Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining

Taheri-Dehkordi, Ayat; Naderi, Roohangiz; Martinelli, Federico; Salami, Seyed Alireza

doi:10.1007/s00425-021-03761-7

Cited by 13 publications

(4 citation statements)

References 104 publications

(122 reference statements)

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“…Max or Min of X i also represents the highest/lowest actual values of that the i metric of the given assembler. To achieve an ultimate perspective of each assembler performance, an overall normalized metric score (ONMS) was calculated by summing all of the normalized values for each assembler 53 .…”

Section: Methodsmentioning

confidence: 99%

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Ahmadi,

Sheikh-Assadi,

Fatahi

et al. 2023

Sci Rep

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Non-erroneous and well-optimized transcriptome assembly is a crucial prerequisite for authentic downstream analyses. Each de novo assembler has its own algorithm-dependent pros and cons to handle the assembly issues and should be specifically tested for each dataset. Here, we examined efficiency of seven state-of-art assemblers on ~ 30 Gb data obtained from mRNA-sequencing of Thymus daenensis. In an ensemble workflow, combining the outputs of different assemblers associated with an additional redundancy-reducing step could generate an optimized outcome in terms of completeness, annotatability, and ORF richness. Based on the normalized scores of 16 benchmarking metrics, EvidentialGene, BinPacker, Trinity, rnaSPAdes, CAP3, IDBA-trans, and Velvet-Oases performed better, respectively. EvidentialGene, as the best assembler, totally produced 316,786 transcripts, of which 235,730 (74%) were predicted to have a unique protein hit (on uniref100), and also half of its transcripts contained an ORF. The total number of unique BLAST hits for EvidentialGene was approximately three times greater than that of the worst assembler (Velvet-Oases). EvidentialGene could even capture 17% and 7% more average BLAST hits than BinPacker and Trinity. Although BinPacker and CAP3 produced longer transcripts, the EvidentialGene showed a higher collinearity between transcript size and ORF length. Compared with the other programs, EvidentialGene yielded a higher number of optimal transcript sets, further full-length transcripts, and lower possible misassemblies. Our finding corroborates that in non-model species, relying on a single assembler may not give an entirely satisfactory result. Therefore, this study proposes an ensemble approach of accompanying EvidentialGene pipelines to acquire a superior assembly for T. daenensis.

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Section: Methodsmentioning

confidence: 99%

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Ahmadi,

Sheikh-Assadi,

Fatahi

et al. 2023

Sci Rep

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“…The role of lncRNA and long intergenic ncRNAs (lincRNAs) in this species in graft tolerance and hybrid vigor is also reported ( Yin et al, 2021 ) Supplementary Table 7 . In saffron, flowering regulation has been reported with the role of miRNA, with its targeted genes mainly encodes for transcription factors ( Taheri-Dehkordi et al, 2021 ) and putative lncRNAs (>70,000) ( Choudhary et al, 2019 ). Recent discoveries on high-throughput sequencing-based identification of miRNAs from the curry leaf and their functional implications in secondary metabolite biosynthesis open a new avenue for miRNAs based regulation underlying spice accumulation ( Gutierrez-Garcia et al, 2021 ).…”

Section: Noncoding Rnas: Switch Guiding Switch Resourcesmentioning

confidence: 99%

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

Das,

Chandra,

Negi

et al. 2023

Current Research in Food Science

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“…MicroRNAs (miRNAs) are small non-coding RNAs of 19-24 nucleotides (nt) in lenght involved in post-transcriptional gene regulation by repressing target gene expression (Li et al 2018;Taheri-Dehkordi et al 2021). Plant miRNAs regulate gene expression by identifying targets through base complementarity, followed by cleavage, translational repression, and destabilization of the target mRNA (Xie et al 2015;Moro et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Deciphering miRNA‐lncRNA‐mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan

Chowdhury,

Chatterjee,

Ghosh

et al. 2024

Plant Biol J

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Pigeon pea (Cajanus cajan) is widely cultivated for its nutritional and medicinal value yet remains an orphan crop as productivity has not been improved because of a lack of genome and non‐coding genome information. Non‐coding RNAs, like miRNAs and long non‐coding RNAs (lncRNAs), are involved in regulation of growth, metabolism, development, and stress response, and have a critical role in post‐transcriptional gene regulation (PTGR). We attempted to elucidate the roles of miRNAs and lncRNAs in pigeon pea through experimental validation of computationally predicted miRNAs and lncRNAs and targets of miRNAs on mRNAs. We experimentally validated 20 miRNAs and 11 lncRNAs. We predicted cleavage sites of three miRNA targets: serine/threonine‐protein kinase, polygalacturonase, beta‐galactosidase. We identified 469 targets of 265 miRNAs and their functional annotations using computational methods. We built a miRNA‐mRNA‐lncRNA network model, with the miRNAs targeting both mRNAs and lncRNAs, to obtain information on the interplay of these three molecules. A confirmed interaction through experimental validation was established between miRNA, namely cca‐miR1535a targeting the mRNA for beta‐galactosidase, as well as the lncRNA cca‐lnc‐020033. Our findings increase knowledge of the non‐coding genome of pigeon pea and their roles in PTGR and in improving agronomic traits of this pulse crop.

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Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining

Abstract: Main conclusion A robust workflow for the identification of miRNAs and their targets in saffron was developed. MicroRNA-mediated gene regulation in saffron is potentially involved in several biological processes, including the biosynthesis of highly valuable apocarotenoids.

Cited by 13 publications

References 104 publications

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

Deciphering miRNA‐lncRNA‐mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan

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