Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

Trypanosoma vivax is the earliest branching African trypanosome. This crucial phylogenetic position makes T. vivax a fascinating model to tackle fundamental questions concerning the origin and evolution of several features that characterize African trypanosomes, such as the Variant Surface Glycoproteins (VSGs) upon which antibody clearing and antigenic variation are based. Other features like gene content and trans-splicing patterns are worth analyzing in this species for comparative purposes.

Motivation: Transposable elements (TEs) are interspersed repetitive sequences that are major constituents of most eukaryotic genomes and are crucial for genome evolution. Despite the existence of multiple tools for their classification and annotation, none of them can achieve completely reliable results making it a challenge for genomic studies. In this work, we introduce TEclass2, a new software that uses a deep learning approach based upon a linear Transformer architecture with a k-mer to-kenizer and further adaptations to handle DNA sequences. This software has an easy configuration that allows training models on new datasets and the classification of TE models providing multiple metrics for a reliable evaluation of the results. Results: This work shows a successful adaptation of deep learning with Transformers for the classification of TE models from consensus sequences, and these results lay a foundation for novel methodologies in bioinformatics. We provide a tool for the training of models and the classification of consensus sequences from TE models on custom data and a web page interface with a pre-trained dataset based on curated and non-curated TE libraries allowing a fast and simple classification of TEs. Availability: https://bioinformatics.uni-muenster.de/tools/teclass2/index.pl Contact: wojmak@uni-muenster.de Supplementary information: Supplementary data are available at Bioinformatics online.

Transposable elements (TEs) constitute a significant portion of eukaryotic genomes and play crucial roles in genome evolution, yet their diverse and complex sequences pose challenges for accurate classification. Existing tools often lack reliability in TE classification, limiting genomic analyses. Here, we present TEclass2, a software employing a deep learning approach based on a linear transformer architecture with k-mer tokenization and sequence-specific adaptations to classify TE consensus sequences into sixteen superfamilies. TEclass2 demonstrates improved classification performance and offers flexible model training on custom datasets. Accessible via a web interface with pre-trained models, TEclass2 facilitates rapid and reliable TE classification. These advancements provide a foundation for enhanced genomic annotation and support further bioinformatics research involving transposable elements.

Transposable elements (TEs) are mobile genetic elements found in the majority of eukaryotic genomes. Genomic studies of protozoan parasites from the phylum Apicomplexa have only reported a handful of TEs in some species and a complete absence in others. Here, we studied sixty-four Apicomplexa genomes available in public databases, using a ‘de novo’ approach to build candidate TE models and multiple strategies from known TE sequence databases, pattern recognition of TEs, and protein domain databases, to identify possible TEs. We offer an insight into the distribution and the type of TEs that are present in these genomes, aiming to shed some light on the process of gains and losses of TEs in this phylum. We found that TEs comprise a very small portion in these genomes compared to other organisms, and in many cases, there are no apparent traces of TEs. We were able to build and classify 151 models from the TE consensus sequences obtained with RepeatModeler, 96 LTR TEs with LTRpred, and 44 LINE TEs with MGEScan. We found LTR Gypsy-like TEs in Eimeria, Gregarines, Haemoproteus, and Plasmodium genera. Additionally, we described LINE-like TEs in some species from the genera Babesia and Theileria. Finally, we confirmed the absence of TEs in the genus Cryptosporidium. Interestingly, Apicomplexa seem to be devoid of Class II transposons.

Although the genome of Trypanosoma cruzi , the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degree of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi´s genome since they permit directly determining the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, allows not only accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (DTU TcVI) and the non-hybrid Dm28c (DTU TcI), determined by PacBio SMRT technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome of T. cruzi is composed of a "core compartment" and a "disruptive compartment" which exhibit opposite gene and GC content composition. New tandem and disperse repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families MUC and trans-sialidases allows now a better overview of these complex groups of genes.