Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Zhao, Xiaobo; Gan, Li‐Ming; Cheng, Yan; Li, Chunjuan; Sun, Quanxi; Wang, Juan; Yuan, Cuiling; Zhang, Hao; Shan, Shiguang; Liu, Jian Ning

doi:10.3390/genes10070536

Cited by 25 publications

(28 citation statements)

References 50 publications

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“…By comparing our results with the published peanut lncRNAs of Zhao [39], in which 50,873 lncRNAs of peanut were identified from 124 samples involving 15 different tissues, we found 39 lncRNAs were identical, accounting for about 2.7% (data shown in Table S10). The low number of identified sequences may simply reflect the small scale of the experiment, which involved only four libraries as opposed to the 124 libraries underlying the above set of lncRNAs in Zhao's [39]. In addition, the selection criteria applied here were more stringent than those commonly used.…”

Section: Discussionmentioning

confidence: 69%

“…Although a growing body of evidence supports the diverse potential roles of lncRNAs in plants, studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. Recently, Zhao et al identified 50,873 lncRNAs of peanut from large-scale published RNA sequencing data, which belonged to 124 samples involving 15 different tissues, and predicted the co-expressions of targeted genes and 386 hub lncRNAs [39].…”

Section: Introductionmentioning

confidence: 99%

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Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

Tian

Guo

Zhang³

et al. 2020

BMC Plant Biol

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Background: Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. Results: A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. Conclusions: This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

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Section: Discussionmentioning

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

Tian

Guo

Zhang³

et al. 2020

BMC Plant Biol

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show abstract

“…The FEELncprogram (version 0.1.1) was used to identify lncRNAs in the transcriptome assemblies. First, the FEELnc lter was used to remove short transcripts (default 200nt) and assess single-exon transcripts [28]. The FEELnc codpot predictors were used to calculate a coding potential score.…”

Section: Identi Cation Of Lncrnasmentioning

confidence: 99%

Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

Feng

Fang

Liu

et al. 2020

Preprint

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Background Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance, the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood. Results The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4–23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 fruit bracts and F423 to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data. Conclusions The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.

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“…The module with the highest correlation coe cient and the smallest p value was designated as the module most relevant to the trait. In this study, a signi cantly correlated module was identi ed based on a correlation coe cient (r) ≥ 0.8 [35] and p < 0.05. The co-expression networks of lncRNAs and…”

Section: Prediction Of Lncrna Functions Based On Co-expressionmentioning

confidence: 99%

Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

Feng

Fang

Liu

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance , the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.Results: The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.Conclusions: The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.

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Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Cited by 25 publications

References 50 publications

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

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