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Genomics of Plasmodiophora brassicae

Stjelja Arvelius, Suzana (2021). Genomics of Plasmodiophora brassicae. Diss. (sammanfattning/summary) Sveriges lantbruksuniv., Acta Universitatis Agriculturae Sueciae, 1652-6880
ISBN 978-91-7760-817-2
eISBN 978-91-7760-818-9
[Doctoral thesis]

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Abstract

Plasmodiophora brassicae is a soil-borne pathogen that infects roots of plants in Brassicaceae and causes enlarged roots or clubs known as the clubroot disease. Details of its complex life cycle and particularly the molecular basis of its strategies to master defenses and alter metabolism of plant hosts are still largely unknown.
The general aim of this thesis was to enhance the genomic knowledge on P. brassicae and its intimate relationship with a plant host. We developed a protocol for extraction of large amounts of high-quality DNA from pathogen resting spores that allowed us to apply long-read PacBio sequencing. De-novo assembly of the P. brassicae e3 strain generated a 25.2 Mb nuclear genome and a mitochondrial genome (114.6 kb). Twenty nuclear contigs were assembled of which 13 from telomere-to-telomere, thanks to the resolution of highly repetitive sequences. As much as 11.5% of the genome was assigned to repetitive sequences, a higher proportion than previously estimated. The most abundant were transposable elements (TEs) such as Copia and Gypsy and unclassified interspersed repeats. They were particularly clustered in telomeric, sub-telomeric and large regions with complex structural variation found on each contig. Among 9,231 predicted protein-coding genes in the nuclear genome, we identified 314 small, secreted proteins as P. brassicae effector candidates. They were distributed along all contigs. TEs and unclassified repeats were found within a 3 kb distance from more than a third of the predicted effectors. We further detected enrichment of the effector candidates with a motif rich in valine, leucine and alanine amino acids. Annotation of the circular mitochondrial genome revealed a compact and complex sequence organization with intron-rich genes, a new splicing mechanism and a previously not resolved 12 kb repetitive region.
Our findings and the new genome sequences, currently representing the only P. brassicae long-read assembly, form a valuable resource for comparative and functional analyses.

Authors/Creators:Stjelja Arvelius, Suzana
Title:Genomics of Plasmodiophora brassicae
Series Name/Journal:Acta Universitatis Agriculturae Sueciae
Year of publishing :2021
Number:2021:70
Number of Pages:73
Publisher:Swedish University of Agricultural Sciences
ISBN for printed version:978-91-7760-817-2
ISBN for electronic version:978-91-7760-818-9
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Article category:Other scientific
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:chromosome, clubroot, effector, genome, PacBio long-read sequencing, Plasmodiophora brassicae, repetitive sequences
URN:NBN:urn:nbn:se:slu:epsilon-p-114497
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-114497
ID Code:26285
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
Deposited By: SLUpub Connector
Deposited On:08 Dec 2021 08:32
Metadata Last Modified:10 Dec 2021 11:36

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