a semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes半定量,synteny-based方法改善功能预测假设和不带注释的细菌和古细菌的基因.pdfVIP

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes 1 1 2¤a 2¤b 3 Alexis P. Yelton , Brian C. Thomas , Sheri L. Simmons , Paul Wilmes , Adam Zemla , Michael P. 3 4 1,2 Thelen , Nicholas Justice , Jillian F. Banfield * 1 Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America, 2 Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America, 3 Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America, 4 Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America Abstract During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation. We applied the phylogenetic pairwise comparison method to establish and model a strong correlation between synteny and sequence divergence in all 634 available Archaeal and Bacterial genomes from the NCBI database and four newly assembled genomes of uncultivated Archaea from an acid mine drainage (AMD) community. In parallel, we established and modeled the trend between synteny and functional relatedness in the 118 genomes available in the STRING datab