Intra- and Intergenomic variation of Ploidy and Clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan

Barchenger, Derek W.; Lamour, Kurt; Sheu, Z.M.; Shrestha, Sandesh; Kumar, Sanjeet; Lin, Shih-Wen; Burlakoti, Rishi R.; Bosland, Paul W.

doi:10.1007/s11557-017-1330-0

Cited by 25 publications

(28 citation statements)

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“…Removal of the loci residing in LOH tracts helped produce a detailed molecular map and the annotated genome was published in 2012 [10]. Population studies using SNP markers reveal LOH is common in P. capsici and other oomycetes at locations worldwide [2,3,7,12,13,15,22,23].…”

Section: Introductionmentioning

confidence: 99%

“…Until recently, the 917 genetic scaffolds were not arranged into chromosomes (18 linkage groups). In 2017, the map-ordered scaffolds were used to visualize heterozygous allele frequencies for P. capsici recovered from pepper in Taiwan and isolates of the closely related pathogen of taro, P. colocasiae, from Hawaii, Vietnam, China and Nepal [22,23]. Allele frequencies measured using whole genome and targeted-sequencing suggested ploidy varied by chromosome within individual isolates.…”

Section: Introductionmentioning

confidence: 99%

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Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici and the potential for rapid asexual evolution

Shrestha

Zhou

et al. 2020

PLoS ONE

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Oomycete plant pathogens are difficult to control and routine genetic research is challenging. A major problem is instability of isolates. Here we characterize >600 field and single zoospore isolates of Phytophthora capsici for inheritance of mating type, sensitivity to mefenoxam, chromosome copy number and heterozygous allele frequencies. The A2 mating type was highly unstable with 26% of 241 A2 isolates remaining A2. The A1 mating type was stable. Isolates intermediately resistant to mefenoxam produced fully resistant single-spore progeny. Sensitive isolates remained fully sensitive. Genome re-sequencing of single zoospore isolates revealed extreme aneuploidy; a phenomenon dubbed Dynamic Extreme Aneuploidy (DEA). DEA is characterized by the asexual inheritance of diverse intra-genomic combinations of chromosomal ploidy ranging from 2N to 3N and heterozygous allele frequencies that do not strictly correspond to ploidy. Isolates sectoring on agar media showed dramatically altered heterozygous allele frequencies. DEA can explain the rapid increase of advantageous alleles (e.g. drug resistance), mating type switches and copy neutral loss of heterozygosity (LOH). Although the mechanisms driving DEA are unknown, it can play an important role in adaptation and evolution and seriously hinders all aspects of P. capsici research.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici and the potential for rapid asexual evolution

Shrestha

Zhou

et al. 2020

PLoS ONE

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“…Population studies using single-zoospore, hyphal-tip and/or infected-plant derived genomic DNA reveal this is not the case 4 . Field populations, especially during the explosive asexual phase of an epidemic, contain many individuals with slightly differing multi-locus SNP genotypes, inconsistent with the expectations for meiosis as the sole driver of genetic diversity [19][20][21]23,30 .…”

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confidence: 91%

“…Until recently, the 917 genetic scaffolds were not arranged according to the chromosomes (18 linkage groups) 8 . In 2017, the map-ordered scaffolds were used to visualize heterozygous allele frequencies for P. capsici recovered from pepper in Taiwan and isolates of the closely related pathogen of taro, P. colocasiae, from Hawaii, Vietnam, China and Nepal 23,24 . Whole genome and targeted-sequencing revealed ploidy varied by chromosome within individual isolates.…”

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confidence: 99%

Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici sheds light on instant evolution and intractability

