Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey
| Autor: | Li Wu, Amy Du, Mechthild Pohlschroder, Kharissa L Shaw, Mari Gingery, Hamza Khan, Michael Abebe, Sumit Handa, Diego Arambula, Elizabeth Czornyj, Partho Ghosh, Jeff F. Miller, Huatao Guo, Steven Zimmerly, Minghsun Liu |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Retroelements Evolution Sequence Homology Zoology Computational biology Biology Evolution Molecular Nanohaloarchaea 03 medical and health sciences 0302 clinical medicine Information and Computing Sciences Sequence Homology Nucleic Acid Genetic variation Genetics Nanoarchaeota Bacteriophages Amino Acid Sequence Survey and Summary Gene Sequence (medicine) Nucleic Acid Bacteria Base Sequence Sequence Homology Amino Acid Phylum Data Collection Molecular Genetic Variation Genomics Biological Sciences biology.organism_classification Archaea Amino Acid 030104 developmental biology GenBank Scale (map) Environmental Sciences 030217 neurology & neurosurgery Developmental Biology |
| Zdroj: | Nucleic Acids Research Nucleic acids research, vol 46, iss 1 Wu, L; Gingery, M; Abebe, M; Arambula, D; Czornyj, E; Handa, S; et al.(2018). Diversity-generating retroelements: Natural variation, classification and evolution inferred from a large-scale genomic survey. Nucleic Acids Research, 46(1), 11-24. doi: 10.1093/nar/gkx1150. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/1q07714k |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkx1150 |
| Popis: | © The Author(s) 2017. Diversity-generating retroelements (DGRs) are novel genetic elements that use reverse transcription to generate vast numbers of sequence variants in specific target genes. Here, we present a detailed comparative bioinformatic analysis that depicts the landscape of DGR sequences in nature as represented by data in GenBank. Over 350 unique DGRs are identified, which together form a curated reference set of putatively functional DGRs. We classify target genes, variable repeats and DGR cassette architectures, and identify two new accessory genes. The great variability of target genes implies roles of DGRs in many undiscovered biological processes. There is much evidence for horizontal transfers of DGRs, and we identify lineages of DGRs that appear to have specialized properties. Because GenBank contains data from only 10% of described species, the compilation may not be wholly representative of DGRs present in nature. Indeed, many DGR subtypes are present only once in the set and DGRs of the candidate phylum radiation bacteria, and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea archaea, are exceptionally diverse in sequence, with little information available about functions of their target genes. Nonetheless, this study provides a detailed framework for classifying and studying DGRs as they are uncovered and studied in the future. |
| Databáze: | OpenAIRE |
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