Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering

Fan, Tongqiang; Zhang, Qixiang; Hu, Yuanyuan; Wang, Zhengjia; Huang, Yajiang

doi:10.1007/s10142-020-00737-w

Cited by 10 publications

(9 citation statements)

References 90 publications

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“…Compared with protein-coding genes, the effect of AS in lncRNAs was much weaker (Tu et al, 2020). Among these lncRNAs, lincRNA accounted for the largest proportion, a finding that was consistent with reports in poplar and hickory (Carya cathayensis) (Liu et al, 2018;Fan et al, 2020;Guo et al, 2020). Studies have revealed that lincRNAs are involved in transcriptional regulation and signal transduction in soybean (Glycine max) and regulate root development in A. thaliana (Li et al, 2016;Golicz et al, 2018).…”

Section: Discussionsupporting

confidence: 81%

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A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Shen

Wen

et al. 2021

Front. Plant Sci.

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Liriodendron chinense is an economically and ecologically important deciduous tree species. Although the reference genome has been revealed, alternative polyadenylation (APA), transcription factors (TFs), long non-coding RNAs (lncRNAs), and co-expression networks of tissue-specific genes remain incompletely annotated. In this study, we used the bracts, petals, sepals, stamens, pistils, leaves, and shoot apex of L. chinense as materials for hybrid sequencing. On the one hand, we improved the annotation of the genome. We detected 13,139 novel genes, 7,527 lncRNAs, 1,791 TFs, and 6,721 genes with APA sites. On the other hand, we found that tissue-specific genes play a significant role in maintaining tissue characteristics. In total, 2,040 tissue-specific genes were identified, among which 9.2% of tissue-specific genes were affected by APA, and 1,809 tissue-specific genes were represented in seven specific co-expression modules. We also found that bract-specific hub genes were associated plant defense, leaf-specific hub genes were involved in energy metabolism. Moreover, we also found that a stamen-specific hub TF Lchi25777 may be involved in the determination of stamen identity, and a shoot-apex-specific hub TF Lchi05072 may participate in maintaining meristem characteristic. Our study provides a landscape of APA, lncRNAs, TFs, and tissue-specific gene co-expression networks in L. chinense that will improve genome annotation, strengthen our understanding of transcriptome complexity, and drive further research into the regulatory mechanisms of tissue-specific genes.

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Section: Discussionsupporting

confidence: 81%

“…Additionally, we found that the lncRNAs were shorter and smaller than the mRNAs in terms of the exon length and number. This phenomenon was also observed in hickory, rice, and poplar (Liu et al, 2018;Fan et al, 2020;Zhao et al, 2020). These findings provide a genome-wide landscape of lncRNAs in L. chinense.…”

Section: Discussionsupporting

confidence: 66%

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Shen

Wen

et al. 2021

Front. Plant Sci.

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“…3 C,3D). The above findings were consistent with the previous studies in maize [ 24 ], Cleistogenes songorica [ 30 ], Carya cathayensis [ 31 ], and duckweed [ 32 ]. The detailed flowchart for identifying lncRNAs and novel PCTs was shown in Fig.…”

Section: Resultssupporting

confidence: 93%

Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

et al. 2022

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Background Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance. Results The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF. Conclusions The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway.

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“…GO and KEGG analysis showed that these genes were mainly related to oxidation-reduction process, integral component of membrane and metal ion binding. These results indicate that many lncRNAs regulate gene expression through cis-action, which is consistent with previous studies [25,26]. Here, a network of lncRNAs and mRNAs was constructed, which showed that a total of 604 lncRNAs and 1,484 mRNAs had regulatory relationships.…”

Section: Construction Of Lncrnas and Mrnas Network And Prediction Analysis Of Lncrnas Functions Related To Fatty Acid Synthesissupporting

confidence: 91%

Transcriptional Profiles of Long Non-coding RNAs Involved in Fatty Acid Biosynthesis at Filling Stage of Soybean Pods

Khalifa

et al. 2021

Preprint

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Background: Long non-coding RNAs (lncRNAs) are non-coding RNAs of more than 200 nucleotides. To date, the roles of lncRNAs in soybean fatty acid synthesis have not been fully studied. Here, the low-linolenic acid ‘mutant 72’ (MT72) and the wild-type control ‘JiNong 18’(JN18) were used. Based on the previously published data on lncRNAs related RNA-seq in young pods of soybean 30 d to 40 d after flowering, lncRNAs and mRNAs from soybean pods 50 d after flowering were identified using high-throughput sequencing. The possible target genes of lncRNAs were predicted, and the functions related to fatty acid synthesis were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).Results: A total of 10,500 lncRNAs and 54,370 mRNAs were identified, and 115 possible target genes of 1,805 differentially expressed lncRNAs were found to be involved in fatty acid synthesis. A network of lncRNAs and mRNAs was constructed, and a total of 604 lncRNAs and 1,484 mRNAs had regulatory relationships. Among them, 115 target genes of 77 lncRNAs were directly or indirectly involved in fatty acid biosynthesis.Conclusions: The function related to fatty acid synthesis was predicted by differential expression of the target gene mRNAs interacting with lncRNAs. In conclusion, our results provide a theoretical basis for studies on fatty acid synthesis of lncRNAs in soybean.

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Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering

Cited by 10 publications

References 90 publications

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

Transcriptional Profiles of Long Non-coding RNAs Involved in Fatty Acid Biosynthesis at Filling Stage of Soybean Pods

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