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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.


Related in: MedlinePlus

Characteristics of NuwaII transposons. a Sequence alignments for NuwaII-2_BFlo family. The terminal inverted repeats (TIRs) and flanking sequences (10 bp) are shown. b Examples of alignments of the flanking sequences of NuwaII-2_BFlo insertions with a paralogous sequences found within the same genome but devoid of the transposon. The TIRs of the element are underlined. c Structure of NuwaII-2_BFlo. Black triangles and solid black boxes represent the TIRs and ORFs, respectively, and the position of the DDE triad is shown. d Predicted secondary structure of the DDE motif-containing transposase of the NuwaII-2_BFlo. The DDE triads is marked with red triangles below the sequence
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Fig5: Characteristics of NuwaII transposons. a Sequence alignments for NuwaII-2_BFlo family. The terminal inverted repeats (TIRs) and flanking sequences (10 bp) are shown. b Examples of alignments of the flanking sequences of NuwaII-2_BFlo insertions with a paralogous sequences found within the same genome but devoid of the transposon. The TIRs of the element are underlined. c Structure of NuwaII-2_BFlo. Black triangles and solid black boxes represent the TIRs and ORFs, respectively, and the position of the DDE triad is shown. d Predicted secondary structure of the DDE motif-containing transposase of the NuwaII-2_BFlo. The DDE triads is marked with red triangles below the sequence

Mentions: There are 30 out of 380 families which belong to the NuwaII families (Additional file 1: Table S7). According to the paralogous empty site, we cannot judge that the TSDs of NuwaII group are 3 bp (TNA) or 5 bp (CTNAG) (Fig. 5). However, most PHIS elements are typically associated with 3-bp TSD. Thus, the TSDs of NuwaII elements are most likely 3-bp TSDs. Meanwhile, there is a conserved single C nucleotide in the flank of 5′ terminal of TSDs and a conserved single G nucleotide in the flank of 3′ terminal of TSDs. Thus, the target of NuwaII is preferentially C/TNA/G (‘N’ represents A, T, C, or G nucleotide, ‘/’ represents the cut site).Fig. 5


The diversification of PHIS transposon superfamily in eukaryotes.

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

Characteristics of NuwaII transposons. a Sequence alignments for NuwaII-2_BFlo family. The terminal inverted repeats (TIRs) and flanking sequences (10 bp) are shown. b Examples of alignments of the flanking sequences of NuwaII-2_BFlo insertions with a paralogous sequences found within the same genome but devoid of the transposon. The TIRs of the element are underlined. c Structure of NuwaII-2_BFlo. Black triangles and solid black boxes represent the TIRs and ORFs, respectively, and the position of the DDE triad is shown. d Predicted secondary structure of the DDE motif-containing transposase of the NuwaII-2_BFlo. The DDE triads is marked with red triangles below the sequence
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Characteristics of NuwaII transposons. a Sequence alignments for NuwaII-2_BFlo family. The terminal inverted repeats (TIRs) and flanking sequences (10 bp) are shown. b Examples of alignments of the flanking sequences of NuwaII-2_BFlo insertions with a paralogous sequences found within the same genome but devoid of the transposon. The TIRs of the element are underlined. c Structure of NuwaII-2_BFlo. Black triangles and solid black boxes represent the TIRs and ORFs, respectively, and the position of the DDE triad is shown. d Predicted secondary structure of the DDE motif-containing transposase of the NuwaII-2_BFlo. The DDE triads is marked with red triangles below the sequence
Mentions: There are 30 out of 380 families which belong to the NuwaII families (Additional file 1: Table S7). According to the paralogous empty site, we cannot judge that the TSDs of NuwaII group are 3 bp (TNA) or 5 bp (CTNAG) (Fig. 5). However, most PHIS elements are typically associated with 3-bp TSD. Thus, the TSDs of NuwaII elements are most likely 3-bp TSDs. Meanwhile, there is a conserved single C nucleotide in the flank of 5′ terminal of TSDs and a conserved single G nucleotide in the flank of 3′ terminal of TSDs. Thus, the target of NuwaII is preferentially C/TNA/G (‘N’ represents A, T, C, or G nucleotide, ‘/’ represents the cut site).Fig. 5

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.


Related in: MedlinePlus