Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.08.26.672483

Exploring the Repetitive DNA Diversity in Solanum betaceum (Solanaceae)

Sader, M. A.·Vaio, M.·Trenchi, A.·Zapata, M. J.·Chiarini, F.·Lopez, A.·Urdampilleta, J.
View original source ↗Export metadata ↓

Abstract

The Solanaceae family, known for its diverse and economically important crops, includes the genus Solanum, which comprises 1,245 species. Solanum betaceum (tree tomato), native to the Andes and cultivated globally, is a promising species due to its nutritional value and market potential. The Cyphomandra clade, which includes the tree tomato, is characterized by huge genomes and chromosomes, with repetitive DNA elements (e.g., retrotransposons and satellite DNA) playing crucial roles in genomic and evolutionary studies. Despite its importance, genetic research on S. betaceum remains limited. This study addresses this knowledge gap by characterizing the repetitive DNA fraction to better understand intraspecific variation and develop molecular markers. Samples from five populations in northwestern Argentina were cultivated, and genome size was assessed via flow cytometry. Illumina HiSeq sequencing combined with RepeatExplorer analysis was used to identify repetitive DNA elements. Cytogenetic techniques, including CMA/DAPI staining and fluorescence in situ hybridization (FISH), were employed to detect satellite DNA patterns. Genome size analysis revealed slight variation among populations. Repetitive DNA accounted for 63.5% of the genome, with Ty3-gypsy retrotransposons being the most abundant (51.44%). Satellite DNA and rDNA were less prevalent, comprising 0.93% and 0.30% of the genome, respectively. Population comparisons showed consistent proportions of repetitive DNA overall, with notable differences in Ty3-gypsy-Tekay and satellite DNA fractions. This study provides a detailed profile of the repetitive DNA landscape in S. betaceum, uncovering intraspecific differences and delivering valuable genomic insights for future breeding and conservation efforts.

Source connections

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sader, M. A., Vaio, M., Trenchi, A., Zapata, M. J., Chiarini, F., Lopez, A., Urdampilleta, J.. 2025-08-30. Exploring the Repetitive DNA Diversity in Solanum betaceum (Solanaceae). https://doi.org/10.1101/2025.08.26.672483

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

MicroDUET: a dual-headed genomic foundation model for pathogen surveillance

Pathogen genomic surveillance works from raw reads, assembled genomes and alignments, representations that are slow and costly to compare at scale. Compact embeddings from genomic language models offer an alternative, but surveillance requires resolving both evolutionary ancestry (phylogeny) and phenotypic capability (function) - which need not co-vary. Here we present MicroDUET, which adapts a 26.6-million-parameter ProkBERT backbone with two 3.5-million-parameter adapter heads: a phylogeny head trained contrastively on genome windows from the same microbes, and a function head trained to identify genes across taxa. On held-out retrieval benchmarks, the phylogeny head returned the correct species for 80.3% and 66.6% of cellular and viral queries, and the function head the correct gene family for 97.3% and 97.2%, reaching 74.4% accuracy on an independent antimicrobial resistance-class benchmark. Across all three benchmarks MicroDUET outranked 17 other genomic encoders. Without training on lineage, clade or drug-susceptibility tasks, MicroDUET identified Mycobacterium tuberculosis and mpox virus lineages and clades (0.965, 0.975 accuracy), discriminated rifampicin resistance without lineage adjustment (AUROC 0.985), and retrospectively identified an emerging mpox lineage as anomalous (AUROC 0.974). MicroDUET operates 10^3 - 10^4 times faster than single-threaded sequence-based alignments. MicroDUET therefore provides a compact, reusable representation for scalable pathogen surveillance and sequence triage.

genomics↗
bioRxiv2026

A chromosome-level genome assembly of northern dragonhead, Dracocephalum ruyschiana L., 1753

We present a chromosome-level genome assembly for the vascular plant northern dragonhead, Dracocephalum ruyschiana. The assembly comprises two pseudo-haplotypes, hap1 and hap2, of 661 Mb and 681 Mb, with 93.6% and 92.5%, respectively, scaffolded into seven chromosomes each - in line with the known karyotype. Assembly quality was high, with conserved single-copy ortholog completeness scores of 97.9% and 97.8%, combined k-mer completeness of 98.1%, and 38,141 and 38,617 annotated protein-coding genes for hap1 and hap2, respectively. This assembly provides a high-quality genomic resource for future research and conservation of northern dragonhead, as well as the endangered northern dragonhead sap beetle, which depends on the plant for reproduction and whose genome assembly is described in a complementary genome note.

genomics↗
bioRxiv2026

Elucidating Bat SuperImmunity: Insights from the Bent-Wing Bat Genome Assembly and Multi-Omics Analysis

Bats have evolved a range of unique adaptations, including powered flight, echolocation, and exceptional longevity. They have also attracted considerable scientific attention, particularly since the COVID-19 pandemic, due to their association with a broad diversity of viruses and their potential role in zoonotic transmission and emerging infectious diseases. Despite hosting numerous viruses, bats often exhibit limited clinical manifestations of infection, suggesting the evolution of distinctive mechanisms of immune regulation and tolerance. Understanding the molecular basis of these mechanisms has become a major focus of current research, with genome-wide analyses providing important insights into the genetic adaptations underlying bat immunity. Nevertheless, the regulatory complexity of bat genomes, particularly the contribution of non-coding RNAs and post-transcriptional RNA editing, remains comparatively underexplored. Here, we present an integrated multi-omic framework for the common bent-wing bat (Miniopterus schreibersii), combining a contiguous chromosome-scale genome assembly with multi-tissue transcriptomic profiling, long non-coding RNA (lncRNA) identification and synteny analysis, endogenous viral elements (EVE) mapping, and same-individual RNA editomic analyses. This study provides a comprehensive resource for investigating genome organization, transcriptional regulation, evolutionary relationships, and post-transcriptional modifications in this species. In particular, it offers an opportunity to explore the potential contribution of non-coding regulatory elements and RNA editing to the molecular mechanisms underlying viral interactions and immune regulation in bats. Collectively, these resources provide a valuable foundation for advancing our understanding of bat genome evolution and the regulatory mechanisms potentially associated with their distinctive responses to viral infections.

genomics↗