Related Content
Search Google Scholar for:
|
|
Science 13 April 2007:
Vol. 316. no. 5822, pp. 238 - 240
DOI: 10.1126/science.1139462
|
|
Reports
Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome
Kyudong Han1*,
Miriam K. Konkel1*,
Jinchuan Xing1* ,
Hui Wang1*,
Jungnam Lee1,
Thomas J. Meyer1,
Charles T. Huang1,
Erin Sandifer1,
Kristi Hebert1,
Erin W. Barnes1,
Robert Hubley2,
Webb Miller3,
Arian F. A. Smit2,
Brygg Ullmer4 and
Mark A. Batzer1
1 Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.
2 Institute for Systems Biology, Seattle, WA98103, USA.
3 Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
4 Department of Computer Science, Center for Computation and Technology (CCT), Louisiana State University, Baton Rouge, LA70803, USA.
|
Fig. 1. Phylogenetic tree of retroviruses based on full-length Pol proteins. Common infectious retroviruses and endogenous retroviruses, present in fish, birds, mammals (nonprimate), and primates, were included in the analysis. Color identifications for each group are shown in the upper right corner. Asterisks and circles show deep-rooted branches with >95 and >75% bootstrap values, respectively. The ERVs identified in this study that invaded the OWM genome horizontally (i.e., through external germline infection) are indicated with red letters. For all ERVs shown in blue letters, the original insertion occurred in the common ancestor of humans and rhesus macaques (i.e., vertically) and is present in both genomes. All ERVs indicated with blue letters also generated new insertions in the OWM lineage. The scale bar indicates 10% divergence in the amino acid sequence.
[View Larger Version of this Image (97K GIF file)]
|
|
|
Fig. 2. Median-joining network of OWM-specific L1 subfamilies. Subfamilies are represented by circles, with the circle size symbolizing the relative size of each subfamily. The length of the lines corresponds to the number of substitutions. The scale of a single substitution is shown in the upper left corner. Broken lines indicate segments not drawn to scale. Gray circles represent the subfamilies belonging to the L1CER-3 lineage, which include an 18–base pair (bp) duplication in their 3' untranslated region (3'UTR), and green-edged circles contain intact full-length L1 elements. The dashed line and red arrow represent two alternative pathways for the origin of the L1CER-4 subfamily. The subfamilies in the blue and pink ovals share the same diagnostic mutations but do not share the 18-bp duplication. My, million years.
[View Larger Version of this Image (12K GIF file)]
|
|
|
Fig. 3. Median-joining network of OWM-specific Alu subfamilies. Subfamilies are represented by circles. The length of the lines corresponds to the number of substitutions, and the scale of a single substitution is shown in the upper left corner. Broken lines indicate segments not drawn to scale. Gray circles represent all subfamilies belonging to the AluYRb lineage containing a 12-bp deletion. Red-edged circles denote the youngest Alu subfamily within each lineage, and the blue-edged circle indicates the AluY subfamily consensus sequence.
[View Larger Version of this Image (18K GIF file)]
|
|
|
|
