Research article
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution
-
* Corresponding author: Wolfgang Frank wolfgang.frank@biologie.uni-freiburg.de
1 Faculty of Biology, Institute of Biology II, Plant Biotechnology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
2 Faculty of Biology, Institute of Biology II, Experimental Bioinformatics, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
BMC Plant Biology 2007, 7:13 doi:10.1186/1471-2229-7-13
Published: 14 March 2007Additional files
Additional file 1:
Non redundant set of cloned sRNA sequences after filtering. The table shows the complete non-redundant set of sRNA sequences which have been obtained from the sRNA cloning approach. Only those sRNA sequences are listed which did not show homologies to rRNA, tRNA or chloroplast encoded RNA sequences deposited in Rfam.
Format: PDF Size: 98KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 2:
Precursor structures of Physcomitrella miRNAs. Fold back analysis of identified potential precursor sequences. Genomic sequences and EST sequences harboring regions identical to sequences of cloned and predicted sRNAs were trimmed and clustered. The non-redundant set of singlets and contigs was used for structural analysis using the RNAshapes program. The mature miRNA sequences within the precursors are highlighted in red.
Format: PDF Size: 383KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
miRBase annotations of identified Physcomitrella miRNAs. The table shows annotations of the identified Physcomitrella miRNAs which were deposited in miRBase.
Format: PDF Size: 39KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
Precursor of a putative rice homolog of Physcomitrella miRNA 4–12. The reciprocal search with microHARVESTER using all Physcomitrella miRNAs without previously found homologs in other plants identified a putative homolog for miRNA 4–12 in rice. The corresponding precursor structure of this rice miRNA is depicted in this figure.
Format: PDF Size: 21KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 5:
Comparison of conserved plant miRNAs. In order to analyze conserved plant miRNA families all Physcomitrella miRNAs, as well as all plant miRNAs deposited in miRBase, were compared. miRNA sequences which were at least present in two different plant species are listed and the numbers of corresponding precursor sequences are provided.
Format: PDF Size: 275KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 6:
Sequence alignments of Physcomitrella miRNAs and their putative targets. The figure shows all sequence alignments between Physcomitrella miRNAs and their putative targets detected in a Physcomitrella EST database using the RNAhybrid program.
Format: PDF Size: 72KB Download file
This file can be viewed with: Adobe Acrobat Reader