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Because recombination at these intermediate repeats is infrequent, the rearranged genomic forms are present at substoichiometric levels relative to the predominant genomic form, and the substoichiometric forms are often undetectable by southern blotting (fig. 2 B; Small et al. 1987; Janska et al. 1998; Tsumura et al. 2000; Shedge et al. 2007).
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As a control, the same protocol failed to connect the genome termini within the Mononegavirales, suggesting the circular genomic form is unique to the chuviruses.
This circular genomic form was also observed in both segments of the segmented chuviruses.
Furthermore, this circular genomic form was also present in both segments of the segmented chuviruses.
The circular genomic form, which was confirmed by 'around-the-genome' RT-PCR and by the mapping of sequencing reads to the genome, is a unique feature of the Chuviridae and can be distinguished from a pseudo-circular structure seen in some other negative-sense RNA viruses including the family Bunyaviridae and the family Orthomyxoviridae.
Another issue is that of the "minimal genome": equating minimal genomes reconstructed by comparative-genomic approaches with ancestral life forms is incorrect and does not reflect the original view of the authors of the minimal genome notion (of which ref. 27 in the present manuscript is a proper reflection).
Following extraction of total genomic nucleic acids, all viral RNA forms were quantified by real-time RT-PCR using the TaqMan technology (see Table S1 for primers and probes sequences).
For the self cleavage ribozyme in the human delta virus (HDV), both the genomic form and the antigenomic form are captured in the pseudoknot structure (Figs. 1b and c) [16].
Alternatively spliced forms were identified by sequence alignment between the cDNA sequence and the genomic sequences.
To quantify the relative frequency of the two isomeric genomic forms, Illumina paired-end reads were mapped to the genome using Bowtie 2 with default parameters.
Unexpectedly, the virus evolved towards genomic forms with internal deletions that were packaged into separate particles and that required complementation to produce infectious progeny and kill cells [5],[7].
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