Research article
Evolutionary maintenance of filovirus-like genes in bat genomes
Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA
BMC Evolutionary Biology 2011, 11:336 doi:10.1186/1471-2148-11-336
Published: 17 November 2011Additional files
Additional file 1:
Table S1. tblastn results in subjects of the Whole Genome Shotgun Sequences (WGS) database using three filovirus-like queries. tblastn results (sequences producing significant alignments) using A. the filovirus-like VP35 element of Myotis lucifugus as a query, B. the filovirus-like VP35 element of Marburgvirus NC_001608.3 as a query, and C. the filovirus-like NP element of Marburgvirus NC_001608.3 as a query
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Additional file 2:
Figure S1. Chromosome maps showing synteny of regions flanking the filovirus-like VP35 elements in rat and mouse genomes. A. whole chromosome view showing the five synteny blocks found between CHR 1 of the mouse and CHR 9 of the rat and B. local view showing the pronounced positional homology of the filovirus-like elements and flanking genes.
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Additional file 3:
Figure S2. Midpoint rooted maximum likelihood phylograms with support values. A. mitochondrial Cytochrome Oxidase I gene for bats of the genus Myotis, B. NP gene amino acid sequences from filoviruses and related mammalian genomic elements, and C. VP35-like gene amino acid sequences from filoviruses and related mammalian genomic elements. Note that hamster and wallaby sequences are positioned within the known modern filoviruses.
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Additional file 4:
Figure S3. Alignment of filovirus VP35-like nucleotide sequences isolated from bat genomes showing open reading frames. A graphical alignment of the VP35-like region in Myotis with open reading frames followed by a FASTA formatted alignment. Note that the two large indels fail to disrupt the open reading frames.
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Additional file 5:
Figure S4. Alignment of filovirus nucleoprotein (NP)-like nucleotide sequences isolated from bat genomes. A graphical alignment of the NP-like region in Myotis followed by a FASTA formatted alignment.
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Additional file 6:
Table S2. Site-by-site selection results and statistics for the open reading frame alignment of VP35-like genes in Myotis using two methods. Results of different site-specific tests of positive selection (Bayesian Ka/Ks with model M8; REL analysis in HyPhy) for the filovirus VP35-like gene in Myotis bats.
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Additional file 7:
Figure S5. RT-PCR of VP35-like region from Myotis lucifugus. RT-PCR of the filovirus VP35-like region and actin controls in Myotis lucifugus from two replicates each from two tissues.
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Additional file 8:
Table S3. Table showing the specimen details for bats assayed for filovirus-like sequences. Origin of specimens used for the attempted isolation of filovirus-like sequences in the present study.
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