Mutational profiles of myelodysplastic syndromes (MDS) have established that a relatively small number of genetic aberrations, including SF3B1 and SRSF2 spliceosome mutations, lead to specific phenotypes and prognostic subgrouping. We performed a multi-omics factor analysis (MOFA) on two published MDS cohorts of bone marrow mononuclear cells (BMMNCs) and CD34 + cells with three data modalities (clinical, genotype, and transcriptomics). Seven different views, including immune profile, inflammation/aging, retrotransposon (RTE) expression, and cell-type composition, were derived from these modalities to identify the latent factors with significant impact on MDS prognosis. SF3B1 was the only mutation among 13 mutations in the BMMNC cohort, indicating a significant association with high inflammation. This trend was also observed to a lesser extent in the CD34 + cohort. Interestingly, the MOFA factor representing the inflammation shows a good prognosis for MDS patients with high inflammation. In contrast, SRSF2 mutant cases show a granulocyte-monocyte progenitor (GMP) pattern and high levels of senescence, immunosenescence, and malignant myeloid cells, consistent with their poor prognosis. Furthermore, MOFA identified RTE expression as a risk factor for MDS. This work elucidates the efficacy of our integrative approach to assess the MDS risk that goes beyond all the scoring systems described thus far for MDS.

Satellite DNA repeats are repetitive DNA sequences found in eukaryotic genomes, typically consisting of short DNA motifs repeated in tandem arrays. Despite the vast body of literature on satellite DNA repeats in other taxa, investigations specifically targeting Tettigoniidae remain conspicuously absent. Our study aims to fill a critical gap in our understanding of satellitome evolutionary processes shaping Tettigoniidae genomes. Repeatome analysis revealed that the Meconema thalassinum genome comprises 92%, and Phryganogryllacris superangulata had the lowest value of 34%, with an average of 67% in other Tettigoniidae species. The analysis reveals significant variation in the number of satellite DNA repeats across species of the Tettigoniidae family, with M. thalassinum exhibiting the highest count, 246, reported in insects to date and the lowest count, 10, in Pholidoptera griseoptera. Ruspolia dubia and Ruspolia yunnana, which are congeneric species, showcase distinct counts of 104 and 84 families, respectively. Satellite DNA repeats in R. dubia exhibit the highest abundance, constituting 17.2% of the total genome, while the lowest abundance was reported in P. griseoptera, at 5.65%. The genome size correlates weakly with the satellite DNA family count (rs = 0.42, p = 0.29), but a strong correlation exists between satellite abundance and family number (rs = 0.73, p = 0.03). Moreover, the analysis of satellite DNA gain and loss patterns provides insights into the amplification and homogenization of satellite DNA families within the genome, with species-specific repeats exhibiting a positive trend toward amplification. The chromosomal distribution in M. thalassinum displayed that the highest accumulation was observed on Chr12, Chr01, and Chr04, constituting 17.79%, 17.4%, and 17.22% of the total chromosome size, respectively. The chromosome-specific propagation of satellite DNA families was evident, with MthSat01 solely on chromosome 1 and MthSat170 on chromosome 2, sharing 1.64% and 2.33%. The observed conservation and variations in satellite DNA number and abundances, along with distinct patterns of gain and loss, indicate the influence of potentially diverse evolutionary processes shaping the genomic landscape of these insects, which requires further investigation. Furthermore, the differential accumulation of satellite DNA on specific chromosomes implies that potential chromosome-specific functions or structural features influence the retention and proliferation of satellite sequences.

UNASSIGNED: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics.
UNASSIGNED: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized.
UNASSIGNED: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method.
UNASSIGNED: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes\' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

Transposable elements make up substantial proportions of eukaryotic genomes and many are thought to be remnants of ancient viral infections. Current research has begun to highlight the role transposable elements can play in the immune system response to infections. However, most of our knowledge about transposable element expression during infection is limited by the specific host and pathogen factors from each study, making it difficult to compare studies and develop broader patterns regarding the role of transposable elements during infection. Here, we use the tools and resources available in the model, Drosophila melanogaster, to analyze multiple gene expression datasets of flies subject to bacterial, fungal, and viral infections. We analyzed differences in pathogen species, host genotype, host tissue, and sex to understand how these factors impact transposable element expression during infection. Our results highlight both shared and unique transposable element expression patterns between pathogens and suggest a larger effect of pathogen factors over host factors for influencing transposable element expression.

Strong selection on complex traits can lead to skewed trait means and reduced trait variability in populations. An example of this phenomenon can be evidenced in allele frequency changes and skewed trait distributions driven by persistent human-directed selective pressures in domesticated species. Dog domestication is linked to several genomic variants; however, the functional impacts of these variants may not always be straightforward when found in non-coding regions of the genome. Four polymorphic transposable elements (TE) found within non-coding sites along a 5 Mb region on canine CFA6 have evolved due to directional selection associated with heightened human-directed hyper-sociability in domesticated dogs. We found that the polymorphic TE in intron 17 of the canine GTF2I gene, which was previously reported to be negatively correlated with canid human-directed hyper-sociability, is associated with altered chromatin looping and hence distinct cis-regulatory landscapes. We reported supporting evidence of an E2F1-DNA binding peak concordant with the altered loop and higher expression of GTF2I exon 18, indicative of alternative splicing. Globally, we discovered differences in pathways regulating the extra-cellular matrix with respect to TE copy number. Overall, we reported evidence suggesting an intriguing molecular convergence between the emergence of hypersocial behaviors in dogs and the same genes that, when hemizygous, produce human Williams Beuren Syndrome characterized by cranio-facial defects and heightened social behaviors. Our results additionally emphasize the often-overlooked potential role of chromatin architecture in social evolution.

