We report a Danio rerio transposon named DrTRT, for D. rerio Transposon Related to Tc1. The complete sequence of the DrTRT transposon is 1,563 base pairs (bp) in length, and its transposase putatively encodes a 338-amino acid protein that harbors a DD37E motif in its catalytic domain. We present evidence based on searches of publicly available genomes that TRT elements commonly occur in vertebrates and protozoa. Phylogenetic and functional domain comparisons confirm that TRT constitutes a new subfamily within the Tc1 family. Hallmark features of having no premature termination codons within the transposase, the presence of all expected functional domains, and its occurrence in the bony fish transcriptome suggest that TRT might have current or recent activity in these species. Further analysis showed that the activity of TRT elements in these species might have arisen about between 4 and 19 Ma. Interestingly, our results also implied that the widespread distribution of TRT among fishes, frog, and snakes is the result of multiple independent HT events, probably from bony fishes to snakes or frog. Finally, the mechanisms underlying horizontal transfer of TRT elements are discussed.

BackgroundTransposable elements (TEs) are common and often present with high copy numbers in cellular genomes. Unlike in cellular organisms, TEs were previously thought to be either rare or absent in viruses. Almost all reported TEs display only one or two copies per viral genome. In addition, the discovery of pandoraviruses with genomes up to 2.5-Mb emphasizes the need for biologists to rethink the fundamental nature of the relationship between viruses and cellular life.ResultsHerein, we performed the first comprehensive analysis of miniature inverted-repeat transposable elements (MITEs) in the 5170 viral genomes for which sequences are currently available. Four hundred and fifty one copies of ten miniature inverted-repeat transposable elements (MITEs) were found and each MITE had reached relatively large copy numbers (some up to 90) in viruses. Eight MITEs belonging to two DNA superfamilies (hobo/Activator/Tam3 and Chapaev–Mirage–CACTA) were for the first time identified in viruses, further expanding the organismal range of these two superfamilies. TEs may play important roles in shaping the evolution of pandoravirus genomes, which were here found to be very rich in MITEs. We also show that putative autonomous partners of seven MITEs are present in the genomes of viral hosts, suggesting that viruses may borrow the transpositional machinery of their cellular hosts’ autonomous elements to spread MITEs and colonize their own genomes. The presence of seven similar MITEs in viral hosts, suggesting horizontal transfers (HTs) as the major mechanism for MITEs propagation.ConclusionsOur discovery highlights that TEs contribute to shape genome evolution of pandoraviruses. We concluded that as for cellular organisms, TEs are part of the pandoraviruses’ diverse mobilome.Electronic supplementary materialThe online version of this article (10.1186/s13100-018-0125-4) contains supplementary material, which is available to authorized users.

Ancherythroculter nigrocauda is a cyprinid fish endemic of the upper reaches of the Yangtze River in China, where it is an important aquaculture and commercial species. It is also a threatened species as a result of overfishing, dam construction and water pollution. In this study, a chromosome-level genome assembly of A. nigrocauda is reported and built using PacBio sequencing and the Hi-C technology. The 1.04-Gb sequenced genome of A. nigrocauda contained 2,403 contigs, with an N50 length of 3.12 Mb. Then, 1,297 contigs, which represented 54.0% of all contigs and 97.2% of the whole content of the genome nucleotide base, were assembled into 24 chromosomes. Combined with transcriptome data from 10 tissues, 27,042 (78.5%) genes were functionally annotated out of 34,414 predicted protein-coding genes. Interestingly, high expression of many positively selected genes and expanded gene families in the brain suggested that these genes might play important roles in brain development in A. nigrocauda. Finally, we found tissue-specific expression of 10,732 genes. Functional analyses showed that they were mainly composed of genes related to (a) environmental information processing, (b) the circulatory system, and (c) development, suggesting they might be important for adaptation to different environments and for development of A. nigrocauda. The high-quality genome obtained in this study not only provides a valuable genomic resource for future studies of A. nigrocauda populations and conservation, but is also an important resource for further functional genomics studies of fishes.

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Horizontal transfer (HT), the exchange of genetic material between species, plays important roles in transposon biology and genome evolution. In this study, we provide the first documented example of a new Academ transposon involved in recent and distant HTs into the genomes of species belonging to seven different orders of insects: Lepidoptera, Hymenoptera, Neuroptera, Embioptera, Dermaptera, Trichoptera and Zoraptera. These results suggest that HT of DNA transposons amongst insects has occurred on a broader scale than previously appreciated. The Academ transposon discovered in the Lepidoptera and parasitic wasps is of particular interest because the intimate association between wasps and their lepidopteran hosts might provide an opportunity for HT of transposons.