Cargando…

Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mi...

Descripción completa

Detalles Bibliográficos
Autores principales: Fields, Peter D., Waneka, Gus, Naish, Matthew, Schatz, Michael C., Henderson, Ian R., Sloan, Daniel B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9071559/
https://www.ncbi.nlm.nih.gov/pubmed/35446419
http://dx.doi.org/10.1093/gbe/evac059
_version_ 1784700864967999488
author Fields, Peter D.
Waneka, Gus
Naish, Matthew
Schatz, Michael C.
Henderson, Ian R.
Sloan, Daniel B.
author_facet Fields, Peter D.
Waneka, Gus
Naish, Matthew
Schatz, Michael C.
Henderson, Ian R.
Sloan, Daniel B.
author_sort Fields, Peter D.
collection PubMed
description Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent data sets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641 kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations.
format Online
Article
Text
id pubmed-9071559
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-90715592022-05-06 Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome Fields, Peter D. Waneka, Gus Naish, Matthew Schatz, Michael C. Henderson, Ian R. Sloan, Daniel B. Genome Biol Evol Letter Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent data sets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641 kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations. Oxford University Press 2022-04-21 /pmc/articles/PMC9071559/ /pubmed/35446419 http://dx.doi.org/10.1093/gbe/evac059 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Letter
Fields, Peter D.
Waneka, Gus
Naish, Matthew
Schatz, Michael C.
Henderson, Ian R.
Sloan, Daniel B.
Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome
title Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome
title_full Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome
title_fullStr Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome
title_full_unstemmed Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome
title_short Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome
title_sort complete sequence of a 641-kb insertion of mitochondrial dna in the arabidopsis thaliana nuclear genome
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9071559/
https://www.ncbi.nlm.nih.gov/pubmed/35446419
http://dx.doi.org/10.1093/gbe/evac059
work_keys_str_mv AT fieldspeterd completesequenceofa641kbinsertionofmitochondrialdnainthearabidopsisthaliananucleargenome
AT wanekagus completesequenceofa641kbinsertionofmitochondrialdnainthearabidopsisthaliananucleargenome
AT naishmatthew completesequenceofa641kbinsertionofmitochondrialdnainthearabidopsisthaliananucleargenome
AT schatzmichaelc completesequenceofa641kbinsertionofmitochondrialdnainthearabidopsisthaliananucleargenome
AT hendersonianr completesequenceofa641kbinsertionofmitochondrialdnainthearabidopsisthaliananucleargenome
AT sloandanielb completesequenceofa641kbinsertionofmitochondrialdnainthearabidopsisthaliananucleargenome