Open Access Highly Accessed Research article

Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae

Hong Liang123, Ying-Tao Zhao234, Jie-Qiong Zhang12, Xiu-Jie Wang24, Rong-Xiang Fang12* and Yan-Tao Jia12*

Author Affiliations

1 State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China

2 National Center for Plant Gene Research, Beijing 100101, PR China

3 Graduate School of the Chinese Academy of Sciences, Beijing 100039, PR China

4 State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China

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BMC Genomics 2011, 12:87  doi:10.1186/1471-2164-12-87

Published: 30 January 2011

Additional files

Additional file 1:

Outline of procedures used in cDNA library analysis (pdf). Flowchart of the steps used for the cDNA library analysis. Each step is shown on the left, and the corresponding number is listed on the right.

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Additional file 2:

The detailed information of the sequences from the cDNA library (xls).

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Additional file 3:

List of the predicted sRNA candidates in Xoo PXO99A using SIPHT search and the comparison of the results of the cloned sequences with the prediction results (xls).

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Additional file 4:

5' RACE results (xls).

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Additional file 5:

Predicted secondary structure of Xoo sRNAs (pdf). Secondary structures of eight Xoo sRNAs were predicted using MFOLD program.

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Additional file 6:

RT-PCR confirmation of the transcriptional unit of the hfq gene (pdf). (A) The position and direction of ORFs were presented by arrows, and the corresponding names for each ORFs were also showed. The locations of primers used in the following PCR were presented by arrows. (B) RNAs prepared from wild-type cells cultured in rich (R) and minimum (M) medium were used for the reverse transcription using random primers to synthesis cDNA separately. DNA, positive control; +, with reverse transcriptase; -, without reverse transcriptase (a negative control to show no contamination of genomic DNA in the RNA sample).

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Additional file 7:

Growth characteristics of the Δhfq mutant in rich medium (pdf). OD600 values of triplicate cultures in PSA medium were determined in two hour intervals (diamonds: wild-type; squares: Δhfq; triangles: Δhfq-C, hfq complementary strain).

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Additional file 8:

2-DE map of the total proteins from wild-type and the sRNA-deleted mutant strains (pdf). (A) 2-DE maps of total proteins from Xoo wild-type strain and ΔsRNA-Xoo3 mutant. (B) 2-DE maps of total proteins from Xoo wild-type strain and ΔsRNA-Xoo4 mutant. Protein spots indicated by numbers are the differentially expressed proteins. All these spots were identified by MS.

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Additional file 9:

Differentially expressed proteins in ΔsRNA-Xoo3 and ΔsRNA-Xoo4 identified by MS (pdf).

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Additional file 10:

The distribution of cis-encoded sRNA candidates and the functional classification of their putative target genes (xls).

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Additional file 11:

Strains and plasmids used in this study (pdf).

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Additional file 12:

Oligonucleotides used in this study (pdf).

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