Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.

TitleLandscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.
Publication TypeJournal Article
Year of Publication2014
AuthorsRogers, RL, Cridland, JM, Shao, L, Hu, TT, Andolfatto, P, Thornton, KR
JournalMol Biol Evol
Volume31
Issue7
Pagination1750-66
Date Published2014 Jul
ISSN1537-1719
KeywordsAnimals, Drosophila, Evolution, Molecular, Female, Gene Duplication, Genetic Variation, Genome, Genotype, Mutation Rate, Sequence Deletion, Tandem Repeat Sequences
Abstract

<p>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. </p>

DOI10.1093/molbev/msu124
Alternate JournalMol. Biol. Evol.
PubMed ID24710518
PubMed Central IDPMC4069613
Grant ListF32-GM099377 / GM / NIGMS NIH HHS / United States
R01-GM083228 / GM / NIGMS NIH HHS / United States
F32 GM099377 / GM / NIGMS NIH HHS / United States
R01 GM085183 / GM / NIGMS NIH HHS / United States
P30 CA062203 / CA / NCI NIH HHS / United States
R01 GM083228 / GM / NIGMS NIH HHS / United States
R01-GM085183 / GM / NIGMS NIH HHS / United States
P30CA062203 / CA / NCI NIH HHS / United States