Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat

Functional & Integrative Genomics
Himanshu DubeyTilak Raj Sharma

Abstract

Cross-kingdom RNAi is a well-documented phenomenon where sRNAs generated by host and pathogens may govern resistance or susceptible phenotypes during host-pathogen interaction. With the first example of the direct involvement of fungal generated sRNAs in virulence of plant pathogenic fungi Botrytis cinerea and recently from Puccinia striiformis f. sp. tritici, we attempted to identify sRNAs in Puccinia triticina (P. triticina). Four sRNA libraries were prepared and sequenced using Illumina sequencing technology and a total of ~ 1-1.28 million potential sRNAs and two microRNA-like small RNA (mil-RNAs) candidates were identified. Computational prediction of targets using a common set of sRNAs and P. triticina mil-RNAs (pt-mil-RNAs) within P. triticina and wheat revealed the majority of the targets as repetitive elements in P. triticina whereas in wheat, the target genes were identified to be involved in many biological processes including defense-related pathways. We found 9 receptor-like kinases (RLKs) and 14 target genes of each related to reactive oxygen species (ROS) pathway and transcription factors respectively, including significant numbers of target genes from various other categories. Expression analysis of twenty select...Continue Reading

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Citations

May 16, 2020·Frontiers in Plant Science·Bernhard Timo WernerAline Michaela Koch
Jul 25, 2020·Functional & Integrative Genomics·Himanshu DubeyTilak Raj Sharma
Nov 30, 2020·Journal of Plant Physiology·Isabel M L Saur, Ralph Hückelhoven
May 26, 2020·Fungal Biology·Pramod PrasadP K Gupta
Jun 3, 2021·Annual Review of Phytopathology·Yongli QiaoWenbo Ma

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Datasets Mentioned

BETA
PRJNA416416
LACZ00000000

Methods Mentioned

BETA
PCR
ubiquitination

Software Mentioned

Tmhmm
BLASTn
AUGUSTUS
Infernal
PatMaN
BEDtools
RepeatMasker
psRNATarget
REVIGO
TargetP

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