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Open Access Highly Accessed Research article

Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways

Yang Li12, Chaoqun Li3, Guohui Ding4 and Youxin Jin12*

Author Affiliations

1 School of Life Sciences, Shanghai University, 200444, Shanghai, P.R.China

2 State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, 200031, Shanghai, China

3 Department of Gastroenterology, Shanghai Public Health Clinical Center Affiliated to Fudan University, 2901 Caolang Road, 201508, Shanghai, China

4 Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China

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BMC Evolutionary Biology 2011, 11:122  doi:10.1186/1471-2148-11-122

Published: 12 May 2011

Additional files

Additional file 1:

Sequences of the MIR159/319 stem-loops. All the sequences are in DNA form in FASTA format in a plain text file.

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Open Data

Additional file 2:

Structural alignment of the 231 type 1 MIR159/319 precursor stem-loops. The structural annotations are output from ConStruct. Background colours: green for loops, red for consensus base pairs, pink for co-varying pairs; white for non-base pairs in paired regions. The abbreviations for the species are in Methods section.

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Additional file 3:

Reconstructed phylogenetic tree of type 1 MIR159/319 genes. The Bayesian posterior probabilities are indicated by numbers. The major clades of land plants are highlighted: red, eudicots; green, monocots; light blue, other flowering plants; blue, gymnosperms; orange, lycopod; gray, moss. The deduced duplications before the split of monocots and eudicots and related losses are indicated by filled circles and gray lines, respectively. Two ath-MIR319b redundant sequences, Ath-MIR319d (sense) and Ath-MIR319e (antisense), which are enclosed in squares, were joined in the phylogenetic inference. They are clustered together in the tree, and their relationships have been correctly resolved. Repeated runs generated the identical topology with slight differences in the posterior probability and branch lengths. The abbreviations for the species are provided in the Methods.

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Additional file 4:

Overall expression profile of the nine partitions for type 1 MIR159/319 genes. The normalized values of sequencing abundances for each partition are listed in a table.

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Additional file 5:

More examples of the proportion of mature products from MIR159/319 genes. Vertical axis: normalized sequencing abundances of small RNAs; horizontal axis: partitions of the MIR159/319 stem-loops. Normalizations are the same as in Figure 5. A-B and D-J: Related databases and series are the same as in Figure 5. C: Mature miRNA expressions of MIR159 and MIR319 from Arabidopsis lyrata leaves and two replicates of flowers stage 1-12. E: Proportion of mature miRNA from moss MIR319 genes. The color-coded series are: Pt, 7-day-old protonemata; PG, 14-day-old protonemata and young gametophores; GS, 60-day-old gametophores and sporophytes..

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Additional file 6:

Comparison of sequencing abundances of MIR159/319 miRNAs in wild type and siRNA-deficient mutants. The vertical axis indicates the sequencing abundances, and the horizontal axis indicates partitions of MIR159/319 stem-loops. Watermarked parts are reads that also match paralogous genes. The color-coded series indicate the sources of tissue and the genotypes used to construct the small RNA libraries. A: WT, wild type; dcl234a and dcl234b, two replicates of dcl2 dcl3 dcl4 triple mutants; rdr2a and rdr2b, two replicates of rdr2 mutants. B: IFR, inflorescence; LF, leaves; SD, seedling; P1,P3, leaves inoculated with pseudomonas for 1 or 3 hours; mixed, tags with unidentifiable barcodes. C: WT, wild type; mop1, mop1/rdr2 mutants. D: WT_1 and WT_2, two replicates of wild type moss; dcl3-5 and dcl3-10, two lines of dcl3 mutants; rdr6_1 and rdr6_2, two replicates of rdr6 mutants.

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Additional file 7:

Genome resources used for homology search

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Additional file 8:

Small RNA sequencing databases used for MIR159/319 expression analysis

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