Rachel O'Neill

Board of Trustees Distinguished Professor

Molecular and Cell Biology / Genetics and Genomics

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Education: PhD La Trobe University

Research Interests:  My research programs employ molecular genetics, cytogenetics, genomics and computational approaches to study the mechanisms that maintain, and disrupt, genome stability and foster genome innovation. Projects include studying: retroelement transcription and centromere function; global chromosome and genome changes during instability; chromosome and genome evolution; species-specific genomic features linked to unique adaptations; and, methods of genome assembly and annotation. We use a diverse set of rapidly evolving next generation sequencing (NGS) technologies and novel library preparation and computational methodologies for generating telomere-to-telomere (T2T) genome assemblies and characterizing genome sequences and epigenomic features in efforts to establish broad eukaryotic species as models for studying genome biology. Projects include generating genome assemblies and comparative analyses for our own lab work including species from all three mammalian lineages (eutherian, marsupial, monotreme), major vertebrate lineages such as birds, marine species, plants, and insects. Our work is part of larger efforts, including : Human T2T Consortium, Primate T2T Consortium, Gibbon T2T Consortium, Earth Biogenomes Project, Ruminant T2T Consortium, Fly T2T Consortium, Deep Ocean Genomes Project, Antarctic Genomes Consortium, the Colossal Foundation, and UConn’s Biodiversity and Conservation Genomics program.

Select Recent Publications – see: https://roneill.lab.uconn.edu/publications/ for full list

1. Frankenberg, S.R., Lucas, S., Feigin, C., Doronina, L., Steffen,R., Hartley, G.#, Grady, P.G.S.#, Menzies, B.R., De Paoli-Iseppi, R., Donnellan, S., Klein, M., Newton, A., Black, J.R., Clark, M., Cooper, S., O’Neill, R.J., Clark, M., Schmitz, J., Pask, A.J. Unearthing the Secrets of Australia’s Most Enigmatic and Cryptic Mammal, the Marsupial Mole. Science Advances 11:1. 2025. DOI: 10.1126/sciadv.ado4140.\

2. Chabot, B. J., Sun, R., Amjad, A., Hoyt, S. J.#, Ouyang, L., Courret, C., Drennan, R., Leo, L., Larracuente, A. M., Core, L. J., O’Neill, R. J., Mellone, B. G. Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape. Genome Biol 25, 295 2024. PMCID: PMC11575011  https://doi.org/10.1186/s13059-024-03433-1

3. Karginov, T.A., Ménoret¹ A., Leclair, N.K., Chandiran, K., Suarez-Ramirez, J.E., Karlinsey, K., O’Neill, R.J., Murphy, P.A., Adler, A.A., Cauley, L.S., Anczuków, O., Zhou, B., Vella, A.T. 2024. Autoregulated splicing of TRA2 β programs T cell fate in response to antigen-receptor stimulation. Science 385(6714): eadj1979. doi: 10.1126/science.adj1979

4. Kabfleisch, R., McKay, S., Murdoch, B. […72 Consortium Co-Authors…] O’Neill, R.J.**, Smith,T,** Rosen, B.** 2024. The Ruminant Telomere-to-Telomere (RT2T) Consortium. Nature Genetics 56, pp 1566–1573. https://doi.org/10.1038/s41588-024-01835-2 **co-senior author

5. Milton A.M., Marin-Gual L., Lister N.C., McIntyre K.L., Grady P.S.#, Laird M.K., Bond D.M., Hore T.A., O’Neill R.J., Pask A.J., Renfree M.B., Ruiz-Herrera A., Waters P.D. 2024. Imprinted X chromosome inactivation in marsupials: the paternal X arrives at the egg with a silent DNA methylation profile. PNAS 121(36):e241218512. doi: 10.1073/pnas.2412185121

6. Makova K.D.§,  Pickett B.D.§, Harris R.S.§,  Hartley G.A.§#, Cechova M., Pal K., Nurk S., Yoo D-A., Li Q., Hebbar P., McGrath B.C., Antonacci F., Aubel M., Biddanda A., Borchers M., Bornberg-Bauer E., Bouffard G.G., Brooks S.Y., Carbone L., Carrel L., Carroll A., Chang P-C., Chin C-S., Cook D.E., Craig S.J.C., de Gennaro L., Diekhans M., Dutra A., Garcia G.H., Grady P.G.S., Green R.E., Haddad D., Hallast P., Harvey W.T., Hickey G., Hillis D.A., Hoyt S.J., Jeong H., Kamali K., Kosakovsky Pond S.L., LaPolice T.M., Lee C.,  Lewis A.P., Loh Y-H. E., Masterson P., McCoy R.C., Medvedev P., Miga K.H., Munson K.M., Pak E., Paten B., Pinto B.J., Potapova T., Rhie A., Rocha J.L., Ryabov F., Ryder O.A., Sacco S., Shafin K., Shepelev V.A., Slon V., Solar S.J., Storer J.M., Sudmant P.H., Sweeten A., Tassia M.G., Thibaud-Nissen F., Ventura M., Wilson M.A., Young A.C., Zeng H., Zhang X., Szpiech Z.A., Huber C.D., Gerton J.L., Yi S.V., Schatz M.C., Alexandrov I.A., Koren S., O’Neill, R.J., Eichler E.,  Phillippy A.M.. 2024. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. Nature 630 (401-411). https://doi.org/10.1038/s41586-024-07473-2

