murray , Max Collenberg , Adrián Contreras-Garrido , Theresa Schlegel , Leon Ess , Justina Jüttner , Christa Lanz , Oliver Deusch , Joffrey Fitz , and others

   bioRxiv, Aug 2024
4. Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought

   Talia L Karasov , Manuela Neumann , Laura Leventhal , Efthymia Symeonidi , Gautam Shirsekar , Aubrey Hawks , Grey Monroe , Moisés Exposito-Alonso , Joy Bergelson , and others

   Nature Microbiology, Aug 2024
5. The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

   1001 Genomes Plus Consortium , Carlos C Alonso-Blanco , Haim Ashkenazy , Pierre Baduel , Zhigui Bao , Claude Becker , Erwann Caillieux , Vincent Colot , Duncan Crosbie , Louna De Oliveira , and others

   bioRxiv, Aug 2024

2023

1. Cycles of satellite and transposon evolution in Arabidopsis centromeres

   Piotr Wlodzimierz , Fernando A Rabanal , Robin Burns , Matthew Naish , Elias Primetis , Alison Scott , Terezie Mandáková , Nicola Gorringe , Andrew J Tock , Daniel Holland , and others

   Nature, Aug 2023

2022

1. vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA

   Frank Vogt^* , Gautam Shirsekar^* , and Detlef Weigel

   Bioinformatics, Aug 2022

2021

1. Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition

   Derek S Lundberg , Pratchaya Pramoj Na Ayutthaya , Annett Strauß , Gautam Shirsekar , Wen-Sui Lo , Thomas Lahaye , and Detlef Weigel

   Elife, Aug 2021
2. Multiple sources of introduction of north American arabidopsis thaliana from across Eurasia

   Gautam Shirsekar , Jane Devos , Sergio M Latorre , Andreas Blaha , Maique Queiroz Dias , Alba González Hernando , Derek S Lundberg , Hernán A Burbano , Charles B Fenster , and Detlef Weigel

   Molecular biology and evolution, Aug 2021

2020

1. Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves

   Julian Regalado , Derek S Lundberg , Oliver Deusch , Sonja Kersten , Talia Karasov , Karin Poersch , Gautam Shirsekar , and Detlef Weigel

   The ISME journal, Aug 2020
2. What natural variation can teach us about resistance durability

   Talia L Karasov , Gautam Shirsekar , Rebecca Schwab , and Detlef Weigel

   Current opinion in plant biology, Aug 2020

2019

1. Role of lysine residues of the Magnaporthe oryzae effector AvrPiz-t in effector-and PAMP-triggered immunity

   Pengfei Bai , Chan-Ho Park , Gautam Shirsekar , Pattavipha Songkumarn , Maria Bellizzi , and Guo-Liang Wang

   Molecular Plant Pathology, Aug 2019
2. The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere

   Talia L Karasov , Manuela Neumann , Alejandra Duque-Jaramillo , Sonja Kersten , Ilja Bezrukov , Birgit Schröppel , Efthymia Symeonidi , Derek S Lundberg , Julian Regalado , Gautam Shirsekar , and others

   BioRxiv, Aug 2019

2018

1. OsWRKY67 plays a positive role in basal and XA21-mediated resistance in rice

   Kieu TX Vo , Chi-Yeol Kim , Trung V Hoang , Sang-Kyu Lee , Gautam Shirsekar , Young-Su Seo , Sang-Won Lee , Guo-Liang Wang , and Jong-Seong Jeon

   Frontiers in plant science, Aug 2018
2. The monocot-specific receptor-like kinase SDS2 controls cell death and immunity in rice

   Jiangbo Fan , Pengfei Bai , Yuese Ning , Jiyang Wang , Xuetao Shi , Yehui Xiong , Kai Zhang , Feng He , Chongyang Zhang , Ruyi Wang , and others

   Cell host & microbe, Aug 2018

2017

1. Role of lysine residues of the Magnaporthe oryzae effector AvrPiz-t in effector and PAMP-triggered immunity

   Pengfei Bai , Chan Ho Park , Gautam Shirsekar , Pattavipha Songkumarn , Maria D Bellizzi , and Guo-Liang Wang

   In 2017 APS Annual Meeting, Aug 2017

2016

1. The E3 ligase APIP10 connects the effector AvrPiz-t to the NLR receptor Piz-t in rice

   Chan Ho Park^* , Gautam Shirsekar^* , Maria Bellizzi , Songbiao Chen , Pattavipha Songkumarn , Xin Xie , Xuetao Shi , Yuese Ning , Bo Zhou , Pavinee Suttiviriya , and others

