What do transposable elements, satellite DNAs and meiotic drive systems have in common? They are all selfish DNAs and can spread in genomes and populations without offering any benefit, and many times even causing harm, to their hosts. Our lab integrates genomic, cytological and molecular approaches to study selfish DNA and its impact on genome evolution. Our primary interest is in satellite DNA (repetitive DNA typically found at centromeres and telomeres) and meiotic drive. Lab projects focus on three related areas:
I. The functional and evolutionary genomics of satellite DNAs
We use genomic, cytological and molecular approaches to study the functional genomics of satellite DNAs and their dynamic evolution across taxa.
Rapid evolution of the Responder (Rsp) satellite: The Rsp satellite shows dynamic evolution over short evolutionary time periods, like many other satellites. Rsp is unique in D. melanogaster because it is a target of the meiotic drive complex, Segregation Distorter (SD). Figure from Larracuente, 2014.
II. Molecular mechanisms of meiotic drive
Meiotic drivers gain a transmission advantage through the germline. We use genetic, genomic and cytological approaches to determine the molecular mechanism of different drive systems. Our primary focus is on the selfish Segregation Distorter complex of D. melanogaster.
Organization of a Segregation Distorter (SD)chromosome: SD is a selfish gene complex on D. melanogaster chromosome 2. Males heterozygous for SD and a wild type chromosome transmit SD to >95% of their progeny. SD kills sperm with sensitive alleles of its target, the Responder (Rsp)satellite repeat, on chromosome 2R. We use genomic, cytological and molecular methods to study how SD kills Rspssperm.
Sperm killing in Drosophila affinis:Sex ratio meiotic drivers kill Y-bearing sperm after meiosis in D. affinis. This figure shows an example of one phenotype in XSR2/Y testes. Approximately half of the nuclei in this sperm bundle are not properly condensed and will not make functional sperm.
III. Y chromosome evolution
Y chromosomes specialize in male fertility, but are generally gene-poor and dense in repetitive elements such as satellite DNAs. Differences in repeat content between Y chromosomes may impact genome evolution. We use population genomic and molecular methods to study Y chromosome evolution across various Drosophila species.
Y variation: Species of the obscura group segregate for Y chromosomes with different morphologies. This figure shows some of the different Y chromosomes in D. affinis. The arrows point to the Y chromosome and the arrowheads point to X chromosomes. Some D. affinis males lack a Y chromosome and are still fertile (panel C)!
- Evolutionary genetics and genomics
- Intragenomic conflict and the evolution of selfish DNA
- Evolutionary and functional genomics of satellite DNA
- Sex chromosome and dot chromosome evolution in Drosophila
- Larracuente, A.M. and V.H. Meller. 2016. Host–Symbiont Interactions: Male- Killers Exposed. Current Biology 26, R408–R431, May 23, 2016. http://dx.doi.org/10.1016/j.cub.2016.03.057
- Unckless, R., A.M. Larracuente, and A.G. Clark. 2015. Sex-ratio meiotic drive and Y-linked resistance in Drosophila affinis. Genetics. Online 1/8/2015.10.1534/genetics.114.173948
- Larracuente, A.M. and P.M. Ferree. 2015. Simple method for fluorescence DNA in situ hybridization to squashed chromosomes. J. Vis. Exp. 95, e52288. doi:10.3791/52288.
- Larracuente, A.M. 2014. The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive. BMC Evol. Biol. 14: 233. doi:10.1186/s12862-014-0233-9.
- Larracuente, A.M. and A.G. Clark. 2014. Recent selection on the Y-to-dot translocation in Drosophila pseudoobscura. Mol. Biol. Evol. 31(4): 846-856. doi 10.1093/molbev/msu002.
- Larracuente, A.M. and A.G. Clark. 2013. Surprising differences in the variability of Y chromosomes in African and Cosmopolitan populations of Drosophila melanogaster. Genetics. 193: 201-214.
- Larracuente, A.M. and D.C. Presgraves. 2012. The selfish Segregation Distorter gene complex of Drosophila melanogaster. Genetics. 192: 1-21.
- Larracuente, A.M., M.A.F. Noor, A.G. Clark. 2010. Translocation of Y-linked genes to the dot chromosome in Drosophilapseudoobscura. Mol. Biol. Evol. 27 (7): 1612-1620.
- Singh, N.D., A.M. Larracuente, T.B. Sackton, A.G. Clark. 2009. Comparative genomics on the Drosophila Phylogenetic Tree. Annu. Rev. Ecol. Evol. Syst. 40: 459–80.
- Larracuente, A.M., T.B. Sackton*, A.J. Greenberg, A. Wong, N.D. Singh, D. Sturgill, Y. Zhang, B. Oliver, A.G. Clark. 2008. Evolution of protein-coding genes in Drosophila. Trends Genet. 24 (3): 114-123.
- Singh N.D., A.M. Larracuente*, A.G. Clark. 2008. Contrasting the efficacy of selection on the X and autosomes in Drosophila. Mol. Biol. Evol. 25 (2):454-467.
- Drosophila 12 Genomes Consortium: A.G. Clark, M.B. Eisen, D.R. Smith, C.M. Bergman, B. Oliver, T.A. Markow, T.C. Kaufman, M. Kellis, W. Gelbart, V.N. Iyer, D.A. Pollard, T.B. Sackton, A.M. Larracuente et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450 (7167): 203-218.