A Genome-Wide Analysis of Nuclear Mitochondrial DNA Sequences (NUMTs) in Chrysomelidae Species (Coleoptera)

Insects, Journal Year: 2025, Volume and Issue: 16(2), P. 150 - 150

Published: Feb. 2, 2025

Nuclear mitochondrial DNA sequences (NUMTs) are fragments in the nuclear genome, and their unclear distribution Chrysomelidae species hinders selection of accurate molecular markers for identification phylogenetic analysis. Our study presents a genome-wide survey NUMTs 32 species. Filtering strategies based on sequence length open reading frame (ORF) features were employed to identify protein-coding genes (PCGs) minimally affected by NUMTs. Phylogenetic relationships inferred from both PCG datasets COX1 dataset containing results show that chromosomally specific, species-specific, widely distributed. ATP8, COX1, ND1, ND4 identified as relatively reliable markers. analysis is influenced other factors such type saturation. A total 66 independent gene integration events estimated across species, mostly distinct lineages. These findings suggest reflect key evolutionary processes flow lineage diversification. Their prevalence emphasizes need refined analysis, while also highlighting importance understanding contribution species’ history.

Language: Английский

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MANUDB: database and application to retrieve and visualize mammalian NUMTs

Database, Journal Year: 2025, Volume and Issue: 2025

Published: Jan. 1, 2025

There is an ongoing genetic flow from the mitochondrial genome to nuclear genome. The sequences that have integrated into been shown be drivers of evolutionary processes and cancerous transformations. In addition their fundamental biological importance, these significant consequences for assembly phylogenetic forensic analyses as well. Previously, our research group developed a computational pipeline provides uniform way identifying in mammalian genomes. this paper, we publish MANUDB-the MAmmalian NUclear DataBase, which makes results publicly accessible. With MANUDB one can retrieve visualize fragments species. Database URL: manudb.streamlit.app.

Language: Английский

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Liberties of the genome: insertions of mitochondrial DNA fragments into nuclear genome

Vavilov Journal of Genetics and Breeding, Journal Year: 2024, Volume and Issue: 28(5), P. 467 - 475

Published: Sept. 2, 2024

The transition of detached fragments mitochondrial DNA into the nucleus and their integration chromosomal is a special kind genetic variability that highlights relation between two genomes interaction in eukaryotic cell. human genome contains several hundreds insertions mtDNA (NUMTS). This paper presents an overview current state research this area. To date, evidence has been obtained occurrence new nuclear seldom but not exceptionally rare event. occurs during double-strand break repair through non-homologous end joining mechanism. Along with evolutionarily stable “genetic fossils” were integrated millions years ago are shared by many species, there NUMTS could be species-specific, polymorphic or “private”. Partial copies can interfere experimental studies genome, such as genotyping, heteroplasmy assessment, methylation analysis, copy number estimation. In some cases, insertion multiple complete sequence may mimic paternal inheritance mtDNA. functional significance poorly understood. For instance, they source for expression splicing modulation. role cause hereditary diseases negligible, since only few cases caused have described so far. addition, serve markers evolutionary studies. Of particular interest meaning evolution. constant flow functionally inactive sequences from mitochondria its significance studied view modern concepts theory suggesting non-adaptive complexity key stochastic processes formation genomic structure.

Language: Английский

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Characterization of Nuclear Mitochondrial Insertions in Canine Genome Assemblies

Genes, Journal Year: 2024, Volume and Issue: 15(10), P. 1318 - 1318

Published: Oct. 14, 2024

The presence of mitochondrial sequences in the nuclear genome (Numts) confounds analyses sequence variation, and is a potential source false positives disease studies. To improve analysis variation canines, we completed systematic assessment Numt content across assemblies, canine populations carnivore lineage.

Language: Английский

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