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Cramptonomyia has a 113 bp insert between nad6 and cytb, as well as several smaller inserts elsewhere in the coding region.
The possibility that high-depth regions instead represent inserts elsewhere (e.g., in the mitochondrial genome) cannot be excluded, although we did not observe obvious sequence variation in these genes that might be indicative of divergent copies in other genomes.
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Thus, they leave behind the original copy and generate a second copy that is inserted elsewhere in the genome.
It is an LT2 strain containing an nrdA'::ΩSpc'nrdB mutation and an extra nrdEF copy inserted elsewhere in the chromosome (merodiploid) allowing aerobic growth.
(Southern blot analysis usually suffices for such measurements, although it is not foolproof because fragments of the T-DNA may have been inserted elsewhere in the genome and these may not match the Southern probe).
Class 1 elements transpose by an RNA intermediate, whereas class 2 elements excise from one chromosomal locus and insert elsewhere in the genome.
However, since there are >2× copies of B, this segment may have amplified independently or inserted elsewhere in the genome as genome shards.
Retrotransposons move through an RNA intermediate that is reverse transcribed into a DNA copy that can insert elsewhere in the genome (Kumar and Bennetzen 1999).
In addition to sequence analysis of each deletion, we verified that the deleted sequences had not inserted elsewhere in the genome using multiple sets of internal primers for each deletion (supplementary material Fig. S2).
The PCR product (primers 1 & 7) was incubated with HinD III and Nhe I to distinguish whether the μ gene had replaced the HygR-TK gene or inserted elsewhere in the genome.
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CEO of Professional Science Editing for Scientists @ prosciediting.com