Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.
University of Tennessee, Knoxville, TN, USA. klamour@utk.edu
Kurt H
KH
Lamour
Joann
J
Mudge
Daniel
D
Gobena
Oscar P
OP
Hurtado-Gonzales
Jeremy
J
Schmutz
Alan
A
Kuo
Neil A
NA
Miller
Brandon J
BJ
Rice
Sylvain
S
Raffaele
Liliana M
LM
Cano
Arvind K
AK
Bharti
Ryan S
RS
Donahoo
Sabra
S
Finley
Edgar
E
Huitema
Jon
J
Hulvey
Darren
D
Platt
Asaf
A
Salamov
Alon
A
Savidor
Rahul
R
Sharma
Remco
R
Stam
Dylan
D
Storey
Marco
M
Thines
Joe
J
Win
Brian J
BJ
Haas
Darrell L
DL
Dinwiddie
Jerry
J
Jenkins
James R
JR
Knight
Jason P
JP
Affourtit
Cliff S
CS
Han
Olga
O
Chertkov
Erika A
EA
Lindquist
Chris
C
Detter
Igor V
IV
Grigoriev
Sophien
S
Kamoun
Stephen F
SF
Kingsmore
D000222:Adaptation, Physiological; D002212:Capsicum / Q000382:microbiology; D002874:Chromosome Mapping; D028464:Cucurbita / Q000382:microbiology; D005786:Gene Expression Regulation; D008040:Genetic Linkage; D016678:Genome; D005838:Genotype; D010838:Phytophthora / Q000502:physiology*; D010935:Plant Diseases / Q000382:microbiology*; D020641:Polymorphism, Single Nucleotide