Mitochondrial DNA Insertions (from Lough et al., Genetics 2008 178: 47-55)

Figure 1: MtDNA segments hybridized to B73 chromosomes. (A). Linear map of the NB maize mitochondrial genome with cosmid locations. A linearized version of the 569,630 bp NB maize mitochondrial genome is shown (CLIFTON et al. Physiol. 2004) (condensed from (ALLEN et al. Genetics 2007)) with the cosmid positions outlined. Mitochondrial genes, rRNAs, and tRNAs (half-length lines) are represented by vertical lines. Repeats are indicated by colored arrows. The cpDNA insertions are indicated by green rectangles. A scale in kilobases is shown along the bottom. (B) Individual mtDNA-containing cosmids hybridized to B73 chromosomes. Individual cosmid probes containing mtDNA were labeled with Texas Red and hybridized to B73 chromosomes. The white arrowheads mark mtDNA insertion sites and the green arrowheads mark potential cpDNA insertion sites. The eight-mix of karyotyping probes (KATO et al. 2004) was used to identify each chromosome. Only the layer with the Texas Red-labeled mitochondrial probes is shown. The marked mtDNA insertion sites were identified on > 88% of individual chromosomes examined.

Figure 2: MtDNA insertion sites in the chromosomes of ten maize inbred lines. The karyotypes of ten different maize inbred lines are shown. Sites of mtDNA hybridization on the chromosomes, probed with the 19-cosmid mix of mtDNA, are indicated by arrowheads. The eight-mix of karyotyping probes was used to identify the chromosomes. The marked mtDNA insertion sites were identified on > 88% of the chromosomes examined.

Figure 3: Different B73 sources probed with the 19-cosmid mix. The karyotypes of B73 from three different sources are shown. Arrowheads indicate mtDNA insertion sites. White arrowheads indicate insertion sites seen in > 88% of chromosomes observed. Empty arrowheads indicate insertion sites seen in 60-87% of the chromosomes observed. Chromosomes were identified as described in Figure 2.

Figure 4: Different B73 sources (A, B and C) probed with mtDNA segments. Six individual mtDNA-containing cosmids labeled with Texas Red were hybridized to B73 chromosomes of different sources. The white arrowheads mark mtDNA insertion sites and the green arrowheads mark potential cpDNA insertion sites. The eight-mix of karyotyping probes was used to identify each chromosome. Only the layer with the Texas Red-labeled mitochondrial probes is shown. The marked mtDNA insertion sites were identified on > 88% of individual chromosomes examined. Chromosome 8 contained no mtDNA insertion sites and was not included in this figure.

Figure 5: Different W23 sources probed with the 19-cosmid mix. The karyotypes of both W23 sources and their F1 hybrid are included. The top two, separate source karyotypes show both the mtDNA insertion sites and karyotyping probes (color). The bottom karyotype of the hybrid shows only the mtDNA insertion sites. Arrowheads indicate mtDNA insertion sites and are labeled as described in Figure 3.

Figure 6: Two W23 sources (A and B) probed with mtDNA segments. Six individual mtDNA-containing cosmids labeled with Texas Red were hybridized to W23 chromosomes of two sources. The white arrowheads mark mtDNA insertion sites. The eight-mix of karyotyping probes was used to identify each chromosome. Only the layer with the Texas Red-labeled mitochondrial probes is shown.

Plastid DNA Insertions
(from Roark et al., Cytogenetics and Genome Research 2010 129: 17-23)

Figure 1: Chloroplast DNA (cpDNA) segments hybridized to B73 chromosomes. The fourteen PCR-amplified probes (A-N) from chloroplast DNA collectively represent the entire chloroplast genome. Each probe was hybridized individually to the mitotic metaphase chromosome spreads. The ten B73 chromosomes are shown hybridized with each cpDNA-region probe. NUPTs are indicated by green arrowheads. The chromosomes were identified using a mix of eight karyotyping probes. Only the signals identified with the Texas red-labeled chloroplast DNA probes are shown in the figure. Chromosomes 1, 2 and 5 have the most NUPTs.

Figure 2: NUPTs in ten maize inbred lines. Arrowheads indicate sites of chloroplast-DNA probe hybridization. The cpDNA probe used is a mixture of the fourteen PCR-amplified cpDNA regions shown in the figure above. The chromosomes were identified with eight karyotyping probes. The layer with only the Texas red-labeled cpDNA probe is shown on the left; the karyotyping plus cpDNA probes are shown on the right.