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. 2024 Jan;14(1):24.
doi: 10.1007/s13205-023-03867-7. Epub 2023 Dec 29.

Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus

Palanisamy Vignesh #  1 , Channappa Mahadevaiah #  1   2 , Kannan Selvamuthu  1 , Huskur Kumaraswamy Mahadeva Swamy  1 , Venkatarayappa Sreenivasa  1 , Chinnaswamy Appunu  1
Affiliations

Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus

Palanisamy Vignesh et al. 3 Biotech. 2024 Jan.

Abstract

Soil salinity and saline irrigation water are major constraints in sugarcane affecting the production of cane and sugar yield. To understand the salinity induced responses and to identify novel genomic resources, integrated de novo transcriptome and small RNA sequencing in sugarcane wild relative, Erianthus arundinaceus salt tolerant accession IND 99-907 and salt-sensitive sugarcane genotype Co 97010 were performed. A total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND 99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than ten members in both genotypes. The differential expression analysis of miRNA reveals that 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND 99-907 and Co 97010 respectively. A total of 12,693 and 7982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed known miRNAs of IND 99-907 and Co 97010 respectively. The gene ontology (GO) enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR < 0.05) for biological process, molecular function and cellular component respectively. These miRNAs have many targets that associated in regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-023-03867-7.

Keywords: Salinity; Small RNA; Sugarcane; Transcriptome; miRNA; miRNA targets.

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Conflict of interest statement

Conflict of interestThe authors have no relevant financial or non-financial interests to disclose.

Figures

Fig. 1
Fig. 1
Small RNA length distribution of four sequenced libraries
Fig. 2
Fig. 2
Distribution of miRNAs families in IND 99-907 and Co 97010
Fig. 3
Fig. 3
Venn diagram showing the unique and shared miRNAs between IND 99-907 and Co 97010; a total differentially expressed miRNAs, b upregulated miRNAs and c) downregulated miRNAs
Fig. 4
Fig. 4
A Linkage group-wise distribution of predicted novel miRNAs in sugarcane monoploid genome, B predicted hairpin structures of the precursor miRNAs and the mature sequences are marked in red, and C Venn diagram showing the distribution of novel miRNAs in the four libraries
Fig. 5
Fig. 5
Overview of GO annotations of potential target genes of miRNAs derived from the transcriptome studies of E. arundinaceus accession IND 99-907 and salinity sensitive sugarcane cultivar Co 97010. The data represents three GO categories namely biological process, molecular function and cellular component
Fig. 6
Fig. 6
Validation of randomly selected four miRNA and their targets in salt tolerant E. arundinaceus accession IND 99-907 and salinity sensitive sugarcane cultivar Co 97010
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References

    1. Andrews S (2015) FASTQC A quality control tool for high throughput sequence data. In: Babraham Inst. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed Dec 2021
    1. Aravind J, Rinku S, Pooja B, Shikha M, Kaliyugam S, Mallikarjuna MG, Kumar A, Rao AR, Nepolean T. Identification, characterization, and functional validation of drought-responsive microRNAs in subtropical maize inbreds. Front Plant Sci. 2017;8:941. doi: 10.3389/fpls.2017.00941. - DOI - PMC - PubMed
    1. Ashraf F, Ashraf MA, Hu X, Zhang S. A novel computational approach to the silencing of sugarcane Bacilliform Guadeloupe a virus determines potential host-derived MicroRNAs in sugarcane (Saccharum officinarum L.) Peer J. 2020;8:e8359. doi: 10.7717/peerj.8359. - DOI - PMC - PubMed
    1. Auger A, Galarneau L, Altaf M, Nourani A, Doyon Y, Utley RT, Cronier D, Allard S, Cote J. Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants. Mol Cell Biol. 2008;28:2257–2270. doi: 10.1128/mcb.01755-07. - DOI - PMC - PubMed
    1. Augustine SM, Narayan JA, Syamaladevi DP, Appunu C, Chakravarthi M, Ravichandran V, Subramonian N. Erianthus arundinaceus HSP70 (EaHSP70) overexpression increases drought and salinity tolerance in sugarcane (Saccharum spp. hybrid) Plant Sci. 2015;232:23–34. doi: 10.1016/j.plantsci.2014.12.012. - DOI - PubMed

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