Characterization of the genome of a phylogenetically distinct tospovirus and its interactions with the local lesion-induced host Chenopodium quinoa by whole-transcriptome analyses

Abstract

Chenopodium quinoa is a natural local lesion host of numerous plant viruses, including tospoviruses (family Bunyaviridae). Groundnut chlorotic fan-spot tospovirus (GCFSV) has been shown to consistently induce local lesions on the leaves of C. quinoa 4 days post-inoculation (dpi). To reveal the whole genome of GCFSV and its interactions with C. quinoa, RNA-seq was performed to determine the transcriptome profiles of C. quinoa leaves. The high-throughput reads from infected C. quinoa leaves were used to identify the whole genome sequence of GCFSV and its single nucleotide polymorphisms. Our results indicated that GCFSV is a phylogenetically distinct tospovirus. Moreover, 27,170 coding and 29,563 non-coding sequences of C. quinoa were identified through de novo assembly, mixing reads from mock and infected samples. Several key genes involved in the modulation of hypersensitive response (HR) were identified. The expression levels of 4,893 deduced complete genes annotated using the Arabidopsis genome indicated that several HR-related orthologues of pathogenesis-related proteins, transcription factors, mitogen-activated protein kinases, and defense proteins were significantly expressed in leaves that formed local lesions. Here, we also provide new insights into the replication progression of a tospovirus and the molecular regulation of the C. quinoa response to virus infection.

Full-Length Transcriptome Sequencing Reveals the Impact of Cold Stress on Alternative Splicing in Quinoa

“…Schmöckel et al (2017) used a multifaceted approach integrating RNA-seq analyses with comparative genomics and topology prediction to identify 219 candidate genes that were differentially expressed in response to salinity in quinoa [ 58 ]. Other RNA-seq experiments have been used to reveal interactions between environment and quinoa [ 59 , 60 ]. Until now, the effects of cold stress on quinoa gene expression had not been explored.…”

Transcriptomics of plant–virus interactions: a review

“…The RNAseq of Chenopodium quinoa inoculated with the tospovirus Groundnut chlorotic fan-spot virus (GCFSV) allowed to obtain the viral whole genome and its single nucleotide polymorphisms, and the transcriptome profiles of C. quinoa leaves, which identified several key genes involved in the modulation of hypersensitive response (HR), such as pathogenesis-related proteins (CqBG1, CqCHIB and CqPRB1), transcription factors (WRKY family; CqWRKY42, CqWRKY53 and CqWRKY75), mitogenactivated protein kinases (CqMKK1, CqSNAP33 and CqSYR1). Besides that with the nucleotide sequence was possible verify that GCFSV is a phylogenetically distinct tospovirus (Chou et al 2017).…”

Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective

“…amaranticolor (a weed host) and C . quinoa infected with different viruses determined modulation of photosynthesis, hormone signaling, plant-pathogen interaction, secondary metabolites, lipid, amino acid, protein, and carbohydrate metabolism [ 36 – 39 ]. However, there is no knowledge on the impact of virus infection on transcriptome and small RNA profiles of sweet or bitter quinoa varieties.…”