PI: Amanda Larracuente
Graduate Students: Xiaolu Wei, Matthew Lindsay
Postdocs: Beatriz Navarro-Domínguez, Lucas Hemmer, John Sproul, Cécile Courret
Research associates and technicians: Danna Eickbush, Shaun Jones
Undergraduates: Sherif Negm, Eddyson Altidor, Anya Greenberg, Jim Chaffer, Gefei (Vera) Yu, Xuewen Geng, Tuan Pham
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 was the Stephen Biggar and Elisabeth Asaro Fellow in Data Science from 2017-2020.
- 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.
Xiaolu Wei (Ph.D. candidate)
Xiaolu is a Biomedical Genetics student studying how satellite DNA is regulated in the Drosophila germline using functional genomics and cytogenetic approaches. She uses the selfish Segregation Distorter system to understand the consequences of misregulating satellite DNA in the male germline. Xiaolu is Agnes M. Messersmith and George Messersmith fellow for 2020-2021.
Wei,X., Eickbush,D.G., Speece,I., A.M. Larracuente. 2021. Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline. eLife 2021;10:e62375. doi: 10.7554/eLife.62375
Matthew Lindsay (E2G2 graduate student)
Matthew joined our lab after finishing his undergraduate work at the University of Toronto as a technician and began as an E2G2 graduate student in Fall 2020. Matthew is working on the population dynamics of Segregation Distorter and satellite DNA fitness.
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 2018-2020)
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.
- Sproul,J.S., Barton, L.M., D.R. Maddison. 2020. Repetitive DNA profiles Reveal Evidence of Rapid Genome Evolution and Reflect Species Boundaries in Ground Beetles. BIORXIV https://doi.org/10.1101/2020.01.03.894527
- Sproul, J.S.; Maddison, D.R. (2017) Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA. Molecular Ecology Resources, 17 (6): 1183-1201.
- Sproul, J.S.; Maddison, D.R. (2017) Cryptic species in the mountaintops: species delimitation and taxonomy of the breve species group (Carabidae: Bembidion) aided by genomic architecture of a century-old type specimen. Zoological Journal of the Linnean Society, 183 (3): 556-583.
- Kanda, K.; Pflug, J.M.; Sproul, J.S.; Dasenko, M.; Maddison, D.R. (2015) Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS ONE, 10, e0143929.
- Courret C, Gérard PR, Ogereau D, Falque M, Moreau L, Montchamp-Moreau C*. 2019. X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression. Heredity doi: 10.1038/s41437-018-0163-1
- Helleu Q*, Courret C, Ogereau D, Burnham KL, Chaminade N, Chakir M, Aulard S, Montchamp-Moreau C*. 2019 Sex-ratio meiotic drive shapes the evolution of the Y chromosome in Drosophila simulans. Molecular Biology and Evolution.doi: 10.1093/molbev/msz160
- Courret C*, Chang CH, Wei K,Montchamp-Moreau C, Larracuente A. 2019. Meiotic drive mechanisms: lessons from Drosophila. Processing B. doi:10.1098/rspb.2019.1430
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 repeat evolution in Drosophila. He has contributed to several projects ranging from euchromatic satellite DNA evolution to designing a pipeline called RepeatProfiler to study repeats with short read sequence data.
Sherif Negm, Anya D. Greenberg, Amanda M. Larracuente, John S. Sproul. 2020. RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles. BioRxiv 5/26/2020. Molecular Ecology Resources. 12/2020 https://doi.org/10.1111/1755-0998.13305
Eddyson is using molecular methods to study variation in centromeric retroelements in Drosophila.
Vera is using genomic approaches to study patterns of expression in the Segregation Distorter system.
Xuewen Geng (undergraduate; Ecology and Evolutionary Biology)
Xuewen is studying centromeric retroelements in Drosophilaspecies using phylogenetic approaches.
Tuan Pham (undergraduate; Computational Biology)
Tuan is a computational biology major working on modeling satellite DNA evolution.
Fantastic former undergrads recently graduated
Anya is a data science student working on developing a bioinformatic pipeline to study repeats (RepeatProfiler) and using methods in machine learning to study satellite DNA evolution.
Sherif Negm, Anya D. Greenberg, Amanda M. Larracuente, John S. Sproul. 2020. RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles. BioRxiv 5/26/2020 doi: https://doi.org/10.1101/2020.05.22.111252
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. Taylar successfully defended her senior thesis and graduated with honors in research.
Iain is a computational biology major studying the functional genomics of satellite DNAs in D. melanogaster.
- Wei,X., Eickbush,D.G., Speece,I., A.M. Larracuente. 2020. Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline. BioRxiv BIORXIV/2020/268920 8/28/20. https://www.biorxiv.org/content/10.1101/2020.08.26.268920v1
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, Songeun Lee, Lindsey Perrin
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 was a recipient of the Ernst Caspari Fellowship and the Messersmith Fellowship. He is a current postdoc in Harmit Malik’s lab at the Fred Hutchison Cancer Research Center. In 2021, Ching-Ho received the prestigious Larry Sandler award for his outstanding dissertation work.
- 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.
Dani was an E2G2 student working on the evolution and functional genomics of satellite DNA in Drosophila species. She used deep real time single molecule sequencing from Pacific Biosciences to study the structural organization of satellite DNA loci in Drosophila genomes. Dani is now in the Harvard University Bioinformatics group.
- Sproul, J., Khost, D.E.*, Eickbush, D.G., Negm, S., Wei, X., Wong, I., and A.M. Larracuente 2020. Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade. BIORXIV/2019/846238, Molecular Biology and Evolution, msaa078, https://doi.org/10.1093/molbev/msaa078 *co-first author
- 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.