Widespread Horizontal Gene Transfer from Circular Single-stranded DNA Viruses to Eukaryotic Genomes
1 State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P R China
2 The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, P R China
3 Current Address: Purdue-NWAFU Joint Research Center, Northwest A&F University, Yangling, 712100, Shaanxi Province, P R China
4 Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA
BMC Evolutionary Biology 2011, 11:276 doi:10.1186/1471-2148-11-276Published: 26 September 2011
Additional file 1:
supplementary figures. This file includes 9 supplementary figures. Figure S1 illustrates the domain organization of different Rep-like proteins. Figure S2 and S3 show multiple alignments of circovirus, nanovirus or geminivirus Rep-like sequences, respectively. Figure S4 shows the phylogeny of viral Rep-like sequences from eukaryotes, known viruses and viral metagenomes. Figure S5 shows the phylogeny of geminiviral Rep-like sequences in viral metagenomes. Figure S6 shows the alignment of viral insertion loci in a genome. Figure S7 shows the phylogeny of parvovirus-like transposons. Figure S8 and S9 show the phylogenies of full-length, N-terminal and C-terminal regions of circoviral or geminiviral Rep-like proteins, respectively.
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Additional file 2:
supplementary Tabular data. This file contains 5 supplementary Tabular data. Tabular data S1 shows the characterization of eukaryotic circular ssDNA viral Rep-like proteins in other systems. Tabular data S1 gives results of all detected endogenous circular ssDNA virus-like sequences in this study. Tabular data S3 shows the endogenous parvovirus-like sequences in acorn worm genome. Tabular data S4 summarizes the expressed endogenous viral sequences. Tabular data S5 lists the circular ssDNA virus-related ESTs which have not been determined if they were expressed endogenous viral sequences.
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