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Here, we comprehensively analysed the abundance, diversity, and activity of Tc1/mariner transposons in African coelacanth (Latimeria chalumnae). Fifteen Tc1/mariner autonomous transposons were identified and grouped into six clades: DD34E/Tc1, DD34D/mariner, DD35D/Fot, DD31D/pogo, DD30-31D/pogo-like, and DD32-36D/Tigger, belonging to three known families: DD34E/Tc1, DD34D/mariner, and DD*D/pogo (DD35D/Fot, DD31D/pogo, DD30-31D/pogo-like, and DD32-36D/Tigger). Thirty-one miniature inverted-repeat transposable element (MITE) transposons of Tc1/mariner were also identified, and 20 of them display similarity to the identified autonomous transposons. The structural organization of these full Tc1/mariner elements includes a transposase gene flanked by terminal inverted repeats (TIRs) with TA dinucleotides. The transposases contain N-terminal DNA binding domain and a C-terminal catalytic domain characterized by the presence of a conservative D(Asp)DE(Glu)/D triad that is essential for transposase activity. The Tc1/mariner superfamily in coelacanth exhibited very low genome coverage (0.3%), but it experienced an extraordinary difference of proliferation dynamics among the six clades identified; moreover, most of them exhibited a very recent and current proliferation, suggesting that some copies of these transposons are putatively active. Additionally, at least four functional genes derived from Tc1/mariner transposons were found. We provide an up-to-date overview of Tc1/mariner in coelacanth, which may be helpful in determining genome and gene evolution in this living fossil. Key words: Latimeria chalumnae, Tc1/mariner, transposons, evolution, domestication. Dans ce travail, les auteurs analysent de maniere exhaustive l'abondance, la diversite et l'activite des transposons de la famille Tc1/mariner chez le coelacanthe africain (Latimeria chalumnae). Quinze transposons Tc1/mariner autonomes ont ete identifies et groupes en six clades : DD34E/Tc1, DD34D/mariner, DD35D/Fot, DD31D/pogo, DD30-31/type pogo et DD32-36/Tigger, lesquels appartiennent a trois familles connues : DD34E/Tc1, DD34D/mariner et DDxD/pogo (DD35D/Fot, DD31D/pogo, DD30-31/type pogo et DD32-36/Tigger). Trente et un transoposons MITE ('Miniature Inverted Terminal Element') derives de Tc1/mariner ont egalement ete identifies, et vingt d'entre eux presentaient une similarite avec les transposons autonomes identifies. Ces elements Tc1/mariner complets presentaient une organisation incluant un gene codant pour la transposase flanque des repetitions terminales inversees (TIR) avec des dinucleotides TA. Les transposases contiennent un domaine de liaison a l'ADN en N-terminal et un domaine catalytique en C-terminal, lequel est caracterise par la presence d'un trio d'acides amines D(Asp)DE-(Glu)/D qui est essentiel pour l'activite transposase. La superfamille Tc1/mariner chez le coelacanthe compte pour une tres faible part du genome (0,3 %), mais presente une extraordinaire difference dans la dynamique de proliferation parmi les six clades identifies. De plus, la plupart d'entre eux affichent une proliferation tres recente et toujours en cours, ce qui suggere que certaines copies de ces transposons sont potentiellement actives. Aussi, au moins quatre genes fonctionnels derives de transposons Tc1/mariner ont ete trouves. Les auteurs contribuent ici une vue globale a jour des elements Tc1/mariner chez le coelacanthe, laquelle sera possiblement utile pour determiner l'evolution du genome et des genes au sein de ce fossile vivant. [Traduit par la Redaction] Mots-cles : Latimeria chalumnae, Tc1/mariner, transposons, evolution, domestication., Introduction Transposable elements (TEs) are widely distributed in the genome of most organisms. During the processes of biological evolution, TEs have dramatically affected the size and structure of the genomes [...]

Simple Summary: Despite the discovery of the Tigger family of pogo transposons in the mammalian genome, the evolution profile of this family is still incomplete. Here, we conducted a systematic evolution analysis for Tigger in nature. The data revealed that Tigger was found in a broad variety of animals, and extensive invasion of Tigger was observed in mammal genomes. Common horizontal transfer events of Tigger elements were observed across different lineages of animals, including mammals, that may have led to their widespread distribution, while parasites and invasive species may have promoted Tigger HT events. Our results also indicate that the activity of Tigger transposons tends to be low in vertebrates; only one mammalian genome and fish genome may harbor active Tigger. The data of this study revealed that Tigger was found in a wide variety of animal genomes, including 180 species from 36 orders of invertebrates and 145 species from 29 orders of vertebrates. An extensive invasion of Tigger was observed in mammals, with a high copy number. Almost 61% of those species contain more than 50 copies of Tigger; however, 46% harbor intact Tigger elements, although the number of these intact elements is very low. Common HT events of Tigger elements were discovered across different lineages of animals, including mammals, that may have led to their widespread distribution, whereas Helogale parvula and arthropods may have aided Tigger HT incidences. The activity of Tigger seems to be low in the kingdom of animals, most copies were truncated in the mammal genomes and lost their transposition activity, and Tigger transposons only display signs of recent and current activities in a few species of animals. The findings suggest that the Tigger family is important in structuring mammal genomes. [ABSTRACT FROM AUTHOR]

In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds. [ABSTRACT FROM AUTHOR]

Simple Summary: In the class of insects, bees are advanced evolutionary groups that play a pivotal role in ecosystem balance, agriculture, and food security. Transposons are the driving factors of genome evolution and speciation, which shape the genomes of almost all organisms. Among them, the Tc1/mariner and pogo superfamily, as the most widely distributed transposons in nature, are widely reported in insects. However, in bees, the research on transposons has never been systematically reported. Therefore, this study focuses on annotating the transposons of the Tc1/mariner and pogo superfamily of bees that were sequenced, revealing the distribution, diversity, potential activities, evolutionary patterns, and structural characteristics of transposons in different bees. Bees (Apoidea), the largest and most crucial radiation of pollinators, play a vital role in the ecosystem balance. Transposons are widely distributed in nature and are important drivers of species diversity. However, transposons are rarely reported in important pollinators such as bees. Here, we surveyed 37 bee genomesin Apoidea, annotated the pogo and Tc1/mariner transposons in the genome of each species, and performed a phylogenetic analysis and determined their overall distribution. The pogo and Tc1/mariner families showed high diversity and low abundance in the 37 species, and their proportion was significantly higher in solitary bees than in social bees. DD34D/mariner was found to be distributed in almost all species and was found in Apis mellifera, Apis mellifera carnica, Apis mellifera caucasia, and Apis mellifera mellifera, and Euglossa dilemma may still be active. Using horizontal transfer analysis, we found that DD29-30D/Tigger may have experienced horizontal transfer (HT) events. The current study displayed the evolution profiles (including diversity, activity, and abundance) of the pogo and Tc1/mariner transposons across 37 species of Apoidea. Our data revealed their contributions to the genomic variations across these species and facilitated in understanding of the genome evolution of this lineage. [ABSTRACT FROM AUTHOR]