Table S8. Oligonucleotides, Primers and RNA Adaptors Used in This Work

Table S8. Oligonucleotides, primers and RNA adaptors used in this work

Oligonucleotides or primers Sequence (5’ to 3’) source For cDNA library construction Biotin-CAUCGAUCCUGCAGGCUAGAGAC Takara, Dalian, China 3’ Sse8387 I-Adaptor (RNA) AAAGAUCCUGCAGGUGCGUCA Takara, Dalian, China 5’ Sse8387 I-Adaptor (RNA) GTCTCTAGCCTGCAGGATCGATG Takara, Dalian, China Sse8387-I specific reverse primer

(also used as RT-Primer)

Sse8387-I specific forward primer AAAGATCCTGCAGGTGCGTCA Takara, Dalian, China

For cDNA clone screening

M13 f/ M13 erv GTTTTCCCAGTCACGAC/AACAGCTATGACCATG Sangon, Shanghai, China

For sequencing

M13 erv AACAGCTATGACCATG Sangon, Shanghai, China For northern blottingZ

Probe-1(for sRNA-C1) Biotin- This work

GGCGGCCGGGTGCTTGAACACGGTCGTAGGGCCGCCCGCAG Probe-2 (for sRNA-C2) TTTTCCCCTTTCGGGTAT This work Probe-3 for sRNA-C3) Biotin- TTGCATTCTCCGCCATGAC This work Probe-4(for sRNA-C4) Biotin- TCGATGCCGTTGCTGCCTTCCGGCCCT This work Probe-5(for sRNA-C5) This work Biotin- CCCCTGGCGATGACCTACTCTCGCATGGCTTGAGC Probe-6(for sRNA-C6) This work Biotin- CCAGGGGATGGGAGAGATCT Probe-7(for sRNA-C7) This work Biotin- TGGTCAAGCCGCACGGATCATTAG

Biotin- For 5’-Race mappingZ GGAGGTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTCC Abridged Anchor Primer (AAP) Invitrogen, Carlsbad, USA AUAP GACTCCACCCCAGT Invitrogen, Carlsbad, USA 1GSP5-1(sRNA-Xcc1 specific) This work 1GSP5-2(sRNA-Xcc1 specific) GGCCACGCGTCGACTAGTACGGGIIGGGIIGGGIIG (I:deoxyinosine) This work 1GSP5-3(sRNA-Xcc1 specific) GGCCACGCGTCGACTAGTAC This work 2GSP5-1(sRNA-Xcc2 specific) GCGGCCGGGTGCTTG This work 2GSP5-2(sRNA-Xcc2 specific) TGCTTGAACACGGTCGTAGGGCG This work 2GSP5-3(sRNA-Xcc2 specific) AGGGCGCTCGCAGTTTTCCCCTTT This work 3GSP5-1(sRNA-Xcc3 specific) TTGCATTCTCCGCCATGA This work 3GSP5-2(sRNA-Xcc3 specific) CCGCCATGACGATGTGTGCGA 3GSP5-3(sRNA-Xcc3 specific) GGACGTTGTTAGGCCGTCGGGC This work

4GSP5-1(sRNA-Xcc4 specific) GGTGTCCCCGCCGGTT This work

4GSP5-2(sRNA-Xcc4 specific) TCCCCGCCGGTTGACCTCG This work

4GSP5-3(sRNA-Xcc4 specific) TGACCTCGGCGCCCGCATC This work

For 3’-Race mappingZ GCCCCTGGCGATGAC This work

3’- Adaptor (RNA) GGCGATGACCTACTCTCGCATG

3’Adaptor specific reverse primer GACCTACTCTCGCATGGCTTGAG Takara, Dalian, China

(also used as RT-Primer) Takara, Dalian, China

1GSP3-1(sRNA-Xcc1 specific) Biotin-CAUCGAUCCUGCAGGCUAGAGAC 1GSP3-2(sRNA-Xcc1 specific) GTCTCTAGCCTGCAGGATCGATG This work 2GSP3-1(sRNA-Xcc2 specific) This work

2GSP3-1(sRNA-Xcc2 specific) This work GGCCGGGTGGAAGGGCAGCTAT 3GSP3-1(sRNA-Xcc3 specific) This work GCAATACCCGAAAGGGGAAAACTGCG 3GSP3-2(sRNA-Xcc3 specific) This work GCGTTCTCTGCTGTGAACGACGGTGTG 4GSP3-1(sRNA-Xcc4 specific) This work CGGTGTGCAAAACATTCGCCTTGT 4GSP3-2(sRNA-Xcc4 specific) This work CCGCCAGGGCCGGAAGGCA This work AGGCAGCAACGGTATCGATTGATG

CTCAAGCCATGCGAGAGTAGGTCAT

ATGCGAGAGTAGGTCATCGCCAGG z These primers were designed according to the genomic sequence of X. campestris

pv. campestris strain 8004 [S1], and were synthesized and 5’-biotin labeled by Sangon

Biological Engineering Technology & Services Co., Ltd (Shanghai, China).

S1. Qian W, Jia Y, Ren SX, He YQ, Feng JX, Lu LF, Sun Q, Ying G, Tang DJ, Tang

H, Wu W, Hao P, Wang L, Jiang BL, Zeng S, Gu WY, Lu G, Rong L, Tian Y, Yao Z,

Fu G, Chen B, Fang R, Qiang B, Chen Z, Zhao GP, Tang JL, He C: Comparative

and functional genomic analyses of the pathogenicity of phytopathogen

Xanthomonas campestris pv. campestris. Genome Res 2005, 15:757-767.