7. Hartley, Gabrielle*#, Stephen R. Frankenberg, Natasha M. Robinson, Anna J. MacDonald, Rodrigo K. Hamede, Christopher P. Burridge, Menna E. Jones, Tim Faulkner, Hayley Shute, Robert Brewster, Rachel O’Neill, Marilyn B. Renfree, Andrew J. Pask, Charles Y. Feigin. 2024. Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution. Communications Biology, 7, 636; doi: https://doi.org/10.1038/s42003-024-06251-0.

8. Meridia Jane Bryant*, Asher M. Coello*, Adam M. Glendening*, Samuel A. Hilliman III*, Carolina Fernanda Jara*, Samuel S. Pring*, Aviel Rodriguez Rivera*, Jennifer Santiago Membreño*, Lisa Nigro, Nicole Pauloski, Matthew R. Graham, Teisha King, Elizabeth L.Jockusch, Rachel J. O’Neill, Jill L. Wegrzyn, Carlos E. Santibáñez-López, Cynthia N.Webster*. 2024. Unveiling the genetic blueprint of a desert scorpion: A chromosome-level genome of Hadrurus arizonensis provides the first reference for Parvorder Iurida. Under revision at Genome Biology and Evolution. bioRxiv 2024.03.22.586284; doi: https://doi.org/10.1101/2024.03.22.586284 NOTE: RaMP Cohort publication

9. McEvoy, S.L., Grady, P.G.S.*, Pauloski, N., O’Neill, R.J., Wegrzyn, J.L. 2024. Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology. Evolutionary Applications 17, e13669. doi: https://doi.org/10.1111/eva.13669.

10. Escalona M., VanCampen J., Maurer N.W., Haukness M., Okhovat M., Harris R.S., Watwood A., Hartley G.A.*, O’Neill R.J., Medvedev P., Makova K.D., Vollmers C., Carbone L., Green R.E.. Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J Hered. 2023. Mar 16;114(1):35-43. doi: 10.1093/jhered/esac043. PMID: 36146896; PMCID: PMC10019027

11. Castellano, K.R.*, Batta-Lona, P., Bucklin, A., O’Neill, R.J. 2023. Salps in Bloom: Genomics of Salpa thompsoni and Salpa aspera reveal complex genomic features and true hermaphroditic life phases. Scientific Advances 13, 21056. DOI: 10.1038/s41598-023-47429-6

12. Guzman-Torres, C.R. §^, Trybulec, E.§ ^, LeVasseur^*, H.§ ^, Akella, H., Amee, M., Strickland, E., Pauloski, N., Williams, M., Romero-Severson, J., Hoban, S., Woeste, K., Pike, C.C., Karl C. Fetter, K.C.^**, Webster, C.N.^**, Neitzey, M.L.^** *, O’Neill, R.J.^**, Wegrzyn, J.L.^** 2024. Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea) G3 jkad180, DOI: 10.1093/g3journal/jkad189 § co-first author, ^**co-senior author NOTE: Biodiversity and Conservation Genomics Program Cohort publication

13. Rhie, A. §, Nurk, S. §, Cechova, M. §, Hoyt, S.J.* §, Taylor, D.J., Altemose, N., Hook, P.W., Koren, S., Rautiainen, M., Alexandrov, I.A., Allen, J., Asri, M., Bzikadze, A.V., Chen, N-C., Chin, C-S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A., Giron, C.S., Garrison, E., Gershman, A., Gerton, J., Grady, P.G.S.*, Guarracino, A., Haggerty, L., Halabian, R., Hansen, N.F., Harris, R., Hartley, G.A.*, Harvey, W.T., Haukness, M., Heinz, J., Hourlier, T., Hubley, R.M., Hunt, S.E., Hwang, S., Jain, M., Kesharwani, R.K., Lewis, A.P., Li, H., Logsdon, G.A., Lucas, J.K., Makalowski, W., Markovic, C., Martin, F.J., Mc Cartney, A.M., McCoy, R.C., McDaniel, J., McNulty, B.M., Medvedev, P., Mikheenko, A., Munson, K.M., Murphy, T.D., Olsen, H.E., Olson, N.D., Paulin, L.F., Porubsky, D., Potapova, T.,  Ryabov, F.,.Salzberg, S.L., Sauria, M.E.G., Sedlazeck, F.J., Shafin, K., Shepelev, V.A., Shumate, A., Storer, J.M.,  Surapaneni, L., Taravella Oill, A.M., Thibaud-Nissen, F., Timp, W., Tomaszkiewicz, M., Vollger, M.R., Walenz, B.P., Watwood, A.C., Weissensteiner, M.H., Wenger, A.M., Wilson, M.A., Zarate, S., Zhu, Y., Zook, J.M., Eichler, E.E., O’Neill, R., Schatz, M.C., Miga, K.H., Makova, K.D., Phillippy, A.M.2022. bio-Rxiv.12.01.518724, DOI: 10.1101/2022.12.01.518724. Nature 621, 334-354. DOI: 10.1038/s41586-023-06457-y, § co-first author\

