Unravelling lncRNA mediated gene expression as potential mechanism for regulating secondary metabolism in Citrus limon

Bordoloi, Kuntala Sarma; Baruah, Poojamoni; Das, M. R.; Agarwala, Niraj

doi:10.1016/j.fbio.2021.101448

Cited by 14 publications

(9 citation statements)

References 111 publications

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“…[ 55 ]—pointed out the significance of miRNAs in the enhancement of flavonoid biosynthesis; ref. [ 83 ]—characterizes lncRNA mediated gene expression in flavonoids and terpenoids production in Citrus limon (L.) Osbeck; ref. [ 84 ]—describing miRNA role in phenylpropanoid, terpenoid, alkaloid, chlorophyll, and carotenoid biosynthesis; ref.…”

Section: The Involvement Of Mirna In Plant Lignan Biosynthesismentioning

confidence: 99%

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Ražná¹,

Harenčár²,

Kučka³

2022

Cells

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Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.

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Section: The Involvement Of Mirna In Plant Lignan Biosynthesismentioning

confidence: 99%

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Ražná¹,

Harenčár²,

Kučka³

2022

Cells

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“…Quan et al found that some lncRNAs may regulate some protein-coding genes in the lignin biosynthesis pathway in a cis or trans manner, providing new insights into wood formation [ 45 ]. Kuntala et al discovered 113 and 29 lncRNAs involved in the terpenoids and flavonoids metabolic pathway of Citrus limon , respectively [ 46 ]. These studies imply that lncRNAs may have a wide range of functions.…”

Section: Discussionmentioning

confidence: 99%

Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

Shen

Zheng

Liu

et al. 2022

IJMS

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Crocins are valuable bioactive components of gardenia fruit, and their biosynthesis and accumulation have attracted widespread interest. Studies have investigated the biosynthesis and accumulation of crocin based on Illumina sequencing, but there is a lack of reports based on full-length transcriptome sequencing. Utilising SMRT sequencing and high-performance liquid chromatography (HPLC), we explored crocin biosynthesis and accumulation in the fruit of Gardenia jasminoides. HPLC analysis showed that crocins specifically exist in fruit and that the content of crocins increases gradually during fruit development. SMRT sequencing generated 46,715 high-quality full-length isoforms, including 5230 novel isoforms that are not present in the G. jasminoides genome. Furthermore, a total of 46 genes and 91 lncRNAs were involved in the biosynthesis and accumulation of crocin. The qRT-PCR indicated that genes involved in crocin biosynthesis reached a peak in the NOV stage. These findings contributed to our understanding of crocin biosynthesis and accumulation.

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“…Long noncoding RNA (lncRNAs) sequences were identi ed from the these datasets of multiple fungalinfected samples. After comparing gene structure information of samples with known annotations information, ltered out the unquali ed transcript and found 8805 transcript lncRNA based on the ltration cut-off (length < 200, coverage < 3, and exon numbers < 2) with class_code of "i", "o", "u", and "x" [53]. Further, simpli ed by the selective bioinformatics lncRNA predictive tools, including CNCI, FEELnc, PLEK, and CPC2.…”

Section: Screening Of Lncrna In Multiple Fungal-infected Samplesmentioning

confidence: 99%

Complex biological network analysis revealed the regulation of genes under multiple fungal infected silk of Zea mays

Kumar,

Arunachalam,

Lakshmi

2023

Preprint

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Background Maize (Zea mays L.) is a more versatile and multi-purpose crop, primarily grown as food and feed, but now extensively applied in beauty, drug, and biofuel energy. However, the decline in production is reported to be promoted by the fungal pathogens, which invade developing grain using silk channels and hampering the quantity and quality of maize silk. Since understanding the molecular mechanisms will increase the chance of reducing the fungal infection, an integrated omics approach was undertaken on the transcriptome datasets with the multi-fungus at the maize silks. Results The available data sets were classed to A and B for simplicity, but enhancement in the analysis based on the intra and inter-transcriptomic level, keeping control data sets for comparing under the infected conditions. Hence, based on the analysis, the differentially expressed transcript isoforms were identified, which revealed approximately 39651 and 34027 transcript isoforms, 3819 and 3320 alternatively spliced regions along classes A and B. On examination, about 3212 lncRNAs were identified, among which 530 lncRNAs expressed were recognized to play a key role in multiple infectious conditions. Investigation on the complex biological network mediated by the combinations of miRNAs with lncRNAs, lncRNAs with transcript isoforms, lncRNAs with alternatively spliced genes. Interestingly, about 82 lncRNAs exhibited intersectional interactions with miRNAs, AS, and Tiso, which decoded for 103 genes. Conclusions This study might have contributed to key functions of response to stimulus, regulating the metabolic and cellular process during the development and of the plants, which eventually enhanced the plants immune or defence mechanisms.

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Unravelling lncRNA mediated gene expression as potential mechanism for regulating secondary metabolism in Citrus limon

Cited by 14 publications

References 111 publications

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Integrated SMRT and Illumina Sequencing Provide New Insights into Crocin Biosynthesis of Gardenia jasminoides

Complex biological network analysis revealed the regulation of genes under multiple fungal infected silk of Zea mays

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