Selected article for: "LG substitution model and phylogenetic tree"

Author: Shabman, Reed S.; Shrivastava, Susmita; Tsibane, Tshidi; Attie, Oliver; Jayaprakash, Anitha; Mire, Chad E.; Dilley, Kari E.; Puri, Vinita; Stockwell, Timothy B.; Geisbert, Thomas W.; Sachidanandam, Ravi; Basler, Christopher F.
Title: Isolation and Characterization of a Novel Gammaherpesvirus from a Microbat Cell Line
  • Document date: 2016_2_17
  • ID: 1a9u53za_17
    Snippet: To determine the relatedness of BGHV8 to other gammaherpesviruses, a phylogenetic analysis was performed with the gB glycoprotein sequence. gB was chosen in part because, although full sequences of other bat gammaherpesviruses have not been reported, gB sequences have been amplified from bats, suggesting the presence of gammaherpesvirus in these animals. All sequences were trimmed, and the alphaherpesvirus human herpesvirus 1 gB protein served as.....
    Document: To determine the relatedness of BGHV8 to other gammaherpesviruses, a phylogenetic analysis was performed with the gB glycoprotein sequence. gB was chosen in part because, although full sequences of other bat gammaherpesviruses have not been reported, gB sequences have been amplified from bats, suggesting the presence of gammaherpesvirus in these animals. All sequences were trimmed, and the alphaherpesvirus human herpesvirus 1 gB protein served as an outgroup. We then generated a phylogenetic tree for the protein (with the LG substitution model and 100 bootstraps) and rooted it on the outgroup. This analysis confirms that BGHV8 is similar to, but distinct from, other gammaherpesviruses (28) , including other apparent bat gammaherpesviruses, and clusters with gB sequences of multiple rhadinovirus sequences (Fig. 5) . Strikingly, a majority of these rhadinovirus sequences belong to sequences obtained from microbats, highlighted in blue in Fig. 5 . Moreover, the gBs from EHV-2 and EHV-5 also are similar to BGHV8 gB, consistent with the notion that bat and horse species are closely related (29) . A more detailed tree without collapsed sequences and accession numbers is provided as Fig. S1 in the supplemental material. Similar results were obtained with a POLD1 phylogenic analysis (data not shown).

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