PI: Amanda Larracuente
Graduate Students: Danielle Khost, Ching-Ho Chang, Xiaolu Wei
Postdocs: Beatriz Navarro-Domínguez, Lucas Hemmer, John Sproul
Research associates and technicians: Danna Eickbush, Shaun Jones,
Undergraduates: Isaac Wong, Taylar Mouton, Iain Speece, Sherif Negm, Eddyson Altidor, Anya Greenberg
Former lab members
Amanda earned her Ph.D. studying Drosophila genomics and sex chromosome evolution in Dr. Andrew Clark’s lab at Cornell University. During her postdoctoral training, she focused on the evolution of selfish DNA including the Segregation Distorter system of Drosophila melanogaster. Amanda is the Stephen Biggar and Elisabeth Asaro Fellow in Data Science.
- 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.
Dani is an E2G2 student working on the evolution and functional genomics of satellite DNA in Drosophila species. She is using deep real time single molecule sequencing from Pacific Biosciences to study the structural organization of satellite DNA loci in Drosophila genomes.
- Khost, D.E., D. Eickbush, A.M. Larracuente. 2017. Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster. Genome Research . Advanced Access. 4/3/17. http://www.genome.org/cgi/doi/10.1101/gr.213512.116.
Ching-Ho is an E2G2 student working on Segregation Distorter in Drosophila melanogaster and Y chromosome evolution in Drosophila. Before coming to Rochester, Ching-Ho worked with Dr. Chau-Ti Ting at National Taiwan University on neo-sex chromosome evolution in Drosophila albomicans. Ching-Ho is a recipient of the Ernst Caspari Fellowship and the Messersmith Fellowship.
- Chang, C-H, Chavan, A, Palladino, J., Wei, X., Martins, N.M.C., Santinello, B., Chen, C-C, Erceg, J., Beliveau, B.J., Wu, C-T, Larracuente, A.M., and Mellone, B.G. 2019. Islands of retroelements are major components of Drosophila melanogaster centromeres. BioRxiv Epub 2/1/2019. PLoS Biology https://doi.org/10.1371/journal.pbio.3000241.
- Chang, C-H. and A.M. Larracuente. 2019. Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome. BioRxiv 7/25/18. GENETICS 211: 333-348. doi: 10.1534/genetics.118.301765. featured in GENETICS highlights 1/1/2019 http://www.genetics.org/content/211/1/NP
- Chang, C-H. and A.M. Larracuente. 2017. Structural changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura. Evolution. Advanced Access 3/21/17. http://dx.doi.org/ .
- Chang C-c, Ting C-T, Chang C-H, Fang S, Chang H-y (2014) The Persistence of Facultative Parthenogenesis in Drosophila albomicans. PLoS ONE 9(11): e113275. doi:10.1371/journal.pone.0113275
- Chia-Hao Cheng, Ching-Ho Chang, and Hwei-yu Chang (2011) Early-stage evolution of the neo-Y chromosome in Drosophila albomicans. Zoological Studies 50(3): 338-349.
Xiaolu is a Biomedical Genetics student studying how satellite DNA is regulated in the germline using functional genomics and cytogenetics.
Beatriz Navarro-Domínguez, Ph.D. (Postdoc)
Beatriz earned her PhD studying B chromosomes in grasshoppers, in the Evolutionary Genetics Group at the University of Granada (Spain). As a postdoc, she has worked in a variety of organisms, from ferns to turtles, trying to understand how genomes evolve. Beatriz is now studying the population genomics of Segregation Distorter and the role of satellite DNA in genetic incompatibilities. She is jointly advised by Daven Presgraves and Amanda Larracuente.
Selected recent publications. See full list of publications on Beatriz’s google scholar page.
Beatriz Navarro-Domínguez, Francisco J Ruiz-Ruano, Josefa Cabrero, José María Corral, María Dolores López-León, Timothy F Sharbel, Juan Pedro M Camacho. 2017. Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. Scientific reports 7, 45200.
Beatriz Navarro-Domínguez, Josefa Cabrero, Juan Pedro M Camacho, María Dolores López-León. 2016. B-chromosome effects on Hsp70 gene expression does not occur at transcriptional level in the grasshopper Eyprepocnemis plorans. Molecular Genetics and Genomics 291 (5), 1909-1917.