14. Hallast, P., Ebert, P., Loftus, M., Yilmaz, F., Audano, P.A., Logsdon, G.A., Bonder, M.J., Zhou, W., Hops, W., Kim, K., Li, C., Hoyt, S.J. *, Dishuck, P.C., Porubsky, D., Tsetsos, F., Kwon, J.Y., Zhu, Q., Munson, K.M., Hasenfeld, P., Garvey, W.T., Lewis, A.P., Kordosky, J., Hoekzema, K., Human Genome Structural Variation Consortium, O’Neill, R.J., Korbel, J.O., Tyler-Smith, C., Eichler, E.E., Shi, X., Beck, C.R., Marschall, T., Konkel, M.K., Lee, C. 2023. Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation. Nature 621, 355-364. DOI:10.1038/s41586-023-06425-6.

15. Fuller, E.P.*, M.P. Weiner, O’Neill, R.J. 2021. Derivation of Splice Junction-Specific Antibodies Using a Phosphoserine Targeting Strategy and Directed Evolution. New Biotechnology vol 71, pp 1-10. DOI: 10.1016/j.nbt.2022.06.003

16. Hoyt S*, Hartley G*§, Grady P*§, Storer J§, Gershman A§, de Lima L, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Core L, Gerton J, Makalowski W, Olson D, Rosen J, Smit A, Straight A, Vollger M, Wheeler T, Schatz M, Eichler E, Phillippy A, Timp W, Miga K, O’Neill R.J. 2021.  From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. Science vol 376, issue 6588. DOI: 10.1126/science.abk3112  (COVER); § co-second author

17. Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze A, Mikheenko A, Vollger M, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt S*, Diekhans M, Logsdon G, Alonge M, Antonarakis S, Borchers M, Bouffard G, Brooks S, Caldas G, Cheng H, Chin C, Chow W, de Lima L, Dishuck P, Durbin R, Dvorkina T, Fiddes I, Formenti G, Fulton R, Fungtammasan A, Garrison E, Grady P*, Graves-Lindsay T, Hall I, Hansen N, Hartley G*, Haukness M, Howe K, Hunkapiller M, Jain C, Jain M, Jarvis E, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro V, Marschall T, McCartney A, McDaniel J, Miller D, Mullikin J, Myers E, Olson N, Paten B, Peluso P, Pevzner P, Porubsky D, Potapova T, Rogaev E, Rosenfeld J, Salzberg S, Schneider V, Sedlazeck F, Shafin K, Shew C, Shumate A, Sims Y, Smit A, Soto D, Sović I, Storer J, Streets A, Sullivan B, Thibaud-Nissen F, Torrance J, Wagner J, Walenz B, Wenger A, Wood J, Xiao C, Yan S, Young A, Zarate S, Surti U, McCoy R, Dennis M, Alexandrov I, Gerton J, O’Neill R.J., Timp W, Zook J, Schatz M, Eichler E, Miga K, Phillippy A. 2021. The complete sequence of a human genome. Science vol 376, issue 6588. DOI: 10.1126/science.abj6987 (COVER)

18. Gershman A, Sauria M, Hook P, Hoyt S*, Razaghi R, Koren S, Altemose N, Caldas G, Vollger M, Logsdon G, Rhie A, Eichler E, Schatz M, O’Neill R.J., Phillippy A, Miga K, Timp W. 2021.  Epigenetic Patterns in a Complete Human Genome. Science vol 376, issue 6588. DOI: 10.1126/science.abj5089 (COVER)

19. Altemose N, Logsdon G, Bzikadze A, Sidhwani P, Langley S, Caldas G, Hoyt S,* Uralsky L, Ryabov F, Shew C, Sauria M, Borchers M, Gershman A, Mikheenko A, Shepelev V, Dvorkina T, Kunyavskaya O, Vollger M, Rhie A, McCartney A, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, Gomes de Lima L, Potapova T, Hartley G*, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama S, Paten B, Rogaev E, Streets A, Karpen G, Dernburg A, Sullivan B, Straight A, Wheeler T, Gerton J, Eichler E, Phillippy A, Timp W, Dennis M, O’Neill R.J., Zook J, Schatz M, Pevzner P, Diekhans M, Langley C, Alexandrov I, Miga K. 2021. Complete genomic and epigenetic maps of human centromeres. Science vol 376, issue 6588. DOI: 10.1126/science.abl4178 (COVER)

20. Hartley, G.*, Ohkavat, M.#, Carbone, L., O’Neill, R. J.* (Co last authors). 2021. Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition. Molecular Biology and Evolution msab148, DOI: 10.1093/mol-bev/msab148