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 (April 2022) Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome. Genome Biology and Evolution, 14 (5). evac059. ISSN 1759-6653

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Abstract

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.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > analysis and processing organism description > plant > Arabidopsis bioinformatics > genomics and proteomics > Mapping and Rendering organs, tissues, organelles, cell types and functions > organelles, types and functions > mitochondria organs, tissues, organelles, cell types and functions > organelles, types and functions > nucleus organs, tissues, organelles, cell types and functions > organelles, types and functions organs, tissues, organelles, cell types and functions organism description > plant
CSHL Authors:	Schatz, Michael C.
Communities:	CSHL labs > Schatz lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	21 April 2022
Date Deposited:	26 May 2022 17:17
Last Modified:	11 Jan 2024 20:01
PMCID:	PMC9071559
URI:	https://repository.cshl.edu/id/eprint/40639

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