Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

Xiao, Huamei; Yuan, Zhuting; Guo, Dan; Hou, Bofeng; Yin, Chuanlin; Zhang, Wenqing; Li, Fēi

doi:10.1186/s12864-015-1953-y

Cited by 65 publications

(74 citation statements)

References 47 publications

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“…Some mammalian lncRNAs can function in cis as scaffolds to recruit co-activator complexes that mediate chromosome looping between enhancer and promoter regions, controlling chromatin topology and modulating gene expression at the transcriptional level54. Emerging evidence showed that lncRNAs tend to influence the expression of adjacent genes or overlapping genes5556. To investigate the possible functions of cassava lncRNAs, we predicted the potential targets of lincRNAs in cis-regulatory relationships.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Ning

et al. 2017

Sci Rep

116

142

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Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

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Section: Resultsmentioning

confidence: 99%

Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Ning

et al. 2017

Sci Rep

116

142

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“…Although lncRNAs are widely identified in some insect species with the application of RNA‐seq technology (Etebari et al ., ; Jayakodi et al ., ; Jenkins et al ., ; Legeai & Derrien, ; Xiao et al ., ; Chen et al ., ; Wu et al ., ), the information about lncRNAs in the silkworm is relatively rare. A previous study suggested that nine silk gland‐enriched ncRNAs may be involved in the development of silk gland and fibroin synthesis (Li et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…The transcripts in which categories corresponded to “I”, “j”, “o”, “u” or “x” were retained and then the strand unknown transcripts were deleted (Sun et al ., ). Putative lncRNAs were defined as the length of transcript ≥ 200 bp and open reading frames (ORFs) ≤ 100 amino acids (Li et al ., ; Liao et al ., ; Xiao et al ., ). The protein‐coding potential of each transcript was estimated using Coding Potential Calculator (CPC) software (Kong et al ., ).…”

Section: Methodsmentioning

confidence: 97%

“…The protein‐coding potential of each transcript was estimated using Coding Potential Calculator (CPC) software (Kong et al ., ). The candidate transcripts were searched against Pfam databases (http://pfam.xfam.org) with e‐values of 0.001 and non‐significant transcripts were retained (Xiao et al ., ). Transcripts which had alignment length ≥ 100 amino acids and identity ≥ 80% with non‐redundancy (nr) were removed (Pauli et al ., ; Liao et al ., ).…”

Section: Methodsmentioning

confidence: 99%

“…Long non‐coding RNAs (lncRNAs) are a kind of non‐coding RNAs (ncRNAs) with at least 200 nucleotides (nt) and they are transcribed by RNA polymerase II (RNAPII) (Mercer et al ., ; Kornienko et al ., ; Cao, ). As the development of high throughput RNA sequencing technology (RNA‐seq), lncRNAs have been identified across eukaryotes including Drosophila melanogaster , Nilaparvata lugens , Plutella xylostella and Bombyx mori (Young et al ., ; Etebari et al ., ; Legeai & Derrien, ; Xiao et al ., ; Chen et al ., ; Wu et al ., ). Previous studies have revealed that lncRNAs play important regulation roles in various biological processes (Mercer et al ., ; Wang & Chang, ; Cao, ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Identification and comparison of long non‐coding RNAs in the silk gland between domestic and wild silkworms

et al. 2017

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Under long-term artificial selection, the domestic silkworm (Bombyx mori) has increased its silk yield tremendously in comparison with its wild progenitor, Bombyx mandarina. However, the molecular mechanism of silk yield increase is still unknown. Comparative analysis of long non-coding RNAs (lncRNAs) may provide some insights into understanding this phenotypic variation. In this study, using RNA sequencing technology data of silk gland in domestic and wild silkworms, we identified 599 lncRNAs in the silk gland of the silkworm. Compared with protein-coding genes, the silk gland lncRNA genes tend to have fewer exon numbers, shorter transcript length and lower GC-content. Moreover, we found that three lncRNA genes are significantly and differentially expressed between domestic and wild silkworms. The potential targets of two differentially expressed lncRNAs (DELs) (dw4sg_0040 and dw4sg_0483) and the expression-correlated genes with the two DELs are mainly enriched in the related processes of silk protein translation. This implies that these DELs may affect the phenotypic variation in silk yield between the domestic and wild silkworms through the post-transcriptional regulation of silk protein.

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Genome‐wide identification of long non‐coding RNAs (lncRNAs) associated with malathion resistance in Bactrocera dorsalis

Meng

Yuan

Chen

et al. 2021

Pest Management Science

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BACKGROUND Long non‐coding RNAs (lncRNAs) play important roles in the regulation of biological processes and have been identified in many species including insects. However, the association between lncRNAs and pesticide resistance in insect species such as Bactrocera dorsalis is unknown. RESULTS RNA‐seq was performed on malathion resistant (MR1) and susceptible (MS) strains of B. dorsalis and a total of 6171 lncRNAs transcripts were identified. These included 3728 lincRNAs, 653 antisense lncRNAs, 1402 intronic lncRNAs, and 388 sense lncRNAs. A total of 40 and 52 upregulated lncRNAs were found in females and males of the MR1 strain compared to 54 and 49 in the same sexes of the MS strain, respectively. Twenty‐seven of these lncRNAs showed the same trend of expression in both females and males in the MR1 strain, in which 15 lncRNAs were upregulated and 12 were downregulated. RT‐qPCR results indicated that the differentially expressed lncRNAs were associated with malathion resistance. The lnc15010.10 and lnc3774.2 were highly expressed in the cuticle of the MR1 strain, indicating that these two lncRNAs may be related to malathion resistance. RNAi of lnc3774.2 and a bioassay showed that malathion resistance was possibly influenced by changes in the B. dorsalis cuticle. CONCLUSION LncRNAs of B. dorsalis potentially related to the malathion resistance were identified. Two lncRNAs appear to influence malathion resistance via modulating the structure, or components, of the cuticle. © 2021 Society of Chemical Industry

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Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens

Cited by 65 publications

References 47 publications

Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Identification and comparison of long non‐coding RNAs in the silk gland between domestic and wild silkworms

Genome‐wide identification of long non‐coding RNAs (lncRNAs) associated with malathion resistance in Bactrocera dorsalis

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