Selection and mutation on microRNA target sequences during rice evolution

doi:10.1186/1471-2164-9-454

BMC Genomics

Volume 9

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Research article

Selection and mutation on microRNA target sequences during rice evolution

Xingyi Guo¹ , Yijie Gui¹ , Yu Wang¹ , Qian-Hao Zhu² , Chris Helliwell² and Longjiang Fan¹

¹Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, PR China

²CSIRO Plant Industry, Canberra, ACT 2601, Australia

author email corresponding author email

BMC Genomics 2008, 9:454doi:10.1186/1471-2164-9-454


Published:	2 October 2008

Additional files

Additional file 1:

The list of 1,331 gene pairs from the whole genome duplication in rice.

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Additional file 2:

The 17 WGD gene pairs where miRNA binding sites were predicted on only one paralog of the pair.

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Additional file 3:

The 12 WGD gene pairs where miRNA binding site was predicted on both paralogs of the pair.

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Additional file 4:

Primers used for amplification of the genomic fragments containing the miRNA binding sites in six experimentally validated miRNA-targeted genes.

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Additional file 5:

Summary of the sequence divergence of six experimentally validated miRNA binding sites in the wild rice population.n, number of samples; S, number of segregating sites; π, average number of pairwise nucleotide differences per site between two sequences [43]; θ, the Watterson estimator of θ per basepair [42].

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Additional file 6:

miRNA target predictions in the gene families at Additional file 2.

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Additional file 7:

The putative gain of miR535 binding site in a gene family.A: Phylogenetic tree of the gene family (TIGR ID 2995) including Os02g09080. Os02g09080 predicted to be target of miR535 is labelled by an asterisk and the branch node on which the WDG event occurred is indicated in red bold line and the corresponding WGD gene pairs are shown in dot lines. Os: Oryza sativa and At: Arabidopsis thaliana; B: The alignment of the binding sites of gene familiy members. The numbers of mismatch between miRNA and its binding sites are shown in parentheses.

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Additional file 8:

Accession number and geographic origin of the cultivated and wild rice used in this study.

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