Josefa Cabrero, Mohammed Bakkali, Beatriz Navarro-Domínguez, Francisco J Ruíz-Ruano, Rubén Martín-Blázquez, María Dolores López-León, Juan Pedro M Camacho. 2013. The Ku70 DNA-repair protein is involved in centromere function in a grasshopper species. Chromosome research 21 (4), 393-406.
Lucas Hemmer, Ph.D. (Postdoc)
Lucas earned his Ph.D. in Ecology and Evolutionary Biology at the University of Kansas in Justin Blumenstiel’s lab. Lucas studied the evolution of meiotic recombination landscapes in different species of Drosophila in light of selfish genetic elements including transposable elements and centromeres. Lucas joined Amanda’s lab as a postdoc to study centromere evolution in Drosophila.
Hemmer L.W. and Blumenstiel J.P.. 2016. Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila. BMC Evolutionary Biology. 16:91. https://doi.org/10.1186/s12862-016-0670-8.
Blumenstiel J.P., A.A. Erwin, L.W. Hemmer 2016. What Drives Positive Selection in the Drosophila piRNA machinery? The Genomic Autoimmunity Hypothesis. Yale J Biol Med. 2016 Dec; 89(4): 499–512.
Hemmer L.W. and J.P. Blumenstiel 2018. BioRxiv Preprint 6/8/18. The Recombination Landscape of Drosophila virilis is Robust to Transposon Activation in Hybrid Dysgenesis. https://doi.org/10.1101/342824
John Sproul, Ph.D. (NSF postdoctoral fellow)
John earned his PhD in Integrative Biology at Oregon State University in David Maddison’s lab. John studied species delimitation, phylogenomics, and repetitive DNA dynamics in ground beetles, and developed methods to improve sequencing results from historical specimens. John joined Amanda’s lab thorough a NSF-funded fellowship that aims to improve benchmarking and generate pipelines for transposable element annotation software, as well as to increase participation of underrepresented groups in science.
Danna Eickbush, Ph.D. (Research associate)
Danna Eickbush attended the University of Arizona where she was introduced to the wonders of molecular biology and immediately transferred to the newly formed Department of Cellular and Development Biology. She then joined the Ph.D. program in Cellular and Development Biology at Harvard University, characterizing the molecular structure and transcriptional patterns of the 71C-E region of Drosophila melanogaster while in the lab of Dr. Peter Cherbas. After moving to upstate New York, she did a postdoc with Dr. Jack Werren studying the selfish B-chromosome Paternal Sex Ratio (PSR) in the wasp Nasonia vitripennis. For the last 25 years, she has worked as a research associate with Dr. Tom Eickbush at the University of Rochester. The long tenure with her husband allowed Danna to study many aspects of the life cycle of the retrotransposable element R2, including its regulation and transcription. Danna works on the regulation of satellite DNA expression in Drosophila species.
Selected recent publications. Click here to see Danna’s PubMed list.
- Eickbush, T.H. and Eickbush, D.G. 2015. Integration, regulation, and long-term stability of R2 retrotransposons. In Mobile DNA III. ASMscience. Editor Nancy L. Craig (in Press).
- Eickbush, D.G., Burke, W.D. and Eickbush, T.H. 2013. Evolution of the R2 retrotransposon ribozyme and its self-cleavage site. PLoS One 8: e66441.
- Eickbush, D.G. and Eickbush, T.H. 2012. R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements. Mobile DNA 3: 10.
Shaun is a skilled fly wrangler who maintains the lab’s fly lines and helps the lab with various projects.
Sherif is using computational methods to study Segregation Distorter and repeat evolution in Drosophila.
Eddyson is using molecular methods to study variation in centromeric retroelements in Drosophila.
Anya is a data science student working on developing a bioinformatic pipeline to study repeats.
Isaac is using computational and cytogenetic methods to study repeat evolution in fireflies and Drosophila species.
Taylar is studying the function of multi-copy Y-linked gene families in D. melanogaster and the simulans clade species.
Iain is a computational biology major studying the functional genomics of satellite DNAs in D. melanogaster.
Former lab members
Undergraduates: Christian Silva (grad student UC Davis), Thanatcha (Kwan) Khunkhet, Linhe (Alex) Xu (grad student at Vanderbilt ), Danielle Pascua, Arif Kodza (MD student at SUNY Downstate), Taylar Mouton (grad student at Johns Hopkins); Isaac Wong (bioinformatician, Harvard MGH)
Rotating graduate students: Steven Messer, John Bettinger, Omid Saleh Ziabari, Nilima Walunjkar, Yingying Liang, Lauren Gregory