Identification of candidate host-specificity genes in Exserohilum turcicum using comparative genomics and transcriptomics

Krone, Mara J.; Adhikari, Pragya; Singh, Pummi; Jamann, Tiffany M.; Mideros, Santiago X.; Todd, ed., R.

doi:10.1093/g3journal/jkaf084

Title: Identification of candidate host-specificity genes in Exserohilum turcicum using comparative genomics and transcriptomics

Journal Article · 10 April 2025 · G3

DOI: https://doi.org/10.1093/g3journal/jkaf084 · OSTI ID:2564504

; Adhikari, Pragya; Singh, Pummi;

;

; Todd, ed., R.

Abstract Exserohilum turcicum causes northern corn leaf blight and sorghum leaf blight. While the same species cause disease in both crops, the strains are host-specific. Here, we report the sequence and de novo annotated assemblies of one sorghum- and one maize-specific E. turcicum strain. The strains were sequenced using the PacBio Sequel II system. The total genome length for both assemblies was between 44 and 45 Mb with N50 of ∼2.5 Mb. Ninety-eight percent of the Benchmarking Universal Single-Copy Orthologs (BUSCO) for both assemblies had complete status. The estimated number of genes was 11,762 and 12,029 in the sorghum- and maize-specific isolates, respectively. Funannotate, EffectorP, SignalP, and transcriptome data were used to create functional annotation of each genome. The whole-genome comparison identified ten large-scale inversions and three translocations between the maize- and sorghum-specific strains, along with homologous genes and gene duplications. RNA was sequenced from the maize- and sorghum-specific isolate 10 days post-inoculation in maize and sorghum and from axenic cultures. Gene expression data from planta and axenic growth experiments were compared for each strain. Candidate host-specificity genes were identified by combining results from whole-genome comparison, synteny analysis, gene annotations, and transcriptome data. Overall, this study identified several candidate host-specificity genes that provide insights into E. turcicum interaction with its hosts.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0019189

OSTI ID:: 2564504

Journal Information:: G3, Journal Name: G3; ISSN 2160-1836

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (47)

