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.
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Data availability
The Illumina raw reads of samples of transcriptome were deposited in NCBI BIO PROJECT with accession number PRJNA716503 and raw data of Small RNA-Seq of stressed and control samples of IND 99-907 and Co 97010 were deposited in NCBI BIO PROJECT with accession number PRJNA888452, PRJNA888470, PRJNA889536 and PRJNA889539 respectively.
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Acknowledgements
The authors are respectfully thanking and acknowledging the financial support from ‘Science and Engineering Research Board, Department of Science and Technology (DST-SERB)’ under Early Career Research Award (File No.: DST/SERB/ECR/2017/000349). We are also thankful to AgriGenome Labs Pvt Ltd, Cochin, India for transcriptome and small RNA sequencing work. We thankfully acknowledge the ICAR-Sugarcane Breeding Institute, Coimbatore for kind support for the study.
Funding
This research was supported by the financial grant received from ‘Science and Engineering Research Board, Department of Science and Technology (DST-SERB)’ under the “Early Career Research Award (File No.: DST/SERB/ECR/2017/000349)”.
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PV & CM: equal contributions to research work or shared first co-authors and bioinformatics data analysis. CM, CA: project formulation and execution of field work. PV, CM, CA: project formulation, bioinformatics flow of data analysis, designed the experiment for performing genome assembly and differential gene expression. KS, CM, CA: execution of field work. CM: uploaded the raw data of small RNA Seq to NCBI website. CM, VS, HKM, KS: RNA isolation and performed qRT-PCR validation. PS, CM: prepared all tables, figures and wrote the manuscript. CM, CA: overall supervised the experiment. All authors read the manuscript and approved.
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Vignesh, P., Mahadevaiah, C., Selvamuthu, K. et al. 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. 3 Biotech 14, 24 (2024). https://doi.org/10.1007/s13205-023-03867-7
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DOI: https://doi.org/10.1007/s13205-023-03867-7