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 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 percent 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.
Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, USA.
Bradford J
BJ
Condon
Yueqiang
Y
Leng
Dongliang
D
Wu
Kathryn E
KE
Bushley
Robin A
RA
Ohm
Robert
R
Otillar
Joel
J
Martin
Wendy
W
Schackwitz
Jane
J
Grimwood
NurAinizzati
N
MohdZainudin
Chunsheng
C
Xue
Rui
R
Wang
Viola A
VA
Manning
Braham
B
Dhillon
Zheng Jin
ZJ
Tu
Brian J
BJ
Steffenson
Asaf
A
Salamov
Hui
H
Sun
Steve
S
Lowry
Kurt
K
LaButti
James
J
Han
Alex
A
Copeland
Erika
E
Lindquist
Kerrie
K
Barry
Jeremy
J
Schmutz
Scott E
SE
Baker
Lynda M
LM
Ciuffetti
Igor V
IV
Grigoriev
Shaobin
S
Zhong
B Gillian
BG
Turgeon
D001203:Ascomycota / Q000235:genetics* / Q000472:pathogenicity; D001483:Base Sequence; D019143:Evolution, Molecular; D014644:Genetic Variation; D016681:Genome, Fungal; D010453:Peptide Synthases / Q000235:genetics*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000469:parasitology; D048630:Polyketide Synthases / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D014774:Virulence / Q000235:genetics
D048630:Polyketide Synthases; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase