The 25-26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes

Frontiers in Microbiology
Jinbu JiaWeixing Shan

Abstract

Small RNAs (sRNAs) are important non-coding RNA regulators, playing key roles in developmental regulation, transposon suppression, environmental response, host-pathogen interaction and other diverse biological processes. However, their roles in oomycetes are poorly understood. Here, we performed sRNA sequencing and RNA sequencing of Phytophthora parasitica at stages of vegetative growth and infection of Arabidopsis roots to examine diversity and function of sRNAs in P. parasitica, a model hemibiotrophic oomycete plant pathogen. Our results indicate that there are two distinct types of sRNA-generating loci in P. parasitica genome, giving rise to clusters of 25-26 nt and 21 nt sRNAs, respectively, with no significant strand-biases. The 25-26 nt sRNA loci lie predominantly in gene-sparse and repeat-rich regions, and overlap with over 7000 endogenous gene loci. These overlapped genes are typically P. parasitica species-specific, with no homologies to the sister species P. infestans. They include approximately 40% RXLR effector genes, 50% CRN effector genes and some elicitor genes. The transcripts of most of these genes could not be detected at both the vegetative mycelium and infection stages as revealed by RNA sequencing, indicati...Continue Reading

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Citations

Dec 18, 2018·Frontiers in Microbiology·Stephanie R BollmannNiklaus J Grünwald
Sep 27, 2019·Molecular Plant Pathology·Özlem BilirMahmut Tör
Mar 9, 2021·Current Opinion in Plant Biology·Suomeng Dong, Wenbo Ma
Jun 3, 2021·Annual Review of Phytopathology·Yongli QiaoWenbo Ma
Oct 5, 2021·The New Phytologist·Xinyi HuChristina Dixelius

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Datasets Mentioned

BETA
PRJNA382499
AAB29433.1

Methods Mentioned

BETA
co-immunoprecipitation
RNA-seq
electrophoresis
transgenic
AGO CO-IP

Software Mentioned

Blast2go
R
Blastp
Circos
Cuffnorm
topGO
PSI
Hisat2
blastn
Cuffquant

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