The effects of the host gene and its intronic miRNAs must be evaluated together because the intronic miRNAs originating from those missing introns may have critical roles in positive or negative feedback with respect to the expression or function of the host genes or their downstream signaling pathways.
In contrast, the Drosophila genes bro and bgb have no introns, while the C. elegans homologue is missing introns 1 and 4 (with its second intron displaced upstream in the coding sequence with respect to intron 3 of the deuterostome homologues; Fig. 1A).
All missing introns were lost precisely from the genome.
The later duplicate is missing introns II-V and is likely a product of retrotransposition.
A second intron position was also conserved in prtB, C and E (intron position 2, Figure 3A), while a third intron position was conserved in prtB, C and I (intron position 7, Figure 3A) Comparison of the prtI gene with the orthologous pr1A gene from M. anisopliae revealed that the second of three introns in the pr1A gene appears to have been lost from prtI (missing intron position 2, Figure 3A).
Initially three constructs were tested that, collectively, are missing intron 1 positions 5811 to 8167.
To determine the source of these discrepancies between Tiling Assembly and the FL-cDNA, seven different categories of classification were used: extra exon, missing exon, extra intron, missing intron, missing junction, gap, or multiple discrepancies.
Those introns have been inherited vertically.
Evolutionary studies of introns have primarily been based on the Introns-Early (IE) or the Introns-Late (IL) views.
These introns have been called intron 714, intron 723 and intron 870, based on their insertion sites [ 13].
