Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian; Madhani, Hiten D.

doi:10.1371/journal.pgen.1003233

Title: Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Journal Article · Thu Jan 24 00:00:00 EST 2013 · PLoS Genetics

DOI:https://doi.org/10.1371/journal.pgen.1003233· OSTI ID:1508277

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt more »

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1508277

Report Number(s):: PNNL-SA-94188

Journal Information:: PLoS Genetics, Vol. 9, Issue 1; ISSN 1553-7404

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Sexuality and compatibility of Bipolaris sorokiniana and segregation pattern in teleomorph (Cochliobolus sativus): geographic origin and segregation ratio Sultana, S.; Adhikary, S. K.; Rahman, S. M. Mahbubur Indian Phytopathology, Vol. 71, Issue 3 https://doi.org/10.1007/s42360-018-0066-3	journal	September 2018
Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi Mondo, Stephen J.; Lastovetsky, Olga A.; Gaspar, Maria L. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02052-8	journal	November 2017
The genome sequence of Bipolaris cookei reveals mechanisms of pathogenesis underlying target leaf spot of sorghum Zaccaron, Alex Z.; Bluhm, Burton H. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-17476-x	journal	December 2017
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Comparative chemical screening and genetic analysis reveal tentoxin as a new virulence factor in C ochliobolus miyabeanus , the causal agent of brown spot disease on rice: Tentoxin, a new virulence factor of C. miyabeanus De Bruyne, Lieselotte; Van Poucke, Christof; Di Mavungu, Diana Jose Molecular Plant Pathology, Vol. 17, Issue 6 https://doi.org/10.1111/mpp.12329	journal	December 2015
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The controversies of silicon's role in plant biology Coskun, Devrim; Deshmukh, Rupesh; Sonah, Humira New Phytologist, Vol. 221, Issue 1 https://doi.org/10.1111/nph.15343	journal	July 2018
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Genome-wide characterization of cellulases from the hemi-biotrophic plant pathogen, Bipolaris sorokiniana, reveals the presence of a highly stable GH7 endoglucanase Aich, Shritama; Singh, Ravi K.; Kundu, Pritha Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0822-0	journal	May 2017
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Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructans Wingfield, Brenda D.; Liu, Miao; Nguyen, Hai D. T. IMA Fungus, Vol. 9, Issue 2 https://doi.org/10.5598/imafungus.2018.09.02.10	journal	December 2018

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