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Characterization of newly gained introns in Daphnia populations.

Li W, Kuzoff R, Wong CK, Tucker A, Lynch M - Genome Biol Evol (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin wenli@mcw.edu.

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An illustration of parallel gains of new introns at a single locus, Dpul_327924. At this locus, six nonhomologous neointrons were inserted at the same site in six separate evolutionary events. Distinct alleles bearing nonhomologous introns are highlighted with distinct colors. A phylogeny for the alleles bearing the six nonhomologous neointrons was generated by the neighbor-joining method using exon sequences only. Branches with greater than 80% bootstrap support are labeled on the tree. cDNA sequences are indicated by green bracket in the sequence alignment. Further details are available in supplementary fig. S58a–g, Supplementary Material online.
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evu174-F4: An illustration of parallel gains of new introns at a single locus, Dpul_327924. At this locus, six nonhomologous neointrons were inserted at the same site in six separate evolutionary events. Distinct alleles bearing nonhomologous introns are highlighted with distinct colors. A phylogeny for the alleles bearing the six nonhomologous neointrons was generated by the neighbor-joining method using exon sequences only. Branches with greater than 80% bootstrap support are labeled on the tree. cDNA sequences are indicated by green bracket in the sequence alignment. Further details are available in supplementary fig. S58a–g, Supplementary Material online.

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.—


Characterization of newly gained introns in Daphnia populations.

Li W, Kuzoff R, Wong CK, Tucker A, Lynch M - Genome Biol Evol (2014)

An illustration of parallel gains of new introns at a single locus, Dpul_327924. At this locus, six nonhomologous neointrons were inserted at the same site in six separate evolutionary events. Distinct alleles bearing nonhomologous introns are highlighted with distinct colors. A phylogeny for the alleles bearing the six nonhomologous neointrons was generated by the neighbor-joining method using exon sequences only. Branches with greater than 80% bootstrap support are labeled on the tree. cDNA sequences are indicated by green bracket in the sequence alignment. Further details are available in supplementary fig. S58a–g, Supplementary Material online.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4202315&req=5

evu174-F4: An illustration of parallel gains of new introns at a single locus, Dpul_327924. At this locus, six nonhomologous neointrons were inserted at the same site in six separate evolutionary events. Distinct alleles bearing nonhomologous introns are highlighted with distinct colors. A phylogeny for the alleles bearing the six nonhomologous neointrons was generated by the neighbor-joining method using exon sequences only. Branches with greater than 80% bootstrap support are labeled on the tree. cDNA sequences are indicated by green bracket in the sequence alignment. Further details are available in supplementary fig. S58a–g, Supplementary Material online.
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.—

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin wenli@mcw.edu.

Show MeSH