Loading…

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

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...

Full description

Saved in:
Bibliographic Details
Published in:PLoS genetics 2013-01, Vol.9 (1)
Main Authors: 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.
Format: Article
Language:English
Subjects:
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by
cites
container_end_page
container_issue 1
container_start_page
container_title PLoS genetics
container_volume 9
creator 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.
description 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.
format article
fullrecord <record><control><sourceid>osti</sourceid><recordid>TN_cdi_osti_scitechconnect_1508277</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1508277</sourcerecordid><originalsourceid>FETCH-osti_scitechconnect_15082773</originalsourceid><addsrcrecordid>eNqNjc2KwkAQhAdR8PcdGs8KiTFEz8F1L4Kgd2knHTMSp2W6I_j2O4c9ePRURVH1Vc-M0jzPlsU6Wfc__NCMRe5JkuWbbTEyvuTHEwOqexHsyfOD4KShs9oFWsCJLPsKwxsOpHjl1mlM0Vewq2uyygFKrpy_QYlPtE7fgDawSIxt0zqOk07giNrwjbxMzaDGVmj2rxMz_9mdy98li7qLRADZJl76yL6kebJZFUX2VekP87tLlw</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens</title><source>Publicly Available Content Database</source><source>PubMed Central</source><creator>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.</creator><creatorcontrib>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. ; Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><description>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.</description><identifier>ISSN: 1553-7404</identifier><identifier>EISSN: 1553-7404</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>BASIC BIOLOGICAL SCIENCES</subject><ispartof>PLoS genetics, 2013-01, Vol.9 (1)</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885</link.rule.ids><backlink>$$Uhttps://www.osti.gov/servlets/purl/1508277$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Condon, Bradford J.</creatorcontrib><creatorcontrib>Leng, Yueqiang</creatorcontrib><creatorcontrib>Wu, Dongliang</creatorcontrib><creatorcontrib>Bushley, Kathryn E.</creatorcontrib><creatorcontrib>Ohm, Robin A.</creatorcontrib><creatorcontrib>Otillar, Robert</creatorcontrib><creatorcontrib>Martin, Joel</creatorcontrib><creatorcontrib>Schackwitz, Wendy</creatorcontrib><creatorcontrib>Grimwood, Jane</creatorcontrib><creatorcontrib>MohdZainudin, NurAinIzzati</creatorcontrib><creatorcontrib>Xue, Chunsheng</creatorcontrib><creatorcontrib>Wang, Rui</creatorcontrib><creatorcontrib>Manning, Viola A.</creatorcontrib><creatorcontrib>Dhillon, Braham</creatorcontrib><creatorcontrib>Tu, Zheng Jin</creatorcontrib><creatorcontrib>Steffenson, Brian J.</creatorcontrib><creatorcontrib>Salamov, Asaf</creatorcontrib><creatorcontrib>Sun, Hui</creatorcontrib><creatorcontrib>Lowry, Steve</creatorcontrib><creatorcontrib>LaButti, Kurt</creatorcontrib><creatorcontrib>Han, James</creatorcontrib><creatorcontrib>Copeland, Alex</creatorcontrib><creatorcontrib>Lindquist, Erika</creatorcontrib><creatorcontrib>Barry, Kerrie</creatorcontrib><creatorcontrib>Schmutz, Jeremy</creatorcontrib><creatorcontrib>Baker, Scott E.</creatorcontrib><creatorcontrib>Ciuffetti, Lynda M.</creatorcontrib><creatorcontrib>Grigoriev, Igor V.</creatorcontrib><creatorcontrib>Zhong, Shaobin</creatorcontrib><creatorcontrib>Turgeon, B. Gillian</creatorcontrib><creatorcontrib>Madhani, Hiten D.</creatorcontrib><creatorcontrib>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><title>Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens</title><title>PLoS genetics</title><description>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.</description><subject>BASIC BIOLOGICAL SCIENCES</subject><issn>1553-7404</issn><issn>1553-7404</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><recordid>eNqNjc2KwkAQhAdR8PcdGs8KiTFEz8F1L4Kgd2knHTMSp2W6I_j2O4c9ePRURVH1Vc-M0jzPlsU6Wfc__NCMRe5JkuWbbTEyvuTHEwOqexHsyfOD4KShs9oFWsCJLPsKwxsOpHjl1mlM0Vewq2uyygFKrpy_QYlPtE7fgDawSIxt0zqOk07giNrwjbxMzaDGVmj2rxMz_9mdy98li7qLRADZJl76yL6kebJZFUX2VekP87tLlw</recordid><startdate>20130124</startdate><enddate>20130124</enddate><creator>Condon, Bradford J.</creator><creator>Leng, Yueqiang</creator><creator>Wu, Dongliang</creator><creator>Bushley, Kathryn E.</creator><creator>Ohm, Robin A.</creator><creator>Otillar, Robert</creator><creator>Martin, Joel</creator><creator>Schackwitz, Wendy</creator><creator>Grimwood, Jane</creator><creator>MohdZainudin, NurAinIzzati</creator><creator>Xue, Chunsheng</creator><creator>Wang, Rui</creator><creator>Manning, Viola A.</creator><creator>Dhillon, Braham</creator><creator>Tu, Zheng Jin</creator><creator>Steffenson, Brian J.