Quantitative Trait Loci ControllingPhytophthora cactorumResistance in the Cultivated Octoploid Strawberry (Fragariaxananassa)

Nellist, Charlotte F.; Vickerstaff, Robert J.; Sobczyk, Maria K.; Marina-Montes, César; Brain, P.; Wilson, Frank J.; Simpson, D. W.; Whitehouse, A. B.; Harrison, Richard J.

doi:10.1101/249573

Cited by 4 publications

(7 citation statements)

References 46 publications

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“…cactorum is a persistent pathogen of strawberry and an economically significant pathogen of apple [ 41 ]. Genomic resources are available for these hosts [ 84 – 87 ], and recent work has identified resistance-associated QTL for cultivated strawberry [ 19 ]. Despite this, genomic resources for the pathogen are limited to identification of ESTs expressed during infection [ 88 ] and transcript expression during oospore germination characterized [ 49 , 89 ].…”

Section: Discussionmentioning

confidence: 99%

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Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

Armitage¹,

Lysøe

Nellist³

et al. 2018

PLoS ONE

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The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.

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Section: Discussionmentioning

confidence: 99%

“…In contrast to these Phytophthora pathosystems, strawberry resistance to P . cactorum appears to be quantitative [ 19 – 22 ], and no race structure has been reported to date. As such, resistance is not determined by a single gene-for-gene recognition, as often associated with RxLR effectors [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

Armitage¹,

Lysøe

Nellist³

et al. 2018

PLoS ONE

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“…P. cactorum is a persistent pathogen of strawberry and an economically significant pathogen of apple (Erwin and Ribeiro 1996). Genomic resources are available for these hosts (Antanaviciute et al 2012; Hirakawa et al 2014; Davik et al 2015; Daccord et al 2017), and recent work has identified resistance-associated QTL for cultivated strawberry (Nellist et al 2018). Despite this, genomic resources for the pathogen are limited to identification of ESTs expressed during infection (Chen et al 2011) and transcript expression during oospore germination characterized (Chen et al 2014; Chen et al 2017).…”

Section: Discussionmentioning

confidence: 99%

“…Quantitative resistance to Phytophthora diseases has also been associated with basal defence (Vega-Sánchez et al 2005; Thomas et al 2007). Accordingly, this study characterises a broad range of effector genes and provides candidates to investigate the basis of quantitative strawberry resistance to P. cactorum (Denoyes-Rothan et al 2004; Shaw et al 2006; Shaw et al 2008; Nellist et al 2018). RxLR effectors are still priority candidates disease related pathogen genes for functional study of strawberry resistance to P. cactorum , particularly homologs of AvrSmira2 characterised avirulence genes.…”

Section: Discussionmentioning

confidence: 99%

“…This highlights the importance of understanding pathogen populations in the field and the associated genetic variation in effector complements. In contrast to these Phytophthora pathosystems, strawberry resistance to P. cactorum appears to be quantitative (partial; Denoyes-Rothan et al 2004; Shaw et al 2006; Shaw et al 2008; Nellist et al 2018), and no race structure has been reported to date. As such, resistance is not determined by a single gene-for-gene recognition, as often associated with RxLR (arginine, any amino-acid, leucine, arginine) effectors (Anderson et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

Armitage

Lysøe

Nellist

et al. 2018

Preprint

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22The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of 23 cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, cultured 24 from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large 25 number of genes encoding putative secreted effectors in the genome, including nearly 200 26 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families and 27 numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing 28 proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN 29 genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found 30 genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, 31 Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora 32 species of Clade 1A and 1C. The reported P. cactorum genome sequence and associated 33 annotations represent a comprehensive resource for avirulence gene discovery in other 34 Phytophthora species from Clade 1 and will facilitate effector informed breeding strategies in 35 other crops. 36 37 38 39 40 The oomycetes are a diverse class of eukaryotic microorganisms that include pathogens of plants, 41 animals and fungi (Simão et al. 2015). The causal agents of plant diseases are well represented in 42 this phylogenetic class, with over 60% of known oomycetes characterised as plant pathogens 43

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The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing

Yuan

Huang

et al. 2019

Hortic Res

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Strawberry ( Fragaria x ananassa ) is an allopolyploid species with diverse and complex transcripts. The regulatory mechanisms of fruit development and maturation have been extensively studied; however, little is known about the signaling mechanisms that direct this process in octoploid strawberry ( Fragaria x ananassa ). Here, we used long-read sequencing (LRS) technology and RNA-seq analysis to investigate the diversity and complexity of the polyploid transcriptome and differentially expressed transcripts along four successive fruit developmental stages of cultivated strawberry. We obtained a reference transcriptome with 119,897 unique full-length isoforms, including 2017 new isoforms and 2510 long noncoding RNAs. Based on the genome of the plausible progenitor ( Fragaria vesca ), 20,229 alternative splicing (AS) events were identified. Using this transcriptome, we found 17,485 differentially expressed transcripts during strawberry fruit development, including 527 transcription factors (TFs) belonging to 41 families. The expression profiles of all members of the auxin, ABA pathway, and anthocyanin biosynthesis gene families were also examined, and many of them were highly expressed at the ripe fruit stage, strongly indicating that the role of those genes is in the regulation of fruit ripening. We produce a high-quality reference transcriptome for octoploid strawberry, including much of the full-length transcript diversity, to help understand the regulatory mechanisms of fruit development and maturation of polyploid species, particularly via elucidation of the biochemical pathways involved in auxin, ABA, and anthocyanin biosynthesis.

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Quantitative Trait Loci ControllingPhytophthora cactorumResistance in the Cultivated Octoploid Strawberry (Fragariaxananassa)

Cited by 4 publications

References 46 publications

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

The complexity of the Fragaria x ananassa (octoploid) transcriptome by single-molecule long-read sequencing

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