An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the "CCG" class of effectors

Oliver J. Furzer; Volkan Cevik; Sebastian Fairhead; Kate Bailey; Amey Redkar; Christian Schudoma; Dan MacLean; Eric B. Holub; Jonathan D. G. Jones

doi:10.1094/MPMI-04-21-0075-R

An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the "CCG" class of effectors

Oliver J. Furzer, Volkan Cevik, Sebastian Fairhead, Kate Bailey, Amey Redkar, Christian Schudoma, Dan MacLean, Eric B. Holub, Jonathan D. G. Jones

The Sainsbury Laboratory

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7 Citations (Scopus)

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Abstract

Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text]

Original language	English
Pages (from-to)	39-48
Number of pages	10
Journal	Molecular plant-microbe interactions : MPMI
Volume	35
Issue number	1
Early online date	17 Dec 2021
DOIs	https://doi.org/10.1094/MPMI-04-21-0075-R
Publication status	Published - Jan 2022

Keywords

Albugo candida
biotrophy
effectors
genome
genomics
oomycete
oomycete–plant interactions
PacBio
population biology

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10.1094/MPMI-04-21-0075-RLicence: CC BY

mpmi-04-21-0075-rFinal published version, 1.96 MBLicence: CC BY

Cite this

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abstract = "Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as {"}CCG{"} based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text]",

keywords = "Albugo candida, biotrophy, effectors, genome, genomics, oomycete, oomycete–plant interactions, PacBio, population biology",

author = "Furzer, {Oliver J.} and Volkan Cevik and Sebastian Fairhead and Kate Bailey and Amey Redkar and Christian Schudoma and Dan MacLean and Holub, {Eric B.} and Jones, {Jonathan D. G.}",

note = "Funding Information: Funding: Support was provided by the Biotechnology and Biological Sciences Research Council (grant BB/L011646/1 to V. Cevik and grant BB/M003809/1 to O. J. Furzer), European Molecular Biology Organization (long-term fellowship ALTF-842-2015 to A. Redkar), and H2020 European Research Council (grant 233376 to K. Bailey and J. D. G. Jones). The Sainsbury Laboratory is supported by the Gatsby Charitable Foundation.",

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doi = "10.1094/MPMI-04-21-0075-R",

language = "English",

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pages = "39--48",

journal = "Molecular plant-microbe interactions : MPMI",

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AU - Cevik, Volkan

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AU - Redkar, Amey

AU - Schudoma, Christian

AU - MacLean, Dan

AU - Holub, Eric B.

AU - Jones, Jonathan D. G.

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N2 - Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text]

AB - Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text]

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An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the "CCG" class of effectors

Abstract

Keywords

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Gene-for-gene coevolution between Albugo candida and Arabidopsis; mining non-host resistance genes for white rust control in Brassicaceae crops

Cite this

An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the "CCG" class of effectors

Abstract

Keywords

Access to Document

Other files and links

Projects

Gene-for-gene coevolution between Albugo candida and Arabidopsis; mining non-host resistance genes for white rust control in Brassicaceae crops

Cite this