Expression and diversification analysis reveals transposable elements play important roles in the origin of <scp>L</scp>ycopersicon‐specific lnc<scp>RNA</scp>s in tomato

Wang, Xin; Ai, Guo; Zhang, Chunli; Cui, Long; Wang, Jiafa; Li, Hanxia; Zhang, Mengjie; Ye, Zhibiao

doi:10.1111/nph.13718

Cited by 80 publications

(72 citation statements)

References 77 publications

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“…LncRNAs have emerged as potential key regulators of transcription. A large amount of lncRNAs have recently been identified to regulate tomato fruit ripening and response to TYLCV (Wang et al ., , ; Zhu et al ., ). Meanwhile, a number of lncRNAs play important roles in plant–pathogen interactions, such as wheat– P. striiformis , tomato–TYLCV, Arabidopsis –F.…”

Section: Discussionmentioning

confidence: 99%

“…() identified a set of F. oxysporum ‐induced lncRNAs (15 lncNATs and 20 lincRNAs) in Arabidopsis thaliana , which were associated with genes that may be involved in disease resistance. In tomato, lncRNA‐314, a fruit‐specific lncRNA expressed in S. lycopersicum and S. pimpinellifolium , but not in S. pennellii , originated through two evolutionary events: a long terminal repeat retro‐transposition; and the promoter region deletion (Wang et al ., ). Another pair of lncRNAs, lncRNA1459 and lncRNA1840, might also regulate tomato fruit ripening (Zhu et al ., ).…”

Section: Introductionmentioning

confidence: 97%

“…Generally, long non‐coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides (nt) in length that possess no apparent coding sequence (CDS) or open reading frame (Fan et al ., ; Wang et al ., ). A number of lncRNAs have recently been identified in plant species due to rapid progress in omics sequencing technology (Li et al ., ; Zou et al ., ), including Arabidopsis (Ben Amor et al ., ; Liu et al ., ; Di et al ., ; Wang et al ., ), rice (Zhang et al ., ), maize (Li et al ., ; Fan et al ., ), wheat (Xin et al ., ), cotton (Wang et al ., ; Zou et al ., ), tomato (Wang et al ., , ; Zhu et al ., ), cucumber (Hao et al ., ), Chinese cabbage (Song et al ., ), Populus (Shuai et al ., ; Chen et al ., ) and others. In particular, studies on plant lncRNAs are far behind those in humans and animals (Liu et al ., ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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The rapid development of omics sequencing technology has facilitated the identification of thousands of long non-coding (lnc)RNAs in plant species, but the role of lncRNAs in plant-pathogen interactions remains largely unexplored. We used comparative transcriptome analysis of Phytophthora infestans-resistant and -susceptible tomatoes to identify differentially expressed genes (DEGs) and lncRNAs (DELs), and examine lncRNA-mRNA networks. A total of 1037 DEGs and 688 DELs were identified between P. infestans-resistant and -susceptible tomatoes. The co-localization networks, including 128 DEGs and 127 DELs, were performed. We found that lncRNA16397 acted as an antisense transcript of SlGRX22 to regulate its expression, and also induced SlGRX21 expression when lncRNA16397 was overexpressed. In addition, disease symptoms and reactive oxygen species (ROS) accumulation in tomatoes overexpressing lncRNA16397 and SpGRX were fewer and lower than those in wild-type after P. infestans infection. This result suggests that tomato lncRNA16397 induces SlGRX expression to reduce ROS accumulation and alleviate cell membrane injury, resulting in enhanced resistance to P. infestans. Our results provide insight into lncRNAs involved in the response of tomato to P. infestans infection, demonstrate that the lncRNA16397-GRXs network is an important component of the P. infestans network in tomato, and provide candidates for breeding to enhance biotic stress-resistance in tomato.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2017

