Identification of novel microRNAs in the Verticillium wilt-resistant upland cotton variety KV-1 by high-throughput sequencing

Abstract

Plant microRNAs (miRNAs) play essential roles in the post-transcriptional regulation of gene expression during development, flowering, plant growth, metabolism, and stress responses. Verticillium wilt is one of the vascular disease in plants, which is caused by the Verticillium dahlia and leads to yellowing, wilting, lodging, damage to the vascular tissue, and death in cotton plants. Upland cotton varieties KV-1 have shown resistance to Verticillium wilt in multiple levels. However, the knowledge regarding the post-transcriptional regulation of the resistance is limited. Here two novel small RNA (sRNA) libraries were constructed from the seedlings of upland cotton variety KV-1, which is highly resistant to Verticillium wilts and inoculated with the V991 and D07038 Verticillium dahliae (V. dahliae) of different virulence strains. Thirty-seven novel miRNAs were identified after sequencing these two libraries by the Illumina Solexa system. According to sequence homology analysis, potential target genes of these miRNAs were predicted. With no more than three sequence mismatches between the novel miRNAs and the potential target mRNAs, we predicted 49 target mRNAs for 24 of the novel miRNAs.These target mRNAs corresponded to genes were found to be involved in plant–pathogen interactions, endocytosis, the mitogen-activated protein kinase (MAPK) signaling pathway, and the biosynthesis of isoquinoline alkaloid, terpenoid backbone, primary bile acid and secondary metabolites. Our results showed that some of these miRNAs and their relative gene are involved in resistance to Verticillium wilts. The identification and characterization of miRNAs from upland cotton could help further studies on the miRNA regulatory mechanisms of resistance to Verticillium wilt.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-3-564) contains supplementary material, which is available to authorized users.

Long noncoding RNAs involve in resistance to Verticillium dahliae, a fungal disease in cotton

“…However, advanced sequencing data will unveil profiles of lncRNAs and provide new insights and promising lncRNA candidates in this area. There were some small RNAs identified related to cotton defence againt V. dahliae (He et al ., ; Yin et al ., ), but information related to lncRNAs in cotton was restricted to fibre development (Wang et al ., ). The availability of the complete genome sequences of Gossypium barbadense and Gossypium hirsutum has made it possible to conduct a genomewide comparative analysis of lncRNAs associated with disease response (Yuan et al ., ; Zhang et al ., ).…”

The ghr-miR164 and GhNAC100 module participates in cotton plant defence against Verticillium dahliae

“…We identified 378 novel miRNAs from three sRNA libraries of roots inoculated with V. dahliae and the mock-treated control at 7- and 10-dpi when the fungus has entered the inner root tissues. However, previous studies showed that significantly fewer novel miRNAs were identified at 12, 24, 36 or 48 hours after inoculation (He et al ., 2014; Yin et al , 2012; Zhang et al , 2015a). For instance, 14 novel miRNAs were identified from Verticillium-inoculated cotton roots at 12 and 24 hours (Yin et al ., 2012), 37 novel miRNAs were identified from two sRNA libraries of the cotton seedlings inoculated with V. dahliae at 24 and 48 hours (He et al , 2014), and 58 novel miRNAs were identified from sRNA sequencing of the cotton roots inoculated with V. dahliae at 24 hours (Zhang et al ., 2015a).…”

“…miRNA expression sequencing in the early response of the cotton plants to V. dahliae infection has been reported, which showed that many early induction miRNAs were observed that possibly participated in plant defence (Yin et al , 2012; He et al ., 2014; Zhang et al , 2015a). For example, Yin et al (2012) investigated the transcriptional profile of the miRNAs in Verticillium-inoculated cotton roots at 12 and 24 hours and identified 215 miRNA families and 14 novel miRNAs.…”

“…For example, Yin et al (2012) investigated the transcriptional profile of the miRNAs in Verticillium-inoculated cotton roots at 12 and 24 hours and identified 215 miRNA families and 14 novel miRNAs. Two small RNA (sRNA) libraries were constructed from the seedlings of the upland cotton variety KV-1 inoculated with V. dahliae at 24 and 48 hours; 37 novel miRNAs were identified, and potential target genes of these miRNAs were predicted (He et al , 2014). Zhang et al (2015a) conducted sRNA sequencing and degradome sequencing of cotton roots inoculated with V. dahliae at 24 hours and identified 140 known miRNAs and 58 novel miRNAs.…”

New opportunities for the regulation of secondary metabolism in plants: focus on microRNAs

“…Apparently, the effect of each miRNA is specific, and its down-regulation or overexpression will not result in global changes in the plant transcriptome. In Taxus mairei, Catharanthus roseus, Papaver somniferum and other economically important plants, several miRNAs have been identified as regulators of secondary metabolism (Hao et al 2012;Pani and Mahapatra 2013;He et al 2014;Boke et al 2015;Vashisht et al 2015).…”