Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots.

Evgeny A Zorin,Olga A Kulaeva,Alexey M Afonin,Oksana Y Shtark,Emma S Gribchenko,Vladimir A Zhukov

doi:10.3390/plants9121700

Evgeny A Zorin, Olga A Kulaeva + Show 4 more

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https://doi.org/10.3390/plants9121700

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Abstract

Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (Pisum sativum L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization.

Highlights

Legume plants are among the most symbiotically active groups of plants, since they are able to interact with a wide range of beneficial soil microorganisms [1,2]
The trimmed reads of pea mycorrhizal and non-mycorrhizal roots of pea cv
Frisson were mapped to the reference genome of pea cv

Summary

Introduction

Legume plants (family Fabaceae) are among the most symbiotically active groups of plants, since they are able to interact with a wide range of beneficial soil microorganisms [1,2]. In the course of evolution, legumes acquired the unique ability to develop two types of mutualistic endosymbioses: nitrogen-fixing symbiosis (NFS) with nodule bacteria and arbuscular mycorrhiza (AM), an ancient symbiosis with fungi of the division Glomeromycota [3]. The formation of symbiotic relationships between a legume plant and AM fungi or nodule bacteria is controlled by a large number of genes encoding receptors, components of the signal cascade, various transcription factors, and transporters [4]. The application of the “reverse genetics” approach to the study of symbiosis in legume plants led to the identification of hundreds of genes (so called “symbiosins”) that are expressed in plant roots during the development of symbiosis [7]. Recent advances in “omics” technologies, namely, Plants 2020, 9, 1700; doi:10.3390/plants9121700 www.mdpi.com/journal/plants

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