BUSCO: Assessing Genomic Data Quality and Beyond Manni, Mosè; Berkeley, Matthew R.; Seppey, Mathieu Current Protocols, Vol. 1, Issue 12 https://doi.org/10.1002/cpz1.323	journal	December 2021
Disease Resistance in Sorghum Das, I. K.; Rajendrakumar, P. Biotic Stress Resistance in Millets https://doi.org/10.1016/B978-0-12-804549-7.00002-0	book	January 2016
Host-specificity factors in plant pathogenic fungi Li, Jiming; Cornelissen, Ben; Rep, Martijn Fungal Genetics and Biology, Vol. 144 https://doi.org/10.1016/j.fgb.2020.103447	journal	November 2020
Genomic regions associated with virulence in Setosphaeria turcica identified by linkage mapping in a biparental population Singh, Pummi; Huang, Shun-Yuan; Hernandez, Alvaro G. Fungal Genetics and Biology, Vol. 159 https://doi.org/10.1016/j.fgb.2021.103655	journal	April 2022
Evolution and Diversity of Assembly-Line Polyketide Synthases: Focus Review Nivina, Aleksandra; Yuet, Kai P.; Hsu, Jake Chemical Reviews, Vol. 119, Issue 24 https://doi.org/10.1021/acs.chemrev.9b00525	journal	December 2019
The global burden of pathogens and pests on major food crops Savary, Serge; Willocquet, Laetitia; Pethybridge, Sarah Jane Nature Ecology & Evolution, Vol. 3, Issue 3 https://doi.org/10.1038/s41559-018-0793-y	journal	February 2019
SignalP 6.0 predicts all five types of signal peptides using protein language models Teufel, Felix; Almagro Armenteros, José Juan; Johansen, Alexander Rosenberg Nature Biotechnology, Vol. 40, Issue 7 https://doi.org/10.1038/s41587-021-01156-3	journal	January 2022
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm Cheng, Haoyu; Concepcion, Gregory T.; Feng, Xiaowen Nature Methods, Vol. 18, Issue 2 https://doi.org/10.1038/s41592-020-01056-5	journal	February 2021
RepeatModeler2 for automated genomic discovery of transposable element families Flynn, Jullien M.; Hubley, Robert; Goubert, Clément Proceedings of the National Academy of Sciences, Vol. 117, Issue 17 https://doi.org/10.1073/pnas.1921046117	journal	April 2020
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Robinson, M. D.; McCarthy, D. J.; Smyth, G. K. Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp616	journal	November 2009
STAR: ultrafast universal RNA-seq aligner Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix Bioinformatics, Vol. 29, Issue 1 https://doi.org/10.1093/bioinformatics/bts635	journal	October 2012
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Liao, Y.; Smyth, G. K.; Shi, W. Bioinformatics, Vol. 30, Issue 7 https://doi.org/10.1093/bioinformatics/btt656	journal	November 2013
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
Versatile genome assembly evaluation with QUAST-LG Mikheenko, Alla; Prjibelski, Andrey; Saveliev, Vladislav Bioinformatics, Vol. 34, Issue 13 https://doi.org/10.1093/bioinformatics/bty266	journal	June 2018
The Translocation-Associated Tox1 Locus of Cochliobolus heterostrophus Is Two Genetic Elements on Two Different Chromosomes Kodama, M.; Rose, M. S.; Yang, G. Genetics, Vol. 151, Issue 2 https://doi.org/10.1093/genetics/151.2.585	journal	February 1999
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale Cantalapiedra, Carlos P.; Hernández-Plaza, Ana; Letunic, Ivica Molecular Biology and Evolution, Vol. 38, Issue 12 https://doi.org/10.1093/molbev/msab293	journal	October 2021
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity Wang, Y.; Tang, H.; DeBarry, J. D. Nucleic Acids Research, Vol. 40, Issue 7 https://doi.org/10.1093/nar/gkr1293	journal	January 2012
antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers Blin, Kai; Medema, Marnix H.; Kazempour, Daniyal Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt449	journal	May 2013
limma powers differential expression analyses for RNA-sequencing and microarray studies Ritchie, Matthew E.; Phipson, Belinda; Wu, Di Nucleic Acids Research, Vol. 43, Issue 7 https://doi.org/10.1093/nar/gkv007	journal	January 2015
EffectorP 3.0: Prediction of Apoplastic and Cytoplasmic Effectors in Fungi and Oomycetes Sperschneider, Jana; Dodds, Peter N. Molecular Plant-Microbe Interactions®, Vol. 35, Issue 2 https://doi.org/10.1094/MPMI-08-21-0201-R	journal	February 2022
Determinants of Virulence and In Vitro Development Colocalize on a Genetic Map of Setosphaeria turcica Mideros, Santiago X.; Chung, Chia-Lin; Wiesner-Hanks, Tyr Phytopathology®, Vol. 108, Issue 2 https://doi.org/10.1094/PHYTO-01-17-0021-R	journal	February 2018
A Genome Resource of Setosphaeria turcica , Causal Agent of Northern Leaf Blight of Maize Cao, Zhiyan; Zhang, Kang; Guo, Xiaoyue Phytopathology®, Vol. 110, Issue 12 https://doi.org/10.1094/PHYTO-06-20-0225-A	journal	December 2020
Genetic Structure of Setosphaeria turcica Populations in Tropical and Temperate Climates Borchardt, Dorothea S.; Welz, H. Günter; Geiger, Hartwig H. Phytopathology, Vol. 88, Issue 4 https://doi.org/10.1094/PHYTO.1998.88.4.322	journal	April 1998
