Integrated mRNA and microRNA transcriptome analysis reveals miRNA regulation in response to PVA in potato

Abstract

Potato (Solanum tuberosum L.) is the fourth most important crop worldwide. Potato virus A (PVA) is one of the most harmful viruses infecting potatoes. However, the molecular mechanisms governing the responses to PVA infection in potato at the transcriptional and post-transcriptional levels are not well understood. In this study, we performed both mRNA and small RNA sequencing in potato leaves to identify the genes and miRNAs involved in the response to PVA infection. A total of 2,062 differentially expressed genes (DEGs) and 201 miRNAs (DEMs) were identified, respectively. Gene ontology (GO) and KEGG analysis revealed that these DEGs were involved in the transduction of pathogen signals, transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related (PR) genes, and changes in secondary metabolism. Small RNA sequencing revealed 58 miRNA-mRNA interactions related to PVA infection. Some of the miRNAs (stu-miR482d-3p, stu-miR397-5p, etc) which target PR genes showed negative correlations between the DEMs and DEGs. Eight of the DEGs and three DEMs with their target genes were further validated by quantitative real time-PCR (qRT-PCR). Overall, this study provides a transcriptome-wide insight into the molecular basis of resistance to PVA infection in potato leaves and potenital candidate genes for improving resistance cultivars.

Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway

“…Nevertheless, the number of the potato miRNAs (219) deposited in miRBase ( http://www.mirbase.org/ ) was still less than that of rice (1519), Arabidopsis (664), cotton ( Gossypium spp L.) (539) and maize (404). The function of some potato miRNAs were also confirmed, for example, miR172 could induce the potato tuberization ( Martin et al, 2009 ), miR396 , miR156a , miR157a and four miR169s were drought-induced ( Yang et al., 2016 ; Hwang, Shin & Kwon, 2011 ), miR156 could modulate potato architecture and tuberization ( Bhogale et al, 2014 ), miR166 and miR159 were responding to salinity ( Kitazumia et al, 2015 ), miR482e could enhance plant sensitivity to Verticillium dahliae infection ( Yang et al, 2015 ), miR397-5P was involved in the PVA infection ( Li et al, 2017 ), miR164 could mediate the lateral root development ( Zhang et al, 2018 ), and miR160 was associated with local defense and systemic acquired resistance against Phytophthora infestans ( Natarajan et al, 2018 ). Herein, a large number of miRNAs have yet to be discovered, and the functions of most miRNAs remain to be investigated in potato.…”

Plant miR397 and its functions

“…In order to better understand the function of miRNAs in pathogen infection, many studies were conducted to identify the differential expressed miRNAs induced by infection through high-throughput sequencing. MiR397 was identified as one of the delegates (Li et al 2017;Xia et al 2018). However, further investigation is lacking.…”

Transcriptomic Insights into Innate Immunity Responding to Red Rot Disease in Red Alga Pyropia yezoensis

“…Plants suffer from a variety of diseases that are caused by fungi [1,2,3], oomycetes [4,5], bacteria [6], and viruses [7,8,9]. It is evident that plants rely on their innate immune system to resist infection.…”