Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome
Article first published online: 24 SEP 2012
© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd
The Plant Journal
Volume 72, Issue 4, pages 636–651, November 2012
How to Cite
Wollrab, C., Heitkam, T., Holtgräwe, D., Weisshaar, B., Minoche, A. E., Dohm, J. C., Himmelbauer, H. and Schmidt, T. (2012), Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome. The Plant Journal, 72: 636–651. doi: 10.1111/j.1365-313X.2012.05107.x
- Issue published online: 2 NOV 2012
- Article first published online: 24 SEP 2012
- Accepted manuscript online: 14 JUL 2012 10:49AM EST
- Received 12 April 2012; revised 2 July 2012; accepted 11 July 2012; published online 24 September 2012.
Figure S1. Overview of different promotermotifs and putative polyadenylation signals within the longterminal repeat (LTR). Plant-Care was used to scan promoter motifsand putative polyadenylation signals of the 5’-LTR of Elbe1,Elbe2, Elbe3, and Elbe4. The motifs are colored according to thelegend.
Figure S2. Amino acid sequence signatures ofgag-pol polyprotein. The zinc-finger domain of the Gag, theconserved Protease domain, seven conserved domains defining thereverse transcriptase, two conserved RNase H domains are shown. Forthe integrase, the zinc finger domain, the domains harboring theDD35E motif, and the GPY/F motif are shown. For comparison, thedomains of following retrotransposons have been added: Athila4-1(Arabidopsis thaliana), Bagy2-1 (Hordeum vulgare),Cyclops-2 (Pisum sativum), as well as Diaspora and Calypso(Glycine max).
Figure S3. Alignment of the putativeEnv-like protein. For comparison, the followingretrotransposons have been included: gypsy (Drosophilamelanogaster), Calypso (Glycine max), Athila4-2(Arabidopsis thaliana), Cyclops-2 (Pisum sativum),and Cotzilla1 (Beta vulgaris). Shading indicates a homologyof at least 50%.
Figure S4. Prediction of putative transmembrane(TM) domains in the Env amino acid sequences of representativemembers of all Elbe families (examples are also shown in Figure 3).The TMHMM output shows the probability of TM domains (black,left y-Axis). TMpred generates scores based on thelikelihood of encoded TM domains and only scores greater than 500(gray dashed line) are considered significant for a TM domain (darkgray: inside à outside, light gray: outside à inside, right y-axis). The x-axis indicates amino acid sequence position.
Table S1. Primers used for the amplification of domain-specific probes derived from the consensus sequence.
Table S2. Accession numbers of Elbe retrotransposons and other sequences used as references.
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