Figure 2
Phylogenetic analysis of Dicer-like, Argonaute and RDR genes of rice with other organisms. A. Argonautes. Unrooted, neighbor joining tree was constructed by alignment of total protein sequences from rice, Arabidopsis, C. elegans, yeast, Drosophila and humans. Four subgroups are marked, AGO1, MEL1, ZIPPY and AGO4 as described by Nonomura et al., (2007, [15]). Plant-specific clades are shaded and rice Argonautes have been highlighted in red in each group. Accession numbers of sequences are as follows: CeALG-1 (NP510322), CeALG-2 (NP493837), CePRG-1(CAA98113), CePRG-2 (AAB37734), CeRDE-1 (AAF06159), DmAGO1(NP523734), DmAGO2 (AAF49619), DmAUB (CAA64320), MmMIWI1(NP067286), MmMIWI2 (AY135692), MmEIF2C2 (NP694818), MmEIF2C3 (NP700451), MmEIF2C4 (NP694817), SpAGO1 (CAA19275), CeCSR-1 (NP001040938), CeSAGO-1 (NP504610), and CeSAGO-2 (NP490758), AtAGO10 (AAD40098), AtAGO1 (AAC18440), AtAGO7 (AAQ92355) and AtAGO4 (NP_565633), AtAGO2 (Locus:2197545), AtAGO3 (Locus:2197550), AtAGO6 (Locus:2059370), AtAGO8 (Locus:2147072) and AtAGO9 (Locus:2179008). B. RNA-dependent RNA polymerase. Analysis of evolutionary relatedness between rice, Arabidopsis, Maize, Populus, yeast and C. elegans RDR genes using full length RDR protein sequences. The protein sequences of all RDRs except rice were obtained from the Chromatin database, ChromDB http://www.chromdb.org. Plant-specifc clades have been shaded. The Arabidopsis proteins are AtRDR1(At1g14790), AtRDR2 (At4g11130), AtRDR3 (At2g19910), AtRDR4 (At2g19920), AtRDR5(At2g19930), and AtRDR6 (At3g49500). PtRDR901 through PtRDR906 and PtRDR908 are Populus trichocarpa proteins, ZmRDR103, ZmRDR104 and ZmMOP1 are Zea mays RDR proteins, SpRDR601 is from Schizosaccharomyces pombe and CeRDR301-CeRDR303 are from Caenorhabditis elegans. C. Dicer-like proteins. Neighbour-joining tree was constructed after alignment of total protein sequences of rice and Arabidopsis. Protein sequences from Drosophila, humans, yeast and C. elegans were included as outgroups. Plant-specific clades have been shaded. Protein sequences were downloaded from National Center for Biotechnology Information (NCBI). Accession numbers and abbreviations are as follows: HsDcr1, Homo sapiens Dicer-1 (NP_085124); DmDcr1, Drosophila melanogaster, Dicer-1(NP_524453); DmDcr2, Drosophila melanogaster Dicer-2 (NP_523778) CeDcr1, Caenorhabditis elegans, Dcr-1(AAA28101); SpDcr1, Schizosaccaromyces pombe, Dcr-1 (Q09884); AtDCL1, Arabidopsis thaliana DCL1, (NP_171612); AtDCL2, Arabidopsis thaliana DCL2, (NP_566199), AtDCL3, Arabidopsis thaliana DCL3, (NP_189978); AtDCL4, Arabidopsis thaliana DCL4, (NP_197532). Rice Dicer-like proteins are shown as OsDCL1a to OsSHO1/DCL4. Scale bar in each panel represents 0.1 amino acid substitution per site.