Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize

Abstract

The transfer of mitochondrial DNA (mtDNA) into nuclear genomes is a regularly occurring process that has been observed in many species. Few studies, however, have focused on the variation of nuclear-mtDNA sequences (NUMTs) within a species. This study examined mtDNA insertions within chromosomes of a diverse set of Zea mays ssp. mays (maize) inbred lines by the use of fluorescence in situ hybridization. A relatively large NUMT on the long arm of chromosome 9 (9L) was identified at approximately the same position in four inbred lines (B73, M825, HP301, and Oh7B). Further examination of the similarly positioned 9L NUMT in two lines, B73 and M825, indicated that the large size of these sites is due to the presence of a majority of the mitochondrial genome; however, only portions of this NUMT (∼252 kb total) were found in the publically available B73 nuclear sequence for chromosome 9. Fiber-fluorescence in situ hybridization analysis estimated the size of the B73 9L NUMT to be ∼1.8 Mb and revealed that the NUMT is methylated. Two regions of mtDNA (2.4 kb and 3.3 kb) within the 9L NUMT are not present in the B73 mitochondrial NB genome; however, these 2.4-kb and 3.3-kb segments are present in other Zea mitochondrial genomes, including that of Zea mays ssp. parviglumis, a progenitor of domesticated maize.

Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize

“…However, XP-CNV analyses are subject to false discovery. First, organelle sequences homologous to nuclear chromosomes could result in high variation in read depths (Lough et al, 2015 ). The number of organelles, such as mitochondria or chloroplasts, varies in different tissues and the percentage of organelle genomes in DNA samples is subject to DNA extraction procedures.…”

Insertions of mitochondrial DNA into the nucleus—effects and role in cell evolution

“…NUMT variability is found intraspecifically or even intraindividually as well. Lough et al (2008Lough et al ( , 2015 studied NUMTs in a set of maize inbred lines, showing extensive NUMT variation in size and location among lines, suggesting that mtDNA is being incorporated or lost from the maize nuclear genome continuously. The same is true for cpDNA insertions; Roark et al (2010) studied the NUPTs into maize chromosomes of the same lines.…”

“…Michalovova et al (2013) found mtDNA and cpDNA insertions located at the pericentromeric regions of Arabidopsis and rice. Lough et al (2008Lough et al ( , 2015 studied mtDNA insertions in a set of maize inbred lines and found extensive variation in size and location among lines, but in many lines the signals were located near the centromere or the telomere. Caro et al (2010) using FISH in bone marrow cells of young and old rats reported that 10 pairs of chromosomes showed mtDNA signal located always at the pericentromeric region in rats of both ages.…”

Doxorubicin-Induced Translocation of mtDNA into the Nuclear Genome of Human Lymphocytes Detected Using a Molecular-Cytogenetic Approach

“…The ability of doxorubicin to induce DSBs directly due to intercalation into DNA and inhibition of topoisomerase II, and indirectly by the generation of reactive oxygen species has been shown previously [ 17 ]. The successful application of fluorescence in situ hybridization (FISH) for examining the variation in mtDNA insertions in nuclear chromosomes of human [ 8 ], maize [ 18 ], and rat [ 19 ] was the reason for selecting this method in our study.…”