   PLoS pathogens, Aug 2016
2. Quantification of hydrogen peroxide in plant tissues using Amplex Red

   Sourav Chakraborty , Amy L Hill , Gautam Shirsekar , Ahmed J Afzal , Guo-Liang Wang , David Mackey , and Pierluigi Bonello

   Methods, Aug 2016
3. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

   Clemens L Weiß , Verena J Schuenemann , Jane Devos , Gautam Shirsekar , Ella Reiter , Billie A Gould , John R Stinchcombe , Johannes Krause , and Hernán A Burbano

   Royal Society open science, Aug 2016

2015

1. Sources of resistance to Indian pathotypes of Puccinia graminis tritici and P. triticina in durum wheat

   Akhilesh N Mishra , Gautam S Shirsekar , Sitaram Yadav , Kamini Kaushal , Vijay G Dubey , and Sakuru V Sai Prasad

   Plant Breeding, Aug 2015
2. Validation of race non-specific, adult plant leaf rust resistance genes Lr34 and Lr67 in some common wheat (Triticum aestivum L.) cultivars

   AN Mishra , K Kaushal , VG Dubey , GS Shirsekar , and SV Sai Prasad

   INDIAN JOURNAL OF GENETICS AND PLANT BREEDING, Aug 2015

2014

1. Identification and characterization of suppressor mutants of spl11-mediated cell death in rice

   Gautam S Shirsekar^* , Miguel E Vega-Sanchez^* , Alicia Bordeos , Marietta Baraoidan , Andrew Swisshelm , Jiangbo Fan , Chan Ho Park , Hei Leung , and Guo-Liang contribution)

   Molecular Plant-Microbe Interactions, Aug 2014

2013

1. Ubiquitination in Innate Immunity of Rice (Oryza sativa)

   Gautam Shashikant Shirsekar

   The Ohio State University, Aug 2013

2012

1. The U-Box E3 ligase SPL11/PUB13 is a convergence point of defense and flowering signaling in plants

   Jinling Liu , Wei Li , Yuese Ning , Gautam Shirsekar , Yuhui Cai , Xuli Wang , Liangying Dai , Zhilong Wang , Wende Liu , and Guo-Liang Wang

   Plant physiology, Aug 2012
2. The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern–triggered immunity in rice

   Chan-Ho Park^* , Songbiao Chen^* , Gautam Shirsekar^* , Bo Zhou^* , Chang Hyun Khang , Pattavipha Songkumarn , Ahmed J Afzal , Yuese Ning , Ruyi Wang , Maria Bellizzi , and others

   The Plant Cell, Aug 2012
3. The fungal effector AvrPiz-t suppresses host innate immunity by targeting the RING finger E3 ligases APIP6 and APIP10 in rice

   C Park , S Chen , G Shirsekar , B Zhou , C Khang , P Songkumarn , M Bellizzi , Y Ning , B Valent , and G Wang

   In PHYTOPATHOLOGY, Aug 2012

2011

1. Diversity for Resistance to Stem and Leaf Rusts in Indian Wheat Germplasm

   Mishra AN , Yadav SR , Shirsekar GS , Dubey VG , Kaushal K , and Sai Prasad SV

   Indian Journal of Plant Genetic Resources, Aug 2011

2010

1. Role of ubiquitination in plant innate immunity and pathogen virulence

   Gautam Shirsekar , Liangying Dai , Yajun Hu , Xuejun Wang , Lirong Zeng , and Guo-Liang Wang

   Journal of Plant Biology, Aug 2010

2005

1. The linkage between the stem rust resistance gene Sr2 and pseudo-black chaff in wheat can be broken

   Akhilesh Mishra , Kamini Kaushal , Sitaram Yadav , Gautam Shirsekar , and Pandey HN

   Plant Breeding, Aug 2005
2. Genetic basis of seedling-resistance to leaf rust in bread wheat ‘Thatcher’

   Plant Breeding, Aug 2005
3. A leaf rust resistance gene, different from Lr34, associated with leaf tip necrosis in wheat

   A. N. Mishra , K. Kaushal , S. R. Yadav , G. S. Shirsekar , and H. N. Pandey

   Plant Breeding, Aug 2005