Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey.
Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey.
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DOI：
10.1093/nar/gkx1150
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发表时间：
2018-01-09
影响因子：
14.9
通讯作者：
Zimmerly S
中科院分区：
文献类型：
--
作者：
Wu L;Gingery M;Abebe M;Arambula D;Czornyj E;Handa S;Khan H;Liu M;Pohlschroder M;Shaw KL;Du A;Guo H;Ghosh P;Miller JF;Zimmerly S
多样性生成逆转录元件（Diversity-generating retroelements，DGR）是一类利用逆转录作用在特定靶基因上产生大量序列变异的新型遗传元件。在这里，我们提出了一个详细的比较生物信息学分析，描绘了自然界中的DGR序列的景观，在GenBank中的数据表示。鉴定了超过350种独特的DGR，它们一起形成了一组有组织的功能性DGR。我们分类的目标基因，可变重复序列和DGR盒架构，并确定了两个新的辅助基因。靶基因的巨大变异性暗示了DGRs在许多未被发现的生物过程中的作用。有很多证据表明DGRs的水平转移，我们确定了DGRs的谱系，似乎有专门的属性。由于GenBank仅包含10%的描述物种的数据，因此汇编可能无法完全代表自然界中存在的DGR。事实上，许多DGR亚型在该组中仅存在一次，并且候选门辐射细菌和Diapherotrites、Parvarchaeota、Aenigmarchaeota、Nanoarchaeota、Nanohaloarchaea archaea的DGR在序列上异常多样，关于其靶基因的功能的信息很少。尽管如此，这项研究提供了一个详细的框架，分类和研究的DGR，因为他们被发现和研究的未来。
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.
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影响因子：
28.3
作者：
Paul BG;Burstein D;Castelle CJ;Handa S;Arambula D;Czornyj E;Thomas BC;Ghosh P;Miller JF;Banfield JF;Valentine DL
通讯作者：
Valentine DL
影响因子：
14.8
作者：
Kelley LA;Mezulis S;Yates CM;Wass MN;Sternberg MJ
通讯作者：
Sternberg MJ
影响因子：
14.9
作者：
Mistry J;Finn RD;Eddy SR;Bateman A;Punta M
通讯作者：
Punta M
影响因子：
--
作者：
Handa S;Paul BG;Miller JF;Valentine DL;Ghosh P
通讯作者：
Ghosh P
影响因子：
4.5
作者：
Guo, Huatao;Tse, Longping V.;Miller, Jeff F.
通讯作者：
Miller, Jeff F.