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We have used whole genome paired-end Illumina sequence data to identify tandem duplications in 20 isofemale lines of
Drosophila yakuba and 20 isofemale lines of D. simulans and performed genome wide validation with PacBio long
molecule sequencing. We identify 1,415 tandem duplications that are segregating in D. yakuba as well as 975 duplications
in D. simulans, indicating greater variation in D. yakuba. Additionally, we observe high rates of secondary deletions at
duplicated sites, with 8% of duplicated sites in D. simulans and 17% of sites in D. yakuba modified with deletions. These
secondary deletions are consistent with the action of the large loop mismatch repair system acting to remove polymorphic
tandem duplication, resulting in rapid dynamics of gain and loss in duplicated alleles and a richer substrate of
genetic novelty than has been previously reported. Most duplications are present in only single strains, suggesting that
deleterious impacts are common. Drosophila simulans shows larger numbers of whole gene duplications in comparison
to larger proportions of gene fragments in D. yakuba. Drosophila simulans displays an excess of high-frequency
variants on the X chromosome, consistent with adaptive evolution through duplications on the D.
simulans X or demographic forces driving duplicates to high frequency. We identify 78 chimeric genes in D.
yakuba and 38 chimeric genes in D. simulans, as well as 143 cases of recruited noncoding sequence in D. yakuba
and 96 in D. simulans, in agreement with rates of chimeric gene origination in D. melanogaster. Together, these
results suggest that tandem duplications often result in complex variation beyond whole gene duplications that
offers a rich substrate of standing variation that is likely to contribute both to detrimental phenotypes and disease,
as well as to adaptive evolutionary change
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