Congratulations to the first PhD graduate from the Larracuente lab: Danielle Khost! She’s off to a fantastic bioinformatics position in the Harvard Bioinformatics group. We’ll miss her dearly.
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.
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!
Xiaolu passed her quals
Congratulations to Xiaolu for passing her quals this week!
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
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: http://www.rochester.edu/newscenter/firefly-researchers-mapping-worlds-second-most-interesting-genome-269372/.
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!
Congratulations Ching-Ho
Ching-Ho passed his qualifying exam today and lots of people came to help us celebrate. Congrats to the new PhD candidate!
Postdoc in evolutionary genomics:
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!