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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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Related in: MedlinePlus

Mechanisms of new intron formation in D. pulex. Newly discovered introns in D. pulex were initially formed by one of the two mechanisms: (A) An insertion (indicated by green) is formed through repair of a single, blunt DSB or (B) through repair of a single, staggered DSB (insertion shown in blue and red). Subsequent events illustrated in (C)–(G) may expand the size and complexity of an intron. These include the following: (C) A blunt and a staggered DSB occur side-by-side, but in some cases, the order of these events (illustrated in C.1 and C.2) is unclear. In other cases, the order is clear. An initial blunt insertion may be followed by a subsequent staggered insertion (D, secondary insert is in light green and beige) or a subsequent second blunt insertion (E, secondary insert is in beige). Alternatively, an initial staggered insert may be followed by a subsequent staggered insert (F, secondary insert in light red and pale green) or a subsequent blunt insert (G, secondary insert in pale green). Peach boxes in (A)–(G) indicate the structure of the neointron after initial and secondary insertions.
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evu174-F3: Mechanisms of new intron formation in D. pulex. Newly discovered introns in D. pulex were initially formed by one of the two mechanisms: (A) An insertion (indicated by green) is formed through repair of a single, blunt DSB or (B) through repair of a single, staggered DSB (insertion shown in blue and red). Subsequent events illustrated in (C)–(G) may expand the size and complexity of an intron. These include the following: (C) A blunt and a staggered DSB occur side-by-side, but in some cases, the order of these events (illustrated in C.1 and C.2) is unclear. In other cases, the order is clear. An initial blunt insertion may be followed by a subsequent staggered insertion (D, secondary insert is in light green and beige) or a subsequent second blunt insertion (E, secondary insert is in beige). Alternatively, an initial staggered insert may be followed by a subsequent staggered insert (F, secondary insert in light red and pale green) or a subsequent blunt insert (G, secondary insert in pale green). Peach boxes in (A)–(G) indicate the structure of the neointron after initial and secondary insertions.

Mentions: Based on sequence characteristics of these newly gained introns and adjacent exons, observed events of intron gain are associated with initial DSBs. Some appear to have been formed through staggered DSBs, evidenced by direct repeats at opposite ends. Others show evidence of a combination of blunt and staggered DSBs at the same site, although the order of these two events is sometimes unclear (fig. 3 and supplementary figs. S1, S21, S40, and S58c, Supplementary Material online).Fig. 3.—


Characterization of newly gained introns in Daphnia populations.

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

Mechanisms of new intron formation in D. pulex. Newly discovered introns in D. pulex were initially formed by one of the two mechanisms: (A) An insertion (indicated by green) is formed through repair of a single, blunt DSB or (B) through repair of a single, staggered DSB (insertion shown in blue and red). Subsequent events illustrated in (C)–(G) may expand the size and complexity of an intron. These include the following: (C) A blunt and a staggered DSB occur side-by-side, but in some cases, the order of these events (illustrated in C.1 and C.2) is unclear. In other cases, the order is clear. An initial blunt insertion may be followed by a subsequent staggered insertion (D, secondary insert is in light green and beige) or a subsequent second blunt insertion (E, secondary insert is in beige). Alternatively, an initial staggered insert may be followed by a subsequent staggered insert (F, secondary insert in light red and pale green) or a subsequent blunt insert (G, secondary insert in pale green). Peach boxes in (A)–(G) indicate the structure of the neointron after initial and secondary insertions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu174-F3: Mechanisms of new intron formation in D. pulex. Newly discovered introns in D. pulex were initially formed by one of the two mechanisms: (A) An insertion (indicated by green) is formed through repair of a single, blunt DSB or (B) through repair of a single, staggered DSB (insertion shown in blue and red). Subsequent events illustrated in (C)–(G) may expand the size and complexity of an intron. These include the following: (C) A blunt and a staggered DSB occur side-by-side, but in some cases, the order of these events (illustrated in C.1 and C.2) is unclear. In other cases, the order is clear. An initial blunt insertion may be followed by a subsequent staggered insertion (D, secondary insert is in light green and beige) or a subsequent second blunt insertion (E, secondary insert is in beige). Alternatively, an initial staggered insert may be followed by a subsequent staggered insert (F, secondary insert in light red and pale green) or a subsequent blunt insert (G, secondary insert in pale green). Peach boxes in (A)–(G) indicate the structure of the neointron after initial and secondary insertions.
Mentions: Based on sequence characteristics of these newly gained introns and adjacent exons, observed events of intron gain are associated with initial DSBs. Some appear to have been formed through staggered DSBs, evidenced by direct repeats at opposite ends. Others show evidence of a combination of blunt and staggered DSBs at the same site, although the order of these two events is sometimes unclear (fig. 3 and supplementary figs. S1, S21, S40, and S58c, Supplementary Material online).Fig. 3.—

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
Related in: MedlinePlus