Spatial Diversity of Setosphaeria turcica Sampled from the Eastern United States Ferguson, Lisa M.; Carson, M. L. Phytopathology®, Vol. 94, Issue 8 https://doi.org/10.1094/PHYTO.2004.94.8.892	journal	August 2004
Corn Yield Loss Estimates Due to Diseases in the United States and Ontario, Canada, from 2016 to 2019 Mueller, Daren S.; Wise, Kiersten A.; Sisson, Adam J. Plant Health Progress, Vol. 21, Issue 4 https://doi.org/10.1094/Php-05-20-0038-Rs	journal	January 2020
Identification and Genetic Diversity of Formae Speciales of Setosphaeria turcica in China Tang, L.; Gao, Z. G.; Yao, Y. Plant Disease, Vol. 99, Issue 4 https://doi.org/10.1094/pdis-06-14-0570-re	journal	April 2015
Field Crop Yield Loss Calculator for Disease and Invertebrate Pests: An Online Tool from the Crop Protection Network Mueller, Daren S.; Sisson, Adam J.; Eide, Brittany PhytoFrontiers™, Vol. 4, Issue 2 https://doi.org/10.1094/phytofr-08-23-0109-a	journal	April 2024
A Putative Polyketide Synthase/Peptide Synthetase fromMagnaporthe griseaSignals Pathogen Attack to Resistant Rice[W] Böhnert, Heidi U.; Fudal, Isabelle; Dioh, Waly The Plant Cell, Vol. 16, Issue 9 https://doi.org/10.1105/tpc.104.022715	journal	September 2004
Identification, cloning, and characterization of PWL2, a gene for host species specificity in the rice blast fungus. Sweigard, J. A.; Carroll, A. M.; Kang, S. The Plant Cell, Vol. 7, Issue 8 https://doi.org/10.1105/tpc.7.8.1221	journal	August 1995
Chromosomal organization of TOX2, a complex locus controlling host-selective toxin biosynthesis in Cochliobolus carbonum. Ahn, J. H.; Walton, J. D. The Plant Cell, Vol. 8, Issue 5 https://doi.org/10.1105/tpc.8.5.887	journal	May 1996
Using structural variants to understand the ecological and evolutionary dynamics of fungal plant pathogens Hartmann, Fanny E. New Phytologist, Vol. 234, Issue 1 https://doi.org/10.1111/nph.17907	journal	December 2021
Genetic differentiation in populations of Exserohilum turcicum from maize and sorghum in South Africa Nieuwoudt, A.; Human, M. P.; Craven, M. Plant Pathology, Vol. 67, Issue 7 https://doi.org/10.1111/ppa.12858	journal	May 2018
A high level of genetic divergence between Exserohilum turcicum populations from maize and sorghum in Henan province of China revealed by SSR markers Cui, Linkai; Zhao, Linxi; Fang, Yufeng Plant Pathology, Vol. 73, Issue 2 https://doi.org/10.1111/ppa.13818	journal	November 2023
Evolution of the wheat blast fungus through functional losses in a host specificity determinant Inoue, Yoshihiro; Vy, Trinh T. P.; Yoshida, Kentaro Science, Vol. 357, Issue 6346 https://doi.org/10.1126/science.aam9654	journal	July 2017
T-Toxin Virulence Genes: Unconnected Dots in a Sea of Repeats Haridas, Sajeet; González, Jennifer B.; Riley, Robert mBio, Vol. 14, Issue 2 https://doi.org/10.1128/mbio.00261-23	journal	April 2023
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in Aspergilli Theobald, Sebastian; Vesth, Tammi C.; Andersen, Mikael R. BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6114-2	journal	November 2019
Conserved defense responses between maize and sorghum to Exserohilum turcicum Zhang, Xiaoyue; Fernandes, Samuel B.; Kaiser, Christopher BMC Plant Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s12870-020-2275-z	journal	February 2020
OrthoFinder: phylogenetic orthology inference for comparative genomics Emms, David M.; Kelly, Steven Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1832-y	journal	November 2019
Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang PLoS Genetics, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pgen.1003233	journal	January 2013
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard PLoS Pathogens, Vol. 8, Issue 12 https://doi.org/10.1371/journal.ppat.1003037	journal	December 2012
Genetic Diversity and Population Genetic Structure of Setosphaeria turcica From Sorghum in Three Provinces of China Using Single Nucleotide Polymorphism Markers Cui, Linkai; Deng, Junli; Zhao, Linxi Frontiers in Microbiology, Vol. 13 https://doi.org/10.3389/fmicb.2022.853202	journal	March 2022
Comparative genomic analysis reveals cellulase plays an important role in the pathogenicity of Setosphaeria turcica f. sp. zeae Ma, Zhoujie; Huang, Yufei; Zhang, Zhaoran Frontiers in Microbiology, Vol. 13 https://doi.org/10.3389/fmicb.2022.925355	journal	July 2022
Genetics of Resistance and Pathogenicity in the Maize/Setosphaeria turcica Pathosystem and Implications for Breeding Galiano-Carneiro, Ana L.; Miedaner, Thomas Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.01490	journal	August 2017
Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae Bates, Helen J.; Pike, Jamie; Price, R. Jordan Frontiers in Plant Science, Vol. 15 https://doi.org/10.3389/fpls.2024.1415534	journal	October 2024

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