About Lorfish DB

Pipeline

Figure 1 – Analysis workflow. Initially, we (i) obtained the complete DNA genomes of 28 fish species from NCBI; (ii) then processed each genome with RepeatModeler 2 and EDTA to generate consensus libraries of repetitive elements. In parallel, (iii) we gathered TE annotations available in the literature — specifically from FishTEDB and the study by Hildsdorf et al. — and incorporated them into our libraries. For the sequences classified as “unknown,” (iv) we applied TEsorter to infer families based on protein domains. Subsequently, (v) we used CD-HIT and BEDtools to remove redundancies between consensuses and align genomic coordinates. Finally, (vi) we ran RepeatMasker on the 259 genomes collected from NCBI and CNGB with the combined and non-redundant library, producing the definitive annotation of transposable elements that composes LORFISHTEDB.

About

Transposable elements (TEs) are mobile DNA sequences that can change position within the genome, playing key roles in genetic diversity and evolution[1]. They are grouped into two main classes: Class I (retrotransposons), which move via an RNA intermediate (“copy-and-paste”), and Class II (DNA transposons), which mobilize directly through DNA (“cut-and-paste”)[2,3]. In fish, TEs influence genome evolution, adaptation, and speciation [4]. TE accumulation also is linked to sex chromosome differentiation and reproductive isolation[5].

REFERENCES:

¹ Wicker, T. et al. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Gen., 8, 973–982.
² Jerzy, J. et al. (2011) Families of transposable elements, population structure and the origin of species. Biol. Direct, 6, 44.
³ Finnegan, D.J. (1989) Eukaryotic transposable elements and genome evolution. Trends Genet., 5, 103–107.
⁴ Almeida, E. et al. (2025) Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. Genome Biol., 26, 14.
⁵ Dulz, T.A. et al. (2024) Repetitive DNAs and chromosome evolution in Megaleporinus obtusidens and M. reinhardti (Characiformes: Anostomidae). Genetica, 152, 63–70.