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

Abstract

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.

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1165999
Report Number(s):
LBNL-6821E
Journal ID: ISSN 1553-7404
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
PLoS Genetics
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1553-7404
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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, and Madhani, Hiten D. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens. United States: N. p., 2013. Web. doi:10.1371/journal.pgen.1003233.
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. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens. United States. doi:10.1371/journal.pgen.1003233.
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, and Madhani, Hiten D. Thu . "Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens". United States. doi:10.1371/journal.pgen.1003233. https://www.osti.gov/servlets/purl/1165999.
@article{osti_1165999,
title = {Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens},
author = {Condon, Bradford J. and Leng, Yueqiang and Wu, Dongliang and Bushley, Kathryn E. and Ohm, Robin A. and Otillar, Robert and Martin, Joel and Schackwitz, Wendy and Grimwood, Jane and MohdZainudin, NurAinIzzati and Xue, Chunsheng and Wang, Rui and Manning, Viola A. and Dhillon, Braham and Tu, Zheng Jin and Steffenson, Brian J. and Salamov, Asaf and Sun, Hui and Lowry, Steve and LaButti, Kurt and Han, James and Copeland, Alex and Lindquist, Erika and Barry, Kerrie and Schmutz, Jeremy and Baker, Scott E. and Ciuffetti, Lynda M. and Grigoriev, Igor V. and Zhong, Shaobin and Turgeon, B. Gillian and Madhani, Hiten D.},
abstractNote = {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.},
doi = {10.1371/journal.pgen.1003233},
journal = {PLoS Genetics},
issn = {1553-7404},
number = 1,
volume = 9,
place = {United States},
year = {2013},
month = {1}
}

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