</creator><creator>Salamov, Asaf</creator><creator>Sun, Hui</creator><creator>Lowry, Steve</creator><creator>LaButti, Kurt</creator><creator>Han, James</creator><creator>Copeland, Alex</creator><creator>Lindquist, Erika</creator><creator>Barry, Kerrie</creator><creator>Schmutz, Jeremy</creator><creator>Baker, Scott E.</creator><creator>Ciuffetti, Lynda M.</creator><creator>Grigoriev, Igor V.</creator><creator>Zhong, Shaobin</creator><creator>Turgeon, B. Gillian</creator><creator>Madhani, Hiten D.</creator><general>Public Library of Science</general><scope>OIOZB</scope><scope>OTOTI</scope></search><sort><creationdate>20130124</creationdate><title>Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens</title><author>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.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-osti_scitechconnect_15082773</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>BASIC BIOLOGICAL SCIENCES</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Condon, Bradford J.</creatorcontrib><creatorcontrib>Leng, Yueqiang</creatorcontrib><creatorcontrib>Wu, Dongliang</creatorcontrib><creatorcontrib>Bushley, Kathryn E.</creatorcontrib><creatorcontrib>Ohm, Robin A.</creatorcontrib><creatorcontrib>Otillar, Robert</creatorcontrib><creatorcontrib>Martin, Joel</creatorcontrib><creatorcontrib>Schackwitz, Wendy</creatorcontrib><creatorcontrib>Grimwood, Jane</creatorcontrib><creatorcontrib>MohdZainudin, NurAinIzzati</creatorcontrib><creatorcontrib>Xue, Chunsheng</creatorcontrib><creatorcontrib>Wang, Rui</creatorcontrib><creatorcontrib>Manning, Viola A.</creatorcontrib><creatorcontrib>Dhillon, Braham</creatorcontrib><creatorcontrib>Tu, Zheng Jin</creatorcontrib><creatorcontrib>Steffenson, Brian J.</creatorcontrib><creatorcontrib>Salamov, Asaf</creatorcontrib><creatorcontrib>Sun, Hui</creatorcontrib><creatorcontrib>Lowry, Steve</creatorcontrib><creatorcontrib>LaButti, Kurt</creatorcontrib><creatorcontrib>Han, James</creatorcontrib><creatorcontrib>Copeland, Alex</creatorcontrib><creatorcontrib>Lindquist, Erika</creatorcontrib><creatorcontrib>Barry, Kerrie</creatorcontrib><creatorcontrib>Schmutz, Jeremy</creatorcontrib><creatorcontrib>Baker, Scott E.</creatorcontrib><creatorcontrib>Ciuffetti, Lynda M.</creatorcontrib><creatorcontrib>Grigoriev, Igor V.</creatorcontrib><creatorcontrib>Zhong, Shaobin</creatorcontrib><creatorcontrib>Turgeon, B. Gillian</creatorcontrib><creatorcontrib>Madhani, Hiten D.</creatorcontrib><creatorcontrib>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</creatorcontrib><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><jtitle>PLoS genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Condon, Bradford J.</au><au>Leng, Yueqiang</au><au>Wu, Dongliang</au><au>Bushley, Kathryn E.</au><au>Ohm, Robin A.</au><au>Otillar, Robert</au><au>Martin, Joel</au><au>Schackwitz, Wendy</au><au>Grimwood, Jane</au><au>MohdZainudin, NurAinIzzati</au><au>Xue, Chunsheng</au><au>Wang, Rui</au><au>Manning, Viola A.</au><au>Dhillon, Braham</au><au>Tu, Zheng Jin</au><au>Steffenson, Brian J.</au><au>Salamov, Asaf</au><au>Sun, Hui</au><au>Lowry, Steve</au><au>LaButti, Kurt</au><au>Han, James</au><au>Copeland, Alex</au><au>Lindquist, Erika</au><au>Barry, Kerrie</au><au>Schmutz, Jeremy</au><au>Baker, Scott E.</au><au>Ciuffetti, Lynda M.</au><au>Grigoriev, Igor V.</au><au>Zhong, Shaobin</au><au>Turgeon, B. Gillian</au><au>Madhani, Hiten D.</au><aucorp>Pacific Northwest National Lab. (PNNL), Richland, WA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens</atitle><jtitle>PLoS genetics</jtitle><date>2013-01-24</date><risdate>2013</risdate><volume>9</volume><issue>1</issue><issn>1553-7404</issn><eissn>1553-7404</eissn><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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1553-7404
ispartof PLoS genetics, 2013-01, Vol.9 (1)
issn 1553-7404
1553-7404
language eng
recordid cdi_osti_scitechconnect_1508277
source Publicly Available Content Database; PubMed Central
subjects BASIC BIOLOGICAL SCIENCES
title Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T02%3A55%3A54IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-osti&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparative%20Genome%20Structure,%20Secondary%20Metabolite,%20and%20Effector%20Coding%20Capacity%20across%20Cochliobolus%20Pathogens&rft.jtitle=PLoS%20genetics&rft.au=Condon,%20Bradford%20J.&rft.aucorp=Pacific%20Northwest%20National%20Lab.%20(PNNL),%20Richland,%20WA%20(United%20States)&rft.date=2013-01-24&rft.volume=9&rft.issue=1&rft.issn=1553-7404&rft.eissn=1553-7404&rft_id=info:doi/&rft_dat=%3Costi%3E1508277%3C/osti%3E%3Cgrp_id%3Ecdi_FETCH-osti_scitechconnect_15082773%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_id=info:pmid/&rfr_iscdi=true