An Analysis of IS630/Tc1/mariner Transposons in the Genome of a Pacific Oyster, Crassostrea gigas

Пузаков, М. В.; Puzakova, L. V.; Чересиз, С. В.

doi:10.1007/s00239-018-9868-2

Cited by 22 publications

(16 citation statements)

References 59 publications

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“…4). Thus, we corroborated our previous results (Puzakov et al 2018) indicating that TLEWI elements represented a subfamily of Tc1 transposons. Additionally, we compared the exon-intron organization and the length of 21 TLEWI elements with their phylogeny.…”

Section: Evolutionary Relationship Between Tlewi Elements and Itm Trasupporting

confidence: 92%

“…Despite the variability of TIRs, their terminy usually represent a TA dinucleotide target site duplication (TSD) (van Luenen and Plasterk 1994). ITm superfamily is divided into nine families: IS630, mariner, Tc1, pogo, maT, plants, mosquito, rosa and L31 (Shao and Tu 2001;Tellier et al 2015;Zhang et al 2016b;Puzakov et al 2018). The classification of ITm elements is based on phylogenetic analysis and, until recently, it was well correlated with structural features (the length of peptide chain between the second and the third amino acid residues of the catalytic DDE/D triad (Tellier et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…The classification of ITm elements is based on phylogenetic analysis and, until recently, it was well correlated with structural features (the length of peptide chain between the second and the third amino acid residues of the catalytic DDE/D triad (Tellier et al 2015). However, the recent studies have identified, at least, four different groups of ITm elements with DD37E signature: mosquito (Shao and Tu 2001), TRT (Zhang et al 2016a), L18 and L31 (Puzakov et al 2018). Thus, the families of ITm elements cannot be accurately distinguished by the spacer size of DDE/D domains.…”

Section: Introductionmentioning

confidence: 99%

“…Thus, the families of ITm elements cannot be accurately distinguished by the spacer size of DDE/D domains. The study of ITm transposons from a Pacific oyster, Crassostrea gigas, revealed Mariner-35_CGi, which was classified as Tc1-like element (TLE) (Puzakov et al 2018). Unlike the classic TLEs (DD34E), this transposon possesses a non-canonical catalytic domain (DD36E).…”

Section: Introductionmentioning

confidence: 99%

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Why did theTc1-like elements of mollusks acquired the spliceosomal introns?

Пузаков

Puzakova

Чересиз

2019

Preprint

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Transposable elements are the DNA sequences capable of transpositions within the genome and, thus, exerting a considerable influence on the genome functioning and structure and providing the source of new genes. Transposable elements are classified into retrotransposons and the DNA transposons. IS630/Tc1/mariner superfamily of DNA transposons is one of the most diverse groups broadly represented among the eukaryotes. We identified a new group of Tc1-like elements in the mollusks, which we named TLEWI. These DNA transposons are characterized by the low copy number, the lack of terminal inverted repeats and the presence of DD36E signature and the spliceosomal introns in transposase sequence. Their prevalence among the mollusks is limited to subclass Pteriomorpha (Bivalvia). Since TLEWI possess the features of domesticated TE and the structure similar to the eukaryotic genes, which is not typical for the DNA transposons, we consider the hypothesis of co-optation of TLEWI gene by the bivalves.

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Section: Evolutionary Relationship Between Tlewi Elements and Itm Trasupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Why did theTc1-like elements of mollusks acquired the spliceosomal introns?

Пузаков

Puzakova

Чересиз

2019

Preprint

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“…A recent study of Tc1/mariner elements in the genome of the Pacific oyster Crassostrea gigas identified a new subfamily and a new family of elements. Specifically, these new groups were described as a: (i) a Mariner-18_ CGi-like group, DD37E(L18), which appeared to form a new subfamily within the Tc1 family; and, (ii) a Mariner-31_CGi-like group, DD37E(L31), that appeared to form a whole new family more basal to pogo [35]. We included the sequences from this analysis in our sequence alignment (Additional file 4), and found that: (i) the DD37E(L18) subfamily is present in the Tc1 family, but unfortunately it does not group together with Mariner-18_CGi (the C. gigas sequence it was named after) which occurs in Minos (Group 8, Additional File 2); while, (ii) the DD37E(L31) family shares a sister-group relationship with the Tec subfamily, and again unfortunately does not group together with Mariner-31_CGi, which groups as an isolated sequence with the minor families Tec, DD37E(L31), HvSm and TBE ( Fig.…”

Section: The Tc1 Familymentioning

confidence: 99%

Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

et al. 2020

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Background: Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the Tc1/mariner superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on Tc1/mariner elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of Tc1/mariner TEs by performing analyses that consider elements that originate from across host diversity. Results: We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. A total of 5158 Tc1/mariner elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of Tc1/mariner elements. In particular, we identify a new family of plant-genome restricted Tc1/mariner elements, which we call PlantMar. We also show that the pogo family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily. Conclusions: Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. Tc1/mariner TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for Tc1/mariner elements (except the PlantMar family). Meanwhile, the pogo family, which is by far the largest Tc1/mariner family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of pogo elements in vertebrates, including humans, in addition to the well-known example of CENP-B. Collectively, our findings provide a considerable advancement in understanding of Tc1/mariner elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.

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