Integrated single-molecule long-read sequencing and Illumina sequencing reveal the resistance mechanism of Psathyrostachys huashanica in response to barley yellow dwarf virus-GAV

Chuan Shen,Jingyuan Li,Yunfeng Wu,Caiyan Wei,Xudong Zhang

doi:10.1186/s42483-020-00057-8

Chuan Shen, Jingyuan Li + Show 3 more

Open Access

https://doi.org/10.1186/s42483-020-00057-8

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Abstract

Although Psathyrostachys huashanica has excellent potential for resistance gene mining and molecular genetic breeding, no reference genome is available. To date, most studies of P. huashanica have been focused on the creation of translocation lines and additional lines, as well as the development of molecular markers. Therefore, research at the transcriptional level is lacking. In this study, the full-length transcriptome of P. huashanica was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample to explore the potential full-length transcript isoforms. We obtained 112,596 unique transcript isoforms with a total length of 114,957,868 base pairs (bp). Subsequently, Illumina sequencing reads were used to correct and trim the PacBio isoforms. We annotated 103,875 unigenes in at least one functional database, and identified a plethora of differentially-expressed genes (DEGs) that are involved in the defense responses of P. huashanica against barley yellow dwarf virus-GAV (BYDV-GAV). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mostly involved in plant-pathogen interaction, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) signaling pathway. Additionally, we selected twenty of the RNA-seq identified resistance-related up-regulated genes, including MAPKs, cysteine-rich receptor-like protein kinases (CRPKs), calcium-dependent protein kinases (CDPKs), pathogenesis-related protein (PR) proteins, WRKYs, and disease resistance proteins, and validated their up-regulation in response to BYDV-GAV by quantitative real-time PCR. Our results indicate that a series of defense-related genes were induced in P. huashanica during BYDV-GAV infection. The full-length transcriptome dataset will contribute to improved use of stress-resistance genes of P. huashanica, and serves as a reference database for the analysis of transcript expression in P. huashanica.

Highlights

IntroductionIn 1991, scientists began to create hybrid materials between common wheat and P. huashanica
Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) is a perennial cross-pollinating plant, which is a rare and endangered plant and a wild relative of crops in need of protection (Baden1991)
Construction of a long-read reference transcriptome for P. huashanica To obtain the desirable transcript isoforms, high-quality RNA was extracted from four types of P. huashanica tissue to generate four RNA samples, which were subsequently pooled in equal amounts

Summary

Introduction

In 1991, scientists began to create hybrid materials between common wheat and P. huashanica. To study its resistance to stripe rust, genomic in situ hybridization (GISH) and EST-SSR techniques were used to create a Triticum aestivum-P. huashanica Keng monosomic addition line, PW11, with high resistance to stripe rust. This led to the discovery that a small terminal segment of the 3Ns genome carrying new stripe rust resistance genes resulted in high levels of disease resistance (Du et al 2014a). A recent study showed that P. huashanica exhibits high resistance to the barley yellow dwarf virus-GAV (BYDV-GAV) and can disrupt the movement of viral particles from inoculated leaves to new leaves (Song et al 2013)

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