Description and display conventions

Nuclear mitochondrial DNA segments (NUMTs) are a kind of insertion from the mitochondrion to the nucleus, which is an ongoing and frequent process that happens in all eukaryotes. In previous studies, NUMTs have been reported to increase genetic diversity, promote gene and genome evolution, and generate novel nuclear exons. NUMTs can also affect the accuracy when nuclear genomes are assembled.

This track is a collection of Nuclear mitochondrial DNA segments, provided in BED format.

Notice: Alignments to incompletely assembled or unmapped chromosome locations are omitted in this track.

In this track, the BED score is calculated by -10log10(E-value), representing the alignment confidence and is reflected in the level of gray. Scores >=100 (E-values <= 1e-10) are colored black. It is important to note that when a NUMT is a merged result, the score is taken as the highest score among all results.

Methods

This dataset identifies nuclear mitochondrial genome segments (NUMTs) by comparing nuclear and mitochondrial genomes and proteins using LAST alignment tools. The method involves several steps: nuclear genome-mitochondrial genome comparison, nuclear genome-mitochondrial protein comparison, and exclusion of overlapping nuclear ribosomal RNA regions using maf-Bed and seg-suite tools. Results are merged if alignments are consistent across both comparisons, with sequences under 30bp excluded. Bedtools and LAST are used throughout the process for efficient alignment and merging.

For more detailed information on the methods used for detecting NUMTs, please visit the following webpage:

Contact

If you have questions or comments, please write to:

Huang Muyao, 2171272903@edu.k.u-tokyo.ac.jp

References

Kleine T, Maier UG, Leister D. DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol. 2009;60:115-38. DOI: 10.1146/annurev.arplant.043008.092119; PMID: 19014347

Zhang GJ, Dong R, Lan LN, Li SF, Gao WJ, Niu HX. Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants. Int J Mol Sci. 2020 Jan 21;21(3). DOI: 10.3390/ijms21030707; PMID: 31973163; PMC: PMC7037861

Yao Y, Frith MC. Improved DNA-Versus-Protein Homology Search for Protein Fossils. IEEE/ACM Trans Comput Biol Bioinform. 2023 May-Jun;20(3):1691-1699. DOI: 10.1109/TCBB.2022.3177855; PMID: 35617174

Frith MC. A simple method for finding related sequences by adding probabilities of alternative alignments. Genome Res. 2024 Sep 13;. DOI: 10.1101/gr.279464.124; PMID: 39152037