The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements (TEs), have been postulated to shape genome-wide dominance and biased fractionation, leading to a conserved least-fractionated (LF) subgenome and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. In this study, a chromosome-scale assembly of the alpine buckler mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is coupled with transcriptional responses to heat, cold, drought, and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of TEs in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the \"turn a hobby into a job\" model, about one-third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased, but with others showing high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles.

BACKGROUND: Transposable elements (TEs) are major components of eukaryotic genomes. The extensive body of evidence suggests that although they were once considered \"genomic parasites\", transposons and their transcripts perform specific functions, such as regulation of early embryo development. Understanding the role of TEs in such parasites as trematodes is becoming critically important. Fasciola hepatica, a parasite affecting humans and livestock, undergoes a complex life cycle in diverse environments and hosts, and knowledge about its life cycle regulation is scarce so far.
METHODS: We summarized the data regarding the repetitive elements in F. hepatica and conducted bulk RNA-seq analysis across its life cycle stages. TE expression profiles were analyzed, focusing on differential expression and potential homology with previously described long non-coding RNAs (lncRNAs).
RESULTS: Differential expression analysis revealed stage-specific TE transcription patterns, notably peaking during egg and metacercariae stages. Some TEs showed homology with known lncRNAs and contained putative transcription factor binding sites. Interestingly, TE transcription levels were highest in eggs and metacercariae compared to adults, suggesting regulatory roles in trematode life cycle transitions.
CONCLUSIONS: These findings suggest that TEs may play roles in regulating trematode life cycle transitions. Moreover, TE homology with lncRNAs underscores their significance in gene regulation.

Transposable elements (TEs) are found in virtually every eukaryotic genome and are important for generating de novo genetic variation. However, outside of costly and time-consuming whole-genome sequencing approaches, the set of available methods to study TE polymorphisms in non-model species is very limited. The Transposon Display (TD) is a simple yet effective technique to characterize polymorphisms across samples by identifying amplified fragment length polymorphisms using primers targeting specific TE families. So far, this technique has almost exclusively been used in plants. Here, we present an optimized TD protocol for insect species with small genomes such as ants (ca. 200-600 Mb). We characterized TE polymorphisms between two distinct genetic lineages of the invasive ant Cardiocondyla obscurior, as well as between neighboring populations of the New World lineage. We found active LTR/Ty3 retrotransposons, that contributed to the genetic diversification of populations in this species.

The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

Brachypodium grass species have been selected as model plants for functional genomics of grass crops, and to elucidate the origins of allopolyploidy and perenniality in monocots, due to their small genome sizes and feasibility of cultivation. However, genome sizes differ greatly between diploid or polyploid Brachypodium lineages. We have used genome skimming sequencing data to uncover the composition, abundance, and phylogenetic value of repetitive elements in 44 representatives of the major Brachypodium lineages and cytotypes. We also aimed to test the possible mechanisms and consequences of the \"polyploid genome shock hypothesis\" (PGSH) under three different evolutionary scenarios of variation in repeats and genome sizes of Brachypodium allopolyploids. Our data indicated that the proportion of the genome covered by the repeatome in the Brachypodium species showed a 3.3-fold difference between the highest content of B. mexicanum-4x (67.97%) and the lowest of B. stacei-2x (20.77%), and that changes in the sizes of their genomes were a consequence of gains or losses in their repeat elements. LTR-Retand and Tekay retrotransposons were the most frequent repeat elements in the Brachypodium genomes, while Ogre retrotransposons were found exclusively in B. mexicanum. The repeatome phylogenetic network showed a high topological congruence with plastome and nuclear rDNA and transcriptome trees, differentiating the ancestral outcore lineages from the recently evolved core-perennial lineages. The 5S rDNA graph topologies had a strong match with the ploidy levels and nature of the subgenomes of the Brachypodium polyploids. The core-perennial B. sylvaticum presents a large repeatome and characteristics of a potential post-polyploid diploidized origin. Our study evidenced that expansions and contractions in the repeatome were responsible for the three contrasting responses to the PGSH. The exacerbated genome expansion of the ancestral allotetraploid B. mexicanum was a consequence of chromosome-wide proliferation of TEs and not of WGD, the additive repeatome pattern of young allotetraploid B. hybridum of stabilized post-WGD genome evolution, and the genomecontraction of recent core-perennials polyploids (B. pinnatum, B. phoenicoides) of repeat losses through recombination of these highly hybridizing lineages. Our analyses have contributed to unraveling the evolution of the repeatome and the genome size variation in model Brachypodium grasses.