All posts by Amanda Larracuente

Paper on Drosophila melanogaster centromeres is out!

Check out our new paper on the organization of Drosophila melanogaster centromeres. For this paper, our lab collaborated with Barbara Mellone’s lab (University of Connecticut) and Ting Wu’s lab (Harvard University) to discover all of the centromeres in D. melanogaster. Centromeres are genomic regions essential for proper chromosome segregation during cell division. They also are among the most rapidly evolving regions of genomes and can play a role in karyotype evolution and speciation. We know little about the detailed organization of centromeres because they are buried in large blocks of tandem repeats that are difficult to assemble. We combined Ching-Ho’s heterochromatin-enriched assembly methods, with ChIP-seq for the centromere-specific histone variant, CENP-A, and FISH on stretched chromatin fibers to reveal the DNA sequences underlying centromeres. It turns out that centromeres correspond to islands rich in retroelements embedded in a sea of satellite DNA! One retroelement, G2/Jockey-3, is found at all D. melanogaster centromeres and centromeres in D. simulans.

Retroelements are associated with centromeres in a wide range of organisms including fungi, plants, and mammals. This suggests that retroelements may be conserved features of centromeres and may have a role in centromere function. We’re currently working on studying patterns of polymorphism and divergence in G2/Jockey-3 and centromere islands to see how they contribute to centromere evolution and function.

Drosophila centromere organization and widespread presence of retroelements at centromeres.
Figure 7 from the centromere paper. (A) Schematic showing the organization of D. melanogaster centromeres. (B) Phylogenetic tree showing that centromere-associated retroelements are common across highly diverged lineages: Gossypium hirsutum (cotton), Zea mays mays (maize), Oryza sativa (rice), Triticum boeoticum (wild wheat), Cryptococcus, Phyllostomid (bat), Hoolock leuconedys (gibbon), Homo sapiens (human) (and a human neocentromere), Macropus eugenii (tammar wallaby), Phascolarctos cinereus (koala), and D. melanogaster (this study for endogenous centromeres; also in an X-derived minichromosome).

Taylar graduates with honors in research

Taylar successfully defended her senior thesis on suppressors of Segregation Distorter in Drosophila melanogaster and is graduating with honors in research this weekend! Next up for Taylar is the Cell, Development, Molecular Biology and Biophysics PhD program Johns Hopkins, where she will be a Morgan Fellow. Congratulations all around Taylar!

Ching-Ho wins a scholarship

Ching-Ho was awarded a Government Scholarship to Study Abroad from the Taiwan government. He’ll use these funds to study the evolution of a new multi-copy Y-linked gene family specific to the Drosophila simulans clade. Congratulations Ching-Ho!!

Firefly chromosomes

Photinus pyralis mitotic chromosomes Image: Isaac Wong

Firefly season is over. It only lasts a couple of months here in Rochester. We rear fireflies in the lab over the summer to study the chromosomal distributions of their repeats. This is challenging for a number of reasons, one being that Photinus pyralis chromosomes typically appear as amorphous little blobs under the microscope. We spend a few months of each summer trying to find good ways to image chromosomes in the short time that we have with the  fireflies. In the last week of this summer, Isaac Wong (an undergrad in the lab) optimized protocols to find chromosomes – and they don’t look like amorphous blobs! 

A few weeks later, UR wrote an article on fireflies that mentions our work. You can read it here:

Congratulations graduates!

Two fantastic undergrads in the lab graduated and are moving on to bigger and better things. Kwan graduated with BS degrees in Computational Biology and Data Science.  Alex graduated with a BS in Neuroscience with minors in Classical Civilization, Computational Biology, and Psychology as a Social Science. We wish them the best!

Christian graduated


This week marks a big milestone for the Larracuente Lab. Our first undergraduate, Christian Silva, has left the nest. Christian pioneered firefly work in the lab and will be sorely missed. He’s off to UC Davis, where he will start his graduate career in plant biology this fall. Good luck, Christian!

Firefly genome project is a SMRT grant finalist!

We are fortunate to be part of a diverse group of biologists collaborating to sequence the genome of Photinus pyralis- the Big Dipper Firefly. Our firefly genome project was chosen as finalist for PacBio’s “Explore your most interesting genome contest”.  The winner will be decided by popular vote! If you’d like to support our efforts to sequence the firefly genome, please visit our page on and vote.  See details below: Alex Wild Photinus swoosh original

Fireflies! These silent fireworks on warm summer nights fill us with wonder. But so much about these fascinating critters remains shrouded in mystery- from the details of how they light up their lanterns to the way some species are disappearing. A team of biologists has joined forces to sequence the genome of the Big Dipper Firefly, Photinus pyralis, your common backyard firefly. This project is part of the PacBio “Explore your most interesting genome” contest. If you’d like to see the firefly genome sequenced, please go to and vote for the project. Voting opens Monday, April 11 and runs through Sunday, May 1st. One person can vote once per day. Help us shed light on the genome of these captivating creatures!