Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2016 Aug 31;7(1):17. doi: 10.1186/s13100-016-0073-9

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s). 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

PMC Copyright notice

Fig. 3 — Phylogeny of dictyostelid LTR retrotransposons. Alignment of the concatenated core domains of RT, RNH, and IN was generated with ClustalX and analyzed using the Maximum Likelihood method. Numbers next to each node indicate bootstrap values as percentages out of 1000 replicates. All positions containing gaps and missing data were eliminated. The tree is drawn to scale with branch lengths measured in the number of substitutions per site. Analysis of the data using the Neighbor Joining method produced a slightly different tree topology (see Additional file 1: Figure S3). Retrotransposons integrating upstream and downstream of tRNA genes are indicated in red and blue boxes, respectively. The sequence immediately downstream of the left LTR in each retrotransposon is shown, with the TGG signature of a canonical primer binding site (PBS) or the polypyrimidine tract (PPy) highlighted in bold. The lengths of the carboxy-terminal extensions of IN domains in individual retrotransposons are indicated and were calculated from the conserved GPY/F motifs to the carboxyl end. It is also indicated whether the IN extensions contain a chromo domain. Dd: D. discoideum; Dp: D. purpureum; Dl: D. lacteum; Df: D. fasciculatum; Pp: P. pallidum; Pf: Protostelium fungivorum; IN-CTD: carboxy-terminal extension of integrase. n.d.: not determined (*: ORF degenerated; **: length of extension undetermined because LTR is missing)