Shrestha

Zhou

et al. 2018

Preprint

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word summaryOomycete plant pathogens are notoriously difficult to control, and individual isolates are highly unstable; making routine research challenging. Sequencing reveals extreme aneuploidy for single-spore progeny of the vegetable pathogen Phytophthora capsici; a phenomenon dubbed Dynamic Extreme Aneuploidy (DEA). Although extreme, the aneuploidy appears to be moderately stable. A single sporulating plant lesion may produce an armada of genetically unique individuals and helps explain the rapid increase of advantageous alleles (e.g. drug resistance), mating type switches to allow sex and the widely observed phenomenon, loss of heterozygosity (LOH). Investigation of other oomycetes indicate this phenomenon is not unique to P. capsici. Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici sheds light on instant evolution and intractability. Introductory ParagraphAlthough oomycete plant pathogens (water molds) look and act like fungi, they are distantly related and most antifungal compounds have no effect 1 . Oomycetes are notoriously difficult to control 2-4 . In research, isolates are highly unstable; making routine research challenging 5,6 . Here we show that ploidy amongst the chromosomes in an individual isolate varies dramatically for asexual spores of Phytophthora capsici; a phenomenon dubbed Dynamic Extreme Aneuploidy (DEA). The number of individual chromosomes allocated to a single zoospore is highly variable and appears moderately stable. The practical consequence is that infected plants can release an armada of genomically unique individuals -responding quickly to selection pressures. DEA explains the rapid increase of advantageous alleles (e.g. drug resistance) 7 , mating type switches to allow sex and loss of heterozygosity (LOH) 8-10 and may spur novel investigation of yeast and human tumor tissues where loss of heterozygosity is reported 11,12 .The genus Phytophthora has many destructive and pervasive plant pathogens 2 . The 120+ species attack almost all dicot plants and threaten ecosystems and entire plant industries 2,4 . For more than 150 years, scientists have struggled to manage this unwieldy genus and make of it (or, at least one of its members) a model organism 13 . Part of this quest has focused on the vegetable pathogen, P. capsici -a devastating pathogen of vegetables [13][14][15] . Ostensibly, an ideal research model; isolates can be immortalized under liquid nitrogen, grow rapidly on simple media, can be easy to mate in the laboratory, are often highly pathogenic and make copious spores with little coaxing. The problem is -sometimes an isolate will do all the above and sometimes it won't. The intractability of Phytophthora (or success, depending on your point of view) lies in its plasticity 5 . Phytophthora, when needed most (e.g. for a long-term laboratory, greenhouse or field experiments), is entirely unreliable.The ploidy of oomycetes was debated actively for over 75 years and it wasn't until Eva Sansome, in a 1961 Letter to Nature, provided convincin...

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“…The sexual phase requires the interaction of two mating types (A1 and A2), and outcrossing can greatly increase the genetic diversity of field populations and may increase the overall evolutionary potential and the ability to adapt to control measures (Lamour et al, 2012). Recently, variable ploidy has been reported in this pathogen and could affect its ability to adapt to different environments (Barchenger et al, 2017).…”

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Virulence Phenotypes on Chili Pepper for Phytophthora capsici Isolates from Michoacán, Mexico

Reyes-Tena¹,

Castro-Rocha²,

Rodríguez-Alvarado³

et al. 2019

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Phytophthora blight of vegetables caused by Phytophthora capsici causes significant economic losses in production of Solanaceae and Cucurbitaceae crops in Mexico. The development of universal resistant chili pepper cultivars is challenging due to the diverse virulence phenotypes produced by P. capsici. The objective of the study was to characterize the diversity of phenotypic interactions for P. capsici isolates recovered from production fields in Michoacán, Mexico, to facilitate the development of resistant cultivars. Virulence phenotypes were characterized for 12 isolates of P. capsici using 26 Capsicum annuum New Mexico Recombinant Inbred Lines (NMRILs) in greenhouse conditions. Criollo de Morelos CM-334 and California Wonder were used as resistant and susceptible controls, respectively. Seedlings at the four to eight true leaf stage were inoculated with 10,000 zoospores per seedling and disease severity was evaluated at 20 days post-inoculation. Two of the P. capsici isolates did not infect any pepper host even though the isolate was less than a year old. The 10 virulent isolates were designated in 10 virulence phenotypes. The information generated by this study is of utmost importance for efforts of producing resistant cultivars specific for Michoacán producers.

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Intra- and Intergenomic variation of Ploidy and Clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan

Cited by 25 publications

References 41 publications

Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici and the potential for rapid asexual evolution

Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici and the potential for rapid asexual evolution

Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici sheds light on instant evolution and intractability

Virulence Phenotypes on Chili Pepper for Phytophthora capsici Isolates from Michoacán, Mexico

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