Integrative satellitomics reveals distinct patterns of organization, transcription and evolution of satellite DNAs in Tenebrio molitor

Majcen, Patrik; Sermek, Antonio; Ugarković, Đurđica; Oppert, Brenda; Plohl, Miroslav; Šatović-Vukšić, Eva (2026) Integrative satellitomics reveals distinct patterns of organization, transcription and evolution of satellite DNAs in Tenebrio molitor. Biology Direct, 21 (1). ISSN 1745-6150

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Abstract

Satellite DNAs (satDNAs) are repetitive sequences that play important roles in chromosomal architecture, genome evolution, and regulation. Here, we present a comprehensive characterization of Tenebrio molitor satellitome, integrating cytogenetic mapping, in silico genome annotation, divergence profiling, screening of extrachromosomal circular DNA (eccDNA), transcription analysis across developmental stages, and phylogenetic and age analyses. SatDNAs exhibited diverse chromosomal organizations, ranging from widespread to chromosome-restricted distributions. Discrepancies between assembly-based and physical mapping highlight limitations of individual approaches and underscore the importance of their integration. Divergence landscape analyses revealed different homogenization efficiencies and turnover rates, reflecting distinct evolutionary trajectories among individual satDNAs. Phylogenetic reconstruction revealed distinct patterns which include clear species-specific clustering of monomers, mixed interspecific clustering, and dispersed topologies. Comparative analyses across insect orders enabled age estimation, identifying both ancient (≥380 MYA) and lineage-specific satDNAs, apparently restricted to T. molitor. We designed and applied an approach that enables the simultaneous detection of multiple satDNAs within the eccDNA fraction which confirmed the presence of six satDNAs in eccDNA. RNA-seq analyses revealed coordinated, stage-specific transcription of all satDNAs, with elevated expression in late male pupae and early male adults. Together, these results reveal a highly dynamic, heterogeneous, and functionally relevant satDNA landscape in T. molitor and demonstrate the importance of integrative approaches for understanding molecular mechanisms and trajectories of satDNA evolution.

Item Type:	Article
Uncontrolled Keywords:	satellite DNA; satellitome; extrachromosomal circular DNA; transcription; phylogeny; molecular evolution; insect genomics; Tenebrio molitor
Subjects:	NATURAL SCIENCES > Biology > Biochemistry and Molecular Biology NATURAL SCIENCES > Biology > Genetics, Evolution and Phylogenetics NATURAL SCIENCES > Biology > General Biology
Divisions:	Division of Molecular Biology
Projects:	Project title Project leader Project code Project type Rasvjetljavanje uloga „tamne materije“ u funkcioniranju genoma gospodarski važnog kukca kornjaša Tenebrio molitor Eva Šatović Vukšić UNSPECIFIED UNSPECIFIED
Depositing User:	Eva Šatović Vukšić
Date Deposited:	22 May 2026 13:13
URI:	https://fulir.irb.hr:/id/eprint/11996
DOI:	10.1186/s13062-026-00808-1

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