Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

Abstract

Recently, a large number of long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, how lncRNAs function during plant DNA virus infection is largely unknown. We performed strand-specific paired-end RNA sequencing of tomato samples infected with Tomato yellow leaf curl virus (TYLCV) with three biological replicates. Overall, we predicted 1565 lncRNAs including long intergenic ncRNAs (lincRNAs) and natural antisense transcripts (lncNATs) and definitively identified lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS). We also verified the functions of a set of lncRNAs that were differentially expressed between 0 and 7 days post inoculation (dpi). More importantly, we found that several lncRNAs acted as competing endogenous target mimics (eTMs) for tomato microRNAs involved in the TYLCV infection. These results provide new insight into lncRNAs involved in the response to TYLCV infection that are important components of the TYLCV network in tomatoes.

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

“…A significant number of transcripts (26 784) were identified as lncRNAs in rose‐scented geranium. The number of lncRNAs detected in this study was comparable with the previous studies on T. aestivum (44 698 lncRNAs) , maize (20 163 lncRNAs) , Populus trichocarpa (2542 lncRNAs) , Arabidopsis (6480 lncRNAs) , rice (2224 lncRNAs) , sea buckthorn (3428 lncRNAs) , Actinidia chinensis (7051 lncRNAs) , tomato (3558 lncRNAs) , Cajanus cajan (3919 lncRNAs) , and Vitis vinifera (3210 lncRNAs) etc. However, out of the total lncRNAs detected in rose‐scented geranium, only 1.8% could be annotated against the different public lncRNA databases, as high‐confidence lncRNAs.…”

Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co‐expressing glutaredoxin

“…A total of 688 lncRNAs as significant differential expressed lncRNAs were identified ( P ‐value <0.05 and fold change >2 or <−2) in leaves of Sp samples compared with Slz samples, including 277 upregulated lncRNAs and 411 downregulated lncRNAs (Figures a and S2; Table S3). We found more DELs (7.0%) than DEGs (4.5%) between Sp and Slz, suggesting that lncRNAs might have a markedly differential expression pattern compared with protein‐coding genes between Sp and Slz (Wang et al ., ). In addition, we also found 257 and 391 lncRNAs that were specifically expressed in Sp and Slz samples, respectively (Figure e).…”

“…Tritici (Zhang et al ., ). In tomato–TYLCV interaction, it was found that tomato lncRNA Slylnc0195 might function as a competing endogenous RNA by biding to miR166 via target mimicry to protect its targets, class III HD‐Zip transcription factor genes (Wang et al ., ). Meanwhile, Zhu et al .…”

“…In particular, studies on plant lncRNAs are far behind those in humans and animals (Liu et al ., ). Plant lncRNAs have been found to be involved in some biological processes, including gene silencing (Franco‐Zorrilla et al ., ; Wu et al ., ), flowering time regulation (Liu et al ., ; Heo and Sung, ; Wang et al ., ), biotic and abiotic stress responses (Ben Amor et al ., ; Zhu et al ., ; Wang et al ., ), photomorphogenesis (Wang et al ., ) and other important developmental pathways. In studies on plant–pathogen interactions, the expression levels of four lncRNAs from wheat Triticum aestivum L. have been shown to change differentially upon inoculation with Puccinia striiformis f. sp.…”

Long Non-Coding RNAs Responsive to Witches’ Broom Disease in Paulownia tomentosa

“…LncRNAs involved in the responses of plants to biotic stresses have also been identified. For example, in wheat, four lncRNAs involved in the response to stripe rust pathogen infection have been identified [31]; in Arabidopsis, lncRNAs responsive to Fusarium oxysporum infection were revealed and played an important role in antifungal immunity [38]; and in tomato, lncRNAs have been identified as endogenous target mimics for miRNAs in response to Tomato yellow leaf curl virus infection [39], and a lncRNA (lncRNA16397) that conveys resistance to Phytophthora infestans by co-expressing glutaredoxin has also been detected [40]. However, in studies of PaWB, lncRNAs that play important roles in the Paulownia-phytoplasma interaction have not yet been identified.…”