In silico identification of microRNAs and their target genes in watermelon (Citrullus lanatus)

Zakeela, M. C. A.; Safeena, M. I. S.; Komathy, T.

doi:10.1016/j.scienta.2019.02.012

Cited by 10 publications

(6 citation statements)

References 36 publications

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“…In the present study, we considered all the important criteria such as the MFEI values, mismatch inhibition, and sequence length, which have been used for miRNA identification in other plant species. The MFEI values of the 20 identified miRNAs in our work were just above 0.5, which is in accordance with that reported for some miRNAs identified in other plant ESTs (Wang et al, 2012 ; Gupta et al, 2015 ; Patel et al, 2019 ; Zakeel et al, 2019 ). The G + C% of the miR399 members ranged from 37.5% to 38.8%, whereas it was found to be more than 41% for miR5021 mature miRNA sequence.…”

Section: Discussionsupporting

confidence: 92%

Identification of putative miRNAs from Expressed Sequence Tags of Gnetum gnemon L. and their cross-kingdom targets in human

Krishnatreya¹,

Ray²,

Baruah³

et al. 2021

bta

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Wild edible plants are often found to be rich sources of nutrients and medicinally beneficial compounds with pharmacological activities. Gnetum gnemon is a nutritionally important plant and a popular food source in parts of Assam and North-East India. Various microRNAs (miRNAs) have been recently identified in many plants; however, there are no records of identification of miRNAs in any species of Gnetum . The prediction of miRNA-target associations in G. gnemon is an important step to facilitate functional genomics studies in this species. In the present study, all known miRNAs from plants available in public domain were used to search for the conserved G. gnemon miRNA homologues in publicly accessible expressed sequence tags (ESTs) in NCBI database. An aggregate of 20 new potential miRNAs belonging to two diverse miRNA families (miR399 and miR5021) were identified through a homology-based search by following stringent filtering criteria. To investigate the potential cross-kingdom effects of the identified miRNAs, we further identified the putative target genes of G. gnemon miRNAs in human transcriptome and analyzed them against the NCBI non-redundant protein database. The KEGG analysis of the target genes indicated that these genes were involved in different metabolic pathways such as caffeine metabolism, drug metabolism, and nitrotoluene degradation. The target genes of G. gnemon miRNAs in humans were found to be associated with various disorders of both hereditary and non-hereditary origin. These results could help to shed new light on understanding of miRNA-mRNAs functional networks in this species and its potential use as a small RNA-based therapy against some human diseases.

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Section: Discussionsupporting

confidence: 92%

Identification of putative miRNAs from Expressed Sequence Tags of Gnetum gnemon L. and their cross-kingdom targets in human

Krishnatreya¹,

Ray²,

Baruah³

et al. 2021

bta

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“…The recent development of next-generation sequencing technology has led to the discovery of numerous miRNAs in several non-model plant species [8]; however, the overall procedure is expensive, time-consuming, and requires a high technical expertise. In the plant kingdom, multiple miRNAs are evolutionarily conserved, and this feature simplifies the process of characterization of novel miRNA orthologues in new plant species by identifying homologs [10][11][12]. Nonetheless, the only sequence-based in silico homology approaches to identify potential miRNAs in new plant species may yield false-positive results, and hence consideration must be given to the secondary structures as well as other parameters of the pre-miRNAs such as length, GC content, Minimum Folding Free Energy (MFE), and Minimum Folding Free Energy Index (MFEI) in order to increase the precision of the computational prediction by discriminating from other coding or non-coding RNAs [6,12,13].…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs and Their Expression in Leaf Tissues of Guava (Psidium guajava L.) under Salinity Stress

et al. 2020

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Superfruit guava (Psidium guajava L.) is one of the healthiest fruits due to its high antioxidant dietary fiber and vitamin content. However, the growth and development of this plant are severely affected by salinity stress, mostly at the seedling stage. MicroRNAs (miRNAs) are small, noncoding, endogenous, highly conserved RNA molecules that play key regulatory roles in plant development, organ morphogenesis, and stress response signaling. In this study, applying computational approaches and following high stringent filtering criteria, a total of 40 potential microRNAs belonging to 19 families were characterized from guava. The identified miRNA precursors formed stable stem-loop structures and exhibited high sequence conservation among diverse and evolutionarily distant plant species. Differential expression pattern of seven selected guava miRNAs (pgu-miR156f-5p, pgu-miR160c-5p, pgu-miR162-3p, pgu-miR164b-5p, pgu-miR166t, pgu-miR167a-5p, and pgu-miR390b-5p) were recorded under salinity stress and pgu-miR162-3p, pgu-miR164b-5p as well as pgu-miR166t were found to be the most affected ones. Using the psRNATarget tool, a total of 49 potential target transcripts of the characterized guava miRNAs were identified in this study which are mostly involved in metabolic pathways, cellular development, and stress response signaling. A biological network has also been constructed to understand the miRNA mediated gene regulation using the minimum free energy (MFE) values of the miRNA-target interaction. To the best of our knowledge, this is the first report of guava miRNAs and their targets.

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“…miRNAs are essential modulators of transcriptional gene regulation in plants ( Zakeel et al, 2019 ). Up to now, many plant miRNAs have been identified to respond to different stress conditions.…”

Section: Discussionmentioning

confidence: 99%

Characterization of HSP70 family in watermelon (Citrullus lanatus): identification, structure, evolution, and potential function in response to ABA, cold and drought stress

et al. 2023

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Watermelon (Citrullus lanatus) as a crop with important economic value, is widely cultivated around the world. The heat shock protein 70 (HSP70) family in plant is indispensable under stress conditions. However, no comprehensive analysis of watermelon HSP70 family is reported to date. In this study, 12 ClHSP70 genes were identified from watermelon, which were unevenly located in 7 out of 11 chromosomes and divided into three subfamilies. ClHSP70 proteins were predicted to be localized primarily in cytoplasm, chloroplast, and endoplasmic reticulum. Two pairs of segmental repeats and 1 pair of tandem repeats existed in ClHSP70 genes, and ClHSP70s underwent strong purification selection. There were many abscisic acid (ABA) and abiotic stress response elements in ClHSP70 promoters. Additionally, the transcriptional levels of ClHSP70s in roots, stems, true leaves, and cotyledons were also analyzed. Some of ClHSP70 genes were also strongly induced by ABA. Furthermore, ClHSP70s also had different degrees of response to drought and cold stress. The above data indicate that ClHSP70s may be participated in growth and development, signal transduction and abiotic stress response, laying a foundation for further analysis of the function of ClHSP70s in biological processes.

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In silico identification of microRNAs and their target genes in watermelon (Citrullus lanatus)

Cited by 10 publications

References 36 publications

Identification of putative miRNAs from Expressed Sequence Tags of Gnetum gnemon L. and their cross-kingdom targets in human

Identification of putative miRNAs from Expressed Sequence Tags of Gnetum gnemon L. and their cross-kingdom targets in human

Identification of microRNAs and Their Expression in Leaf Tissues of Guava (Psidium guajava L.) under Salinity Stress

Characterization of HSP70 family in watermelon (Citrullus lanatus): identification, structure, evolution, and potential function in response to ABA, cold and drought stress

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