Characterization the coding and non-coding RNA components in the transcriptome of invasion weed Alternanthera philoxeroides

Zhu, Yong‐Guan; Jiang, Xinchen; Han, Xiaofei; Han, Shuo; Chen, Zhongyi; Yin, Junliang; Liu, Yiqing

doi:10.15835/nbha49112242

Cited by 3 publications

(4 citation statements)

References 42 publications

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“…The miRNAs are key post-transcriptional regulators [ 18 ]. They are involved in a broad range of plant growth, development, and stress response processes through cleavage and/or inhibition of translation of functional gene transcripts [ 19 ]. In this study, the post-transcriptional regulatory relationships of miRNAs targeting CsDUF966 transcripts were explored.…”

Section: Discussionmentioning

confidence: 99%

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

Tian

et al. 2022

Plants

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DUF966 genes are widely found in monocotyledons, dicotyledons, mosses, and other species. Current evidence strongly suggests that they are involved in growth regulation and stress tolerance in crops. However, their functions in cucumbers remain unexplored. Here, cucumber CsDUF966 was systemically identified and characterized using bioinformatics. Eight CsDUF966 genes were identified in the cucumber genome. These were phylogenetically separated into three groups. All CsDUF966 proteins were hydrophilic and localized to the nucleus. Moreover, three acidic and five basic proteins were identified. Evolutionary analysis of DUF966 between cucumber and 33 other Cucurbitaceae species/cultivars revealed that most CsDUF966 genes were conserved, whereas CsDUF966_4.c and CsDUF966_7.c were positively selected among the five cucumber cultivars. Expression profiling analysis showed that CsDUF966 had variable expression patterns, and that miRNA164, miRNA166, and Csa-novel-35 were involved in the post-transcriptional regulation of CsDUF966_4.c and CsDUF966_7.c. The expression of CsDUF966_4.c and CsDUF966_7.c, which were under strong neofunctionalization selection, was strictly regulated in fruit and tissues, including seeds, pericarps, peels, and spines, suggesting that these genes are fruit growth regulators and were strongly selected during the cucumber breeding program. In conclusion, the results reveal the roles of CsDUF966s in regulating cucumber fruit development and lay the foundation for further functional studies.

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Section: Discussionmentioning

confidence: 99%

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

Tian

et al. 2022

Plants

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“…Three days later, leaf fluorescence was visualized through confocal microscopy (TCS SP8) with 488 nm exciting light wavelength. Gene Ontology database was used to perform functional annotation of TaLIM genes (Zhu, Jiang et al., 2021).…”

Section: Methodsmentioning

confidence: 99%

Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene

Liu

Xiao

et al. 2022

The Plant Genome

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The Lin‐11, Isl‐1, and Mec‐3 domains (LIM) transcription factors play essential roles in regulating plant biological processes. Despite that, there is a lack of a full understanding of LIMs in wheat (Triticum aestivum L.). In this study, 28 wheat LIM s (TaLIMs) were identified and designated as TaLIM1‐1A to TaLIM12‐7D. The cis‐regulatory element analysis showed that TaLIMs were rich in elements related to biological and abiotic stresses. Expression profiling analysis showed that certain members of TaLIMs were responsive to biotic and abiotic stresses, such as TaLIM1‐1A, TaLIM3‐2B, TaLIM8‐4D, and TaLIM10‐5D, were significantly induced by heat, drought, sodium chloride (NaCl), abscisic acid (ABA) and Fusarium graminearum stresses. Furthermore, the biological function of TaLIM8‐4D was analyzed and results showed that it was subcellular localization in the nucleus and could induce weak cell death in Nicotiana benthamiana leaves. Additionally, overexpression of TaLIM8‐4D could upregulate plant pathogenesis‐related (PR) genes, promoting the infection of hemibiotrophic pathogen, implying that TaLIM8‐4D could function as susceptible gene in the nucleus by upregulating PR genes and inducing cell death to promote the colonization of hemibiotrophic agent F. graminearum. Overall, the systematic identification, characterization, expression profiling, evolutionary, and function analyses provided the ability to understand TaLIMs and laid a foundation for the further function study of LIM family members in wheat.

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“…The expression of lincRNAs was divided into four classes (Fig. 3A): (1) low (FPKM ≤ 1); (2) moderate (1 < FPKM ≤ 10); (3) high (10 < FPKM ≤ 100); and (4) very high (100 < FPKM). In each treatment, the majority of lincRNAs belong to the low (41%) and moderate (48%) classes based on lin-cRNA expression; however, some lincRNAs belonged to the high or very high classes, indicating that the lin-cRNAs exhibit a biological purpose, rather than simply representing transcriptional 'noise' (Fig.…”

Section: Expression Pattern Profiling Of Lincrnasmentioning

confidence: 99%

“…In recent years, a growing body of studies has demonstrated that eukaryotic genomes contain many regions that transcribe functional noncoding RNAs (ncRNAs), which are typically grouped into housekeeping and regulatory ncRNAs [1]. Among the regulatory ncR-NAs, long ncRNAs (lncRNAs) have been suggested to be the critical player during eukaryotic gene regulation [2].…”

Section: Introductionmentioning

confidence: 99%

Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici

et al. 2021

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Background As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. Results In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. Conclusions This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.

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Characterization the coding and non-coding RNA components in the transcriptome of invasion weed Alternanthera philoxeroides

Cited by 3 publications

References 42 publications

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

Genome‐wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8‐4D function as a susceptible gene

Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici

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