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Guo M, Addy GA, Yang N, Asare E, Wu H, Saleh AA, Shi S, Gao B, Song C. PiggyBac Transposon Mining in the Small Genomes of Animals. BIOLOGY 2023; 13:24. [PMID: 38248455 PMCID: PMC10813416 DOI: 10.3390/biology13010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
TEs, including DNA transposons, are major contributors of genome expansions, and have played a very significant role in shaping the evolution of animal genomes, due to their capacity to jump from one genomic position to the other. In this study, we investigated the evolution landscapes of PB transposons, including their distribution, diversity, activity and structure organization in 79 species of small (compact) genomes of animals comprising both vertebrate and invertebrates. Overall, 212 PB transposon types were detected from almost half (37) of the total number of the small genome species (79) investigated. The detected PB transposon types, which were unevenly distributed in various genera and phyla, have been classified into seven distinct clades or families with good bootstrap support (>80%). The PB transposon types that were identified have a length ranging from 1.23 kb to 9.51 kb. They encode transposases of approximately ≥500 amino acids in length, and possess terminal inverted repeats (TIRs) ranging from 4 bp to 24 bp. Though some of the transposon types have long TIRs (528 bp), they still maintain the consistent and reliable 4 bp target site duplication (TSD) of TTAA. However, PiggyBac-2_Cvir transposon originating from the Crassostrea virginica species exhibits a unique TSD of TATG. The TIRs of the transposons in all the seven families display high divergence, with a highly conserved 5' end motif. The core transposase domains (DDD) were better conserved among the seven different families compared to the other protein domains, which were less prevalent in the vertebrate genome. The divergent evolution dynamics analysis also indicated that the majority of the PB transposon types identified in this study are either relatively young or old, with some being active. Additionally, numerous invasions of PB transposons were found in the genomes of both vertebrate and invertebrate animals. The data reveals that the PB superfamily is widely distributed in these species. PB transposons exhibit high diversity and activity in the small genomes of animals, and might play a crucial role in shaping the evolution of these small genomes of animals.
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Affiliation(s)
- Mengke Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - George A. Addy
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Naisu Yang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Emmanuel Asare
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Han Wu
- Department of Immunology, School of Medicine, Shenzhen University, Shenzhen 518060, China;
| | - Ahmed A. Saleh
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City 11865, Egypt
| | - Shasha Shi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (M.G.); (G.A.A.); (N.Y.); (E.A.); (A.A.S.); (S.S.); (B.G.)
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Shi S, Puzakov MV, Puzakova LV, Ulupova YN, Xiang K, Wang B, Gao B, Song C. Hiker, a new family of DNA transposons encoding transposases with DD35E motifs, displays a distinct phylogenetic relationship with most known DNA transposon families of IS630-Tc1-mariner (ITm). Mol Phylogenet Evol 2023; 188:107906. [PMID: 37586577 DOI: 10.1016/j.ympev.2023.107906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/13/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
DNA transposons play a crucial role in determining the size and structure of eukaryotic genomes. In this study, a new family of IS630-Tc1-mariner (ITm) DNA transposons, named Hiker (HK), was identified. HK is characterized by a DD35E catalytic domain and is distinct from all previously known families of the ITm group. Phylogenetic analyses showed that DD35E/Hiker forms a monophyletic clade with DD34E/Gambol, indicating that they may represent a separate superfamily of ITm. A total of 178 Hiker species were identified, with 170 found mainly in Actinopterygii, one in Chondrichthyes, six in Anura and one in Mollusca. Gambol (GM), on the other hand, are found in invertebrates, with 18 in Arthropoda and one in Platyhelminthes. Hiker transposons have a total length ranging from 2.14 to 3.67 kb and contain a single open reading frame that encodes a protein of approximately 370 amino acids (range 311-413 aa). They are flanked by short terminal inverted repeats (TIRs) of 16-30 base pairs and two base pair (TA) target-site duplications. In contrast, most transposons of the Gambol family have a total length of 1.35-5.96 kb, encode a transposase protein of approximately 350 amino acids (range 306-374 aa), and are flanked by TIRs that range from 32 to 1097 bp in length. Both Hiker and Gambol transposases have several conserved motifs, including helix-turn-helix (HTH) motifs and a DDE domain. Our study observed multiple amplification waves and repeated horizontal transfer (HT) events of HK transposons in vertebrate genomes, indicating their role in diversifying and shaping the genomes of Actinopterygii, Chondrichthyes, and Anura. Conversely, GM transposons showed few Horizontal transfer events. According to cell-based transposition assays, most HK transposons are likely inactive due to the truncated DNA binding domains of their transposases. We present an updated classification of the ITm group based on these findings, which will enhance the understanding of both the evolution of ITm transposons and that of their hosts.
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Affiliation(s)
- Shasha Shi
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Mikhail V Puzakov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Lenninsky ave, 38 119991, Moscow, Russia
| | - Ludmila V Puzakova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Lenninsky ave, 38 119991, Moscow, Russia
| | - Yulia N Ulupova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Lenninsky ave, 38 119991, Moscow, Russia
| | - Kuilin Xiang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Binqing Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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Li X, Guan Z, Wang F, Wang Y, Asare E, Shi S, Lin Z, Ji T, Gao B, Song C. Evolution of piggyBac Transposons in Apoidea. INSECTS 2023; 14:402. [PMID: 37103217 PMCID: PMC10140906 DOI: 10.3390/insects14040402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
In this study, we investigated the presence of piggyBac (PB) transposons in 44 bee genomes from the Apoidea order, which is a superfamily within the Hymenoptera, which includes a large number of bee species crucial for pollination. We annotated the PB transposons in these 44 bee genomes and examined their evolution profiles, including structural characteristics, distribution, diversity, activity, and abundance. The mined PB transposons were divided into three clades, with uneven distribution in each genus of PB transposons in Apoidea. The complete PB transposons we discovered are around 2.23-3.52 kb in length and encode transposases of approximately 580 aa, with terminal inverted repeats (TIRs) of about 14 bp and 4 bp (TTAA) target-site duplications. Long TIRs (200 bp, 201 bp, and 493 bp) were also detected in some species of bees. The DDD domains of the three transposon types were more conserved, while the other protein domains were less conserved. Generally, most PB transposons showed low abundance in the genomes of Apoidea. Divergent evolution dynamics of PB were observed in the genomes of Apoidea. PB transposons in some identified species were relatively young, whiles others were older and with some either active or inactive. In addition, multiple invasions of PB were also detected in some genomes of Apoidea. Our findings highlight the contribution of PB transposons to genomic variation in these species and suggest their potential as candidates for future gene transfer tools.
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