Table 1.

Predicted target genes of miRNAs involved in top enriched pathways of drought tolerance in sugarcane

S. No.	Pathway	miRNAs	Target genes	Gene ID
1	Plant-pathogen interaction	Smo-miR408 Mireap-m0077-3p Mireap-m0073-3p Mireap-m0049-5p Mireap-m0016-5p Mireap-m0016-5p Mireap-m0073-3p	Serine/threonine protein kinase transcription factor MYB CERK1; chitin elicitor receptor kinase 1 RPM1; disease resistance protein RPM1 CPK; calcium-dependent protein kinase RBOH; respiratory burst oxidase Carboxypeptidase	31_c37860_g1_i2 41_c56809_g2_i6 31_c35993_g1_i3 51_c41883_g1_i4 51_c45744_g2_i2 41_c55871_g2_i1 41_c57068_g1_i4
2	Plant hormone signal transduction	Tae-miR5384-3p Smo-miR408 Tae-miR5384-3p Tae-miR5384-3p Tae-miR5384-3p Tae-miR5384-3p Tae-miR5384-3p Tae-miR5384-3p Tae-miR5384-3p Sbi-miR396d Sbi-miR397-3p Tae-miR5384-3p Mireap-m0020-5p Mireap-m0043-3p Mireap-m0020-5p Mireap-m0067-5p Mireap-m0049-5p Mireap-m0020-5p Mireap-m0049-5p Mireap-m0049-5p Mireap-m0049-5p	Mitogen-activated protein kinase Phosphoribulokinase Pyruvate dehydrogenase 2C-type protein phosphatase protein (uncharacterized protein) ACC synthase 2 Rhomboid-like protein Putative CRINKLY4-like receptor protein kinase family protein (uncharacterized protein) Protein kinase domain containing protein Calmodulin (uncharacterized protein) Histidine-containing phosphotransfer protein 4 ATP binding protein (uncharacterized protein) 1-Aminocyclopropane-1-carboxylate synthase Jasmonate ZIM domain-containing protein GH3; auxin responsive GH3 gene family TGA; transcription factor TGA putative bZIP transcription factor superfamily protein ARR-B; two-component response regulator ARR-B family JAZ; jasmonate ZIM domain-containing protein Putative snRK/SAPK family protein kinase SNRK2; serine/threonine-protein kinase SRK2 Serine/threonine-protein kinase SAPK6	41_c61679_g1_i3 51_c35422_g1_i2 21_c47811_g1_i4 41_c61886_g1_i2 51_c31538_g1_i1 21_c46681_g2_i1 51_c40570_g1_i2 21_c44921_g3_i1 11_c45593_g1_i2 21_c33465_g1_i2 51_c34821_g1_i2 11_c50950_g2_i1 51_c31421_g1_i1 11_c35859_g1_i5 11_c40163_g1_i1 31_c22010_g1_i2 41_c57376_g1_i1 21_c39304_g1_i2 51_c47267_g3_i5 21_c46764_g1_i2 51_c47267_g3_i4
3	MAPK signaling pathway—plant	Tae-miR5384-3p Mireap-m0075-5p Mireap-m0011-3p Mireap-m0020-5p Mireap-m0067-5p Mireap-m0043-3p Mireap-m0020-5p Mireap-m0016-5p	Mitogen-activated protein kinase WRKY transcription factor 33 ERECTA-like 2 Chitinase 1 ACC synthase 1 PREDICTED: abscisic acid receptor PYL4-like RBOH; respiratory burst oxidase peroxidase activity	41_c89678_g1_i1 41_c34210_g1_i1 21_c51388_g2_i1 41_c49938_g1_i3 31_c40137_g1_i3 31_c25419_g2_i1 41_c47344_g2_i1 41_c55871_g2_i1
4	Phenylpropanoid biosynthesis	Tae-miR5384-3p Tae-miR5384-3p Mireap-m0077-3p Mireap-m0043-3p Mireap-m0049-5p	Peroxidase Glycosyltransferase Peroxidase Peroxidase Laccase	41_c55109_g2_i1 11_c45559_g1_i2 21_c52014_g1_i5 11_c33778_g2_i6 11_c35815_g1_i1
5	General function prediction only	Sbi-miR397-3p Sbi-miR397-3p Osa-miR393b-3p Osa-miR393b-3p Sbi-miR5564c-5p Tae-miR5384-3p Tae-miR5384-3p	Putative polyprotein Caffeic acid 3-O-methyltransferase (EC 2.1.1.6) (caffeic acid-O-methyltransferase) Putative RING zinc finger domain superfamily protein (uncharacterized protein) S-acyltransferase (EC 2.3.1.225) (palmitoyltransferase) Putative gag-pol polyprotein NAD dependent epimerase/dehydratase family protein (uncharacterized protein) Carboxypeptidase	41_c50099_g1_i1 31_c31301_g1_i1 51_c28098_g1_i1 41_c62565_g1_i2 21_c53598_g1_i2 41_c59268_g5_i4 41_c57369_g4_i1
6	Posttranslational modification, protein turnover, chaperones	Sbi-miR397-3p Sbi-miR397-3p Tae-miR5384-3p Tae-miR5384-3p Mireap-m0020-5p Mireap-m0043-3p	Heat shock protein MYB-like transcription factor DIVARICATA Carboxypeptidase (EC 3.4.16.-) Thioredoxin M-type HSP20; HSP20 family protein HSP90B; heat shock protein 90 kDa beta	51_c29439_g1_i4 21_c49879_g1_i2 41_c62042_g1_i4 51_c25511_g1_i1 21_c36141_g1_i1 41_c54140_g1_i3
7	Carbohydrate transport and metabolism	Tae-miR5384-3p Sbi-miR397-3p Sbi-miR397-3p Tae-miR5384-3p Mireap-m0073-3p	Trehalose-6-phosphate synthase component TPS1 and related subunits Glycosyltransferase (EC 2.4.1.-) Fructose-6-phosphate 2-kinase/fructose-2,6-biphosphatase Alpha-galactosidase (EC 3.2.1.22) (melibiase) GAPDH; glyceraldehyde 3-phosphate dehydrogenase [EC:1.2.1.12]	21_c4416_g1_i1 11_c18089_g1_i1 11_c53370_g1_i1 31_c37634_g2_i2 21_c47885_g2_i1
8	Secondary metabolite biosynthesis transport and catabolism	Sbi-miR397-3p Tae-miR5384-3p Tae-miR5384-3p Mireap-m0052-3p	Cytochrome P450 Acc oxidase S-glutathione dehydrogenase/class III alcohol dehydrogenase Cytochrome P450	31_c38488_g1_i2 11_c49592_g2_i2 11_c48315_g1_i1 51_c36473_g1_i1
9	Glutathione metabolism	Tae-miR5384-3p Csi-miR166a Tae-miR5384-3p Mireap-m0086-5p	Multicopper oxidases Glutathione S transferase Glutathione S transferase Glutathione S-transferase	21_c49637_g2_i3 51_c29924_g1_i2 41_c51347_g1_i1 51_c34512_g1_i1

Pathway: pathway in which protein is involved; miRNAs: differentially expressed miRNAs with log2 ratio ≥ 1 up and ≤ 1 down, p ≤ 0.05; target genes: description of genes obtained from GenBank by BLAST search; gene ID: target mRNA ID (sugarcane transcript list available in NCBI BioProject ID—PRJNA590595) to which miRNA binds