The diversification of PHIS transposon superfamily in eukaryotes.
The diversification of PHIS transposon superfamily in eukaryotes.
复制标题
真核生物中 PHIS 转座子超家族的多样化
DOI：
10.1186/s13100-015-0043-7
复制
发表时间：
2015
期刊：
影响因子：
4.9
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Han MJ;Xiong CL;Zhang HB;Zhang MQ;Zhang HH;Zhang Z
背景PHIS转座子超家族属于DNA转座子家族，包括PIF/Harbinger、ISL 2 EU和Spytransposon三大类。这三组具有相似的DDE结构域的转座酶，但是，他们的编码能力，物种分布，和靶位点重复（TSDs）是显着different.ResultsIn这项研究中，我们系统地确定和分析PHIS转座子在836测序真核生物基因组中使用转座酶同源性搜索和结构的方法。在112个基因组中共鉴定出380个PHIS家系，其中168个为首次报道。除了先前鉴定的PIF/Harbinger、ISL 2 EU和Spygroups外，还鉴定了三种新的PHIS超家族类型（称为Pangu、NuwaI和NuwaII），每种类型都有其独特的特征，特别是在TSDs中，Pangu和NuwaII转座子的特征在于5′-ANT-3′和5′-C| TNA| G-3′ TSD。这两种转座子广泛分布于植物、真菌和动物中，NuwaI转座子的特征是5′-CWG-3′ TSDs，主要分布于动物中。在这380个家系中，有168个是本研究首次报道。此外，还鉴定了三种新的PHIS超家族类型。本研究结果不仅丰富了转座子的多样性，而且对提高高等生物基因组序列的组装和注释水平具有重要意义。
BackgroundPHIS transposon superfamily belongs to DNA transposons and includesPIF/Harbinger,ISL2EU, andSpytransposon groups. These three groups have similar DDE domain-containing transposases; however, their coding capacity, species distribution, and target site duplications (TSDs) are significantly different.ResultsIn this study, we systematically identified and analyzed PHIS transposons in 836 sequenced eukaryotic genomes using transposase homology search and structure approach. In total, 380 PHIS families were identified in 112 genomes and 168 of 380 families were firstly reported in this study. Besides previous identifiedPIF/Harbinger,ISL2EU, andSpygroups, three new types (calledPangu,NuwaI, andNuwaII) of PHIS superfamily were identified; each has its own distinctive characteristics, especially in TSDs.PanguandNuwaIItransposons are characterized by 5′-ANT-3′ and 5′-C|TNA|G-3′ TSDs, respectively. Both transposons are widely distributed in plants, fungi, and animals; theNuwaItransposons are characterized by 5′-CWG-3′ TSDs and mainly distributed in animals.ConclusionsHere, in total, 380 PHIS families were identified in eukaryotes. Among these 380 families, 168 were firstly reported in this study. Furthermore, three new types of PHIS superfamily were identified. Our results not only enrich the transposon diversity but also have extensive significance for improving genome sequence assembly and annotation of higher organisms.
登录
查看更多内容
影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
4.5
作者：
de Koning AP;Gu W;Castoe TA;Batzer MA;Pollock DD
通讯作者：
Pollock DD
影响因子：
1.5
作者：
Kapitonov, VV;Jurka, J
通讯作者：
Jurka, J
影响因子：
4.2
作者：
Sanmiguel, P;Bennetzen, JL
通讯作者：
Bennetzen, JL
影响因子：
10.7
作者：
Gilbert, Clement;Hernandez, Sharon S.;Feschotte, Cedric
通讯作者：
Feschotte, Cedric