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The diversification of PHIS transposon superfamily in eukaryotes.

Han MJ, Xiong CL, Zhang HB, Zhang MQ, Zhang HH, Zhang Z - Mob DNA (2015)

Bottom Line: These three groups have similar DDE domain-containing transposases; however, their coding capacity, species distribution, and target site duplications (TSDs) are significantly different.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.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Chongqing University, Chongqing, 400044 China.

ABSTRACT

Background: PHIS transposon superfamily belongs to DNA transposons and includes PIF/Harbinger, ISL2EU, and Spy transposon groups. These three groups have similar DDE domain-containing transposases; however, their coding capacity, species distribution, and target site duplications (TSDs) are significantly different.

Results: In 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 identified PIF/Harbinger, ISL2EU, and Spy groups, three new types (called Pangu, NuwaI, and NuwaII) of PHIS superfamily were identified; each has its own distinctive characteristics, especially in TSDs. Pangu and NuwaII transposons are characterized by 5'-ANT-3' and 5'-C/TNA/G-3' TSDs, respectively. Both transposons are widely distributed in plants, fungi, and animals; the NuwaI transposons are characterized by 5'-CWG-3' TSDs and mainly distributed in animals.

Conclusions: Here, 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.

No MeSH data available.


Phylogenetic tree based on DDE domain sequences of PHIS superfamily
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Fig6: Phylogenetic tree based on DDE domain sequences of PHIS superfamily

Mentions: To investigate the evolutionary relationships of six PHIS transposon groups (PIF/Harbinger, ISL2EU, Spy, Pangu, NuwaI, and NuwaII), the core catalytic DDE domain of 16 representative transposases (include intact DDE domain) of Pangu, 12 NuwaI, 21 NuwaII, 33 PIF/Harbinger, 18 ISL2EU, 11 Spy, and 11 bacterial IS5 were used to perform a Bayesian phylogenetic analysis. The resulting tree (Fig. 6) showed that the eukaryotic PHIS transposases formed five distinct highly supported monophyletic clades beside the individual clade of bacterial IS5 transposons. In the phylogenetic tree, Pangu, PIF/Harbinger, ISL2EU, and SPY transposons formed four separate clades. Meanwhile, NuwaI and NuwaII transposons formed a single clade in the phylogenetic tree.Fig. 6


The diversification of PHIS transposon superfamily in eukaryotes.

Han MJ, Xiong CL, Zhang HB, Zhang MQ, Zhang HH, Zhang Z - Mob DNA (2015)

Phylogenetic tree based on DDE domain sequences of PHIS superfamily
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4482050&req=5

Fig6: Phylogenetic tree based on DDE domain sequences of PHIS superfamily
Mentions: To investigate the evolutionary relationships of six PHIS transposon groups (PIF/Harbinger, ISL2EU, Spy, Pangu, NuwaI, and NuwaII), the core catalytic DDE domain of 16 representative transposases (include intact DDE domain) of Pangu, 12 NuwaI, 21 NuwaII, 33 PIF/Harbinger, 18 ISL2EU, 11 Spy, and 11 bacterial IS5 were used to perform a Bayesian phylogenetic analysis. The resulting tree (Fig. 6) showed that the eukaryotic PHIS transposases formed five distinct highly supported monophyletic clades beside the individual clade of bacterial IS5 transposons. In the phylogenetic tree, Pangu, PIF/Harbinger, ISL2EU, and SPY transposons formed four separate clades. Meanwhile, NuwaI and NuwaII transposons formed a single clade in the phylogenetic tree.Fig. 6

Bottom Line: These three groups have similar DDE domain-containing transposases; however, their coding capacity, species distribution, and target site duplications (TSDs) are significantly different.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.

View Article: PubMed Central - PubMed

Affiliation: School of Life Sciences, Chongqing University, Chongqing, 400044 China.

ABSTRACT

Background: PHIS transposon superfamily belongs to DNA transposons and includes PIF/Harbinger, ISL2EU, and Spy transposon groups. These three groups have similar DDE domain-containing transposases; however, their coding capacity, species distribution, and target site duplications (TSDs) are significantly different.

Results: In 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 identified PIF/Harbinger, ISL2EU, and Spy groups, three new types (called Pangu, NuwaI, and NuwaII) of PHIS superfamily were identified; each has its own distinctive characteristics, especially in TSDs. Pangu and NuwaII transposons are characterized by 5'-ANT-3' and 5'-C/TNA/G-3' TSDs, respectively. Both transposons are widely distributed in plants, fungi, and animals; the NuwaI transposons are characterized by 5'-CWG-3' TSDs and mainly distributed in animals.

Conclusions: Here, 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.

No MeSH data available.