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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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Estimated age distribution of newly gained introns categorized into three groups—all new introns, new introns found in Oregon populations only, and new introns resulting from parallel gains at homologous sites. This plot indicates that new intron-containing alleles range in estimated ages of 14,500–390,000 years, with a spike in new intron establishment between 52,000 and 122,000 years.
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evu174-F2: Estimated age distribution of newly gained introns categorized into three groups—all new introns, new introns found in Oregon populations only, and new introns resulting from parallel gains at homologous sites. This plot indicates that new intron-containing alleles range in estimated ages of 14,500–390,000 years, with a spike in new intron establishment between 52,000 and 122,000 years.

Mentions: Distributions of derived intron-bearing alleles that are still segregating in D. pulex clones are divided into three categories: overall, Oregon, and parallel gains (fig. 2). Our estimate for the average age of all derived intron-bearing alleles that are polymorphic in D. pulex (overall) is 1.40 ± 0.09 × 105 (mean ± SE) years. D. pulex populations in Oregon were thought to have experienced one or more historical bottleneck events (Lynch et al. 1999). Thus, the age estimates of clades formed by derived intron-bearing alleles that are specific to Oregon can potentially provide insights into the historical events associated with new intron gains restricted to this geographic area. Our estimate for the average age of new introns endemic to Oregon populations (Oregon gain) is 1.20 ± 0.09 × 105 (mean ± SE) years.Fig. 2.—


Characterization of newly gained introns in Daphnia populations.

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

Estimated age distribution of newly gained introns categorized into three groups—all new introns, new introns found in Oregon populations only, and new introns resulting from parallel gains at homologous sites. This plot indicates that new intron-containing alleles range in estimated ages of 14,500–390,000 years, with a spike in new intron establishment between 52,000 and 122,000 years.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evu174-F2: Estimated age distribution of newly gained introns categorized into three groups—all new introns, new introns found in Oregon populations only, and new introns resulting from parallel gains at homologous sites. This plot indicates that new intron-containing alleles range in estimated ages of 14,500–390,000 years, with a spike in new intron establishment between 52,000 and 122,000 years.
Mentions: Distributions of derived intron-bearing alleles that are still segregating in D. pulex clones are divided into three categories: overall, Oregon, and parallel gains (fig. 2). Our estimate for the average age of all derived intron-bearing alleles that are polymorphic in D. pulex (overall) is 1.40 ± 0.09 × 105 (mean ± SE) years. D. pulex populations in Oregon were thought to have experienced one or more historical bottleneck events (Lynch et al. 1999). Thus, the age estimates of clades formed by derived intron-bearing alleles that are specific to Oregon can potentially provide insights into the historical events associated with new intron gains restricted to this geographic area. Our estimate for the average age of new introns endemic to Oregon populations (Oregon gain) is 1.20 ± 0.09 × 105 (mean ± SE) years.Fig. 2.—

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