Table 1 All differentially expressed (DE) miRNAs in rice ZH11 plants by combined analysis with the eligible predicted target DE mRNAs after 48 h of Xoo infection

novel_miR_92

Os07g0603100 (Nuclear transport factor 2); Os01g0365000 (Wall-associated receptor kinase 5); Os05g0446600 (DNA glycosylase 704); Os11g0173500 (Probable LRR receptor-like serine/threonine-protein kinase); Oryza_sativa_newGene_4972 (Disease resistance protein RPM1); Os05g0446000 (Exonuclease VII small subunit); Os11g0590700 (Disease resistance protein RPP13); Os11g0565000 (LRR receptor-like serine/threonine-protein kinase FLS2); Os09g0482640 (Wall-associated receptor kinase 3); Os11g0127600(Probable helicase MAGATAMA 3); Os12g0178700 (Dynamin-like protein ARC5); Os10g0155500 (Aldose 1-epimerase); Os12g0203900; Os01g0763100 (RNA processing and modification)

miR528-5p

Os09g0365900 (L-ascorbate oxidase); Os04g0688500 (Cationic peroxidase SPC4); Os11g0167300 (NYN domain; OST-HTH/LOTUS domain)

miR162b

Os03g0127600 (Transcription factor activity, sequence-specific DNA binding); Os07g0182900 [DNA (cytosine-5)-methyltransferase]

miR395a

Os09g0567900 (Probable inactive methyltransferase); Os04g0104900 (Translation, ribosomal structure and biogenesis); Os01g0266000 (Posttranslational modification, protein turnover, chaperones)

miR395p, 395q, 395r, 395 m, 395 l, 395n, 395 k, 395b, 395i, 395 h, 395j, 395y, 395d, 395e, 395 g, 395 s

Os09g0567900 (Nucleotide transport and metabolism)

miR395f

Os03g0151700 (Similar to WD repeat protein); Os01g0266000 (RNA-binding protein)

miR156j-3p

Os08g0558900 (Enzyme inhibitor activity)

miR408-5p

Os11g0189600 (Lipid transport and metabolism); Os10g0538200 (Aspartic proteinase nepenthesin-1); Os10g0537800 (Aspartic proteinase nepenthesin-1)

novel_miR_108

Oryza_sativa_newGene_10065 (Uncharacterized protein LOC4346670 isoform X3)

miR1428g-5p, 1428e-5p, 1428f-5p

Os01g0885000 (Cytochrome C oxidase, cbb3-type, subunit III)

miR5079a, 5079b

Os10g0577600 (JmjC domain, hydroxylase)

miR1428e-3p

Oryza_sativa_new gene_7640 (Putative receptor protein kinase ZmPK1)

miR528-3p

Os02g0132100 (Pentatricopeptide repeat-containing protein); Os05g0133100 (Nitrogen regulatory protein P-II);

miR2118r, 2118e

Oryza_sativa_new gene_717

miR2871a-3p, 2871b-3p

Os02g0663300 (BEACH domain containing protein)

miR169r-5p

Os01g0759900 (Nucleobase-ascorbate transporter 2)

miR1861c

Os10g0160000 (Ubiquitin carboxyl-terminal hydrolase 10); Os01g0856900 (Disease resistance RPP13-like protein 4)

miR169a

Os01g0236300 (Auxin response factor 1)

miR5542

Os02g0143200 (Armadillo-type fold domain containing protein); Os03g0249200 (RF-1 domain)

miR172c

Os12g0177800 (S-Domain receptor like protein-12)