School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai, 201203, China.
BMC Genomics. 2019 Jul 19;20(1):595. doi: 10.1186/s12864-019-5951-3.
Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target proteins. They exist widely in bacteria, archaea, phage and plasmid. However, our understanding about DGRs in natural environments was still very limited.
We developed an efficient computational algorithm to identify DGRs, and applied it to characterize DGRs in more than 80,000 sequenced bacterial genomes as well as more than 4,000 human metagenome datasets. In total, we identified 948 non-redundant DGRs, which expanded the number of known DGRs in bacterial genomes and human microbiomes by about 55%, and provided a much more comprehensive reference for the study of DGRs. Phylogenetic analysis was done for identified DGRs. The putative target genes of DGRs were searched, and the functions of these target genes were investigated with a comprehensive alignment against the nr database.
DGR system is a powerful and universal mechanism to generate diversity. DGR evolution is closely associated with the living environment and their cassette structures. Furthermore, it may impact a wide range of functional processes in addition to receptor-binding. These results significantly improved our understanding about DGRs.
多样性产生的 retroelements（DGRs）是一类独特的 retroelements，通过引入变异和加速目标蛋白的进化，为其宿主带来了 DNA 序列多样性的好处。它们广泛存在于细菌、古菌、噬菌体和质粒中。然而，我们对自然环境中的 DGRs 的了解仍然非常有限。
我们开发了一种有效的计算算法来识别 DGRs，并将其应用于超过 80000 个测序细菌基因组和超过 4000 个人类宏基因组数据集的 DGR 特征描述。总共鉴定了 948 个非冗余的 DGRs，这将细菌基因组和人类微生物组中已知的 DGRs 数量分别增加了约 55%，为 DGRs 的研究提供了一个更全面的参考。对鉴定出的 DGRs 进行了系统发育分析。搜索了 DGR 的假定靶基因，并与 nr 数据库进行了全面比对，研究了这些靶基因的功能。
DGR 系统是一种产生多样性的强大而普遍的机制。DGR 的进化与生活环境及其盒式结构密切相关。此外，除了受体结合之外，它可能还会影响广泛的功能过程。这些结果显著提高了我们对 DGRs 的理解。
