Characterization of newly gained introns in Daphnia populations.
Bottom Line: A disproportionally large number of new introns were found in historically isolated populations in Oregon.A majority (55/90 or 61.1%) of the identified neointrons have associated internal direct repeats with lengths and compositions that are unlikely to occur by chance, suggesting repeated bouts of staggered double-strand breaks (DSBs) during their evolution.Accordingly, internal, staggered DSBs may contribute to a passive trend toward increased length and sequence diversity in nascent introns.
Affiliation: Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin email@example.com.Show MeSH
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Mentions: Twenty genes in D. pulex exhibit a pattern of parallel intron gain. In total, parallel gains account for 51 derived intron-bearing alleles in sampled populations (table 2). An illustrative example is the Dpul_308086 locus, at which three derived intron-bearing alleles were detected (supplementary fig. S55a–d, Supplementary Material online). All outgroup species and a sizeable number of D. pulex clones have alleles with an uninterrupted exon 11. In three independent events, distinct introns were inserted into this exon in geographically diverse clones of D. pulex. We detected 19 additional genes in D. pulex with patterns similar to that observed at Dpul_308086, although the number of alleles per locus and affected exons varied. In one extreme case, locus Dpul_327924, six different, derived introns were identified in close proximity in alignments of one exon (fig. 4 and supplementary fig. S58a–g, Supplementary Material online).Fig. 4.—
Affiliation: Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin firstname.lastname@example.org.