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“…(Yu et al ., ), populus (Shuai et al ., ), Triticum aestivum (wheat; Xin et al ., ), Gossypium spp . (cotton; Wang et al ., ) Gossypium arboreum (cotton; Zou et al ., ), Solanum lycopersicum (tomato; Wang et al ., ; Zhu et al ., ; Wang et al ., ), Cucumis sativus (cucumber; Hao et al ., ) and other plants. Most of these genome‐wide studies have focused on identifying novel lncRNAs and profiling expression patterns, but some of them have assessed transcription factor regulation at the transcriptional level (Di et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Yuan

Yang

et al. 2018

The Plant Journal

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Recently, long non-coding RNAs (lncRNAs) have been demonstrated to be involved in many biological processes of plants; however, a systematic study on transcriptional and, in particular, post-transcriptional regulation of stress-responsive lncRNAs in Oryza sativa (rice) is lacking. We sequenced three types of RNA libraries (poly(A)+, poly(A)- and nuclear RNAs) under four abiotic stresses (cold, heat, drought and salt). Based on an integrative bioinformatics approach and ~200 high-throughput data sets, ~170 of which have been published, we revealed over 7000 lncRNAs, nearly half of which were identified for the first time. Notably, we found that the majority of the ~500 poly(A) lncRNAs that were differentially expressed under stress were significantly downregulated, but approximately 25% were found to have upregulated non-poly(A) forms. Moreover, hundreds of lncRNAs with downregulated polyadenylation (DPA) tend to be highly conserved, show significant nuclear retention and are co-expressed with protein-coding genes that function under stress. Remarkably, these DPA lncRNAs are significantly enriched in quantitative trait loci (QTLs) for stress tolerance or development, suggesting their potential important roles in rice growth under various stresses. In particular, we observed substantially accumulated DPA lncRNAs in plants exposed to drought and salt, which is consistent with the severe reduction of RNA 3'-end processing factors under these conditions. Taken together, the results of this study reveal that polyadenylation and subcellular localization of many rice lncRNAs are likely to be regulated at the post-transcriptional level. Our findings strongly suggest that many upregulated/downregulated lncRNAs previously identified by traditional RNA-seq analyses need to be carefully reviewed to assess the influence of post-transcriptional modification.

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“…Non‐coding RNAs (ncRNAs) that have no or little protein‐coding potential take up a large proportion of the eukaryotic genome and can play roles in various biological processes (Zhang and Chen , Liu et al , Wang et al ). Unlike microRNA (miRNA), small interfering RNA (siRNA) and long non‐coding RNA (lncRNA), studies of which have made great progress in the past few years (Chen , Chekanova , Gao et al ), circular RNAs (circRNAs) are newly discovered endogenous ncRNAs (Salzman et al , , Memczak et al , Wang et al ).…”

Section: Introductionmentioning

confidence: 99%

Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

Wang

Gao

et al. 2017

Physiologia Plantarum

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Circular RNAs (circRNAs) are a large class of non-coding endogenous RNAs that could act as competing endogenous RNAs (ceRNAs) to terminate the mRNA targets' suppression of miRNAs. To elucidate the intricate regulatory roles of circRNAs in the ethylene pathway in tomato fruit, deep sequencing and bioinformatics methods were performed. After strict screening, a total of 318 circRNAs were identified. Among these circRNAs, 282 were significantly differentially expressed among wild-type and sense-/antisense-LeERF1 transgenic tomato fruits. Besides, 1254 target genes were identified and a large amount of them were found to be involved in ethylene pathway. In addition, a sophisticated regulatory model consisting of circRNAs, target genes and ethylene was set up. Importantly, 61 circRNAs were found to be potential ceRNAs to combine with miRNAs and some of the miRNAs had been revealed to participate in the ethylene signaling pathway. This research further raised the possibility that the ethylene pathway in tomato fruit may be under the regulation of various circRNAs and provided a new perspective of the roles of circRNAs.

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Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon‐specific lncRNAs in tomato

Cited by 80 publications

References 77 publications

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

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

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

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