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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...), in contrast with the topology based on all genomic SNPs (Fig. 1). An inspection of the SNP distribution revealed a mosaic pattern in which the IIa Egyptian isolates are either very similar to the IId isolates from Egypt and China (population 1) or to the IIa and IId isolates from Europe (population 2...
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Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
...lineages. Further phylogenetic and population genomic analyses revealed extensive loss of genetic diversity in VNBI, suggestive of a history of population bottlenecks, along with unique evolutionary trajectories for mating type loci. These data highlight the complex evolutionary interplay between...
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Research: Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations
- Liam C. Hunt,
- Jianqin Jiao,
- Yong-Dong Wang,
- David Finkelstein,
- Deepti Rao,
- Michelle Curley,
- Maricela Robles-Murguia,
- Abbas Shirinifard,
- Vishwajeeth R. Pagala,
- Junmin Peng,
- Yiping Fan,
- and Fabio Demontis
Genome Res. August 2019 29: 1262-1276; Published in Advance June 27, 2019, doi:10.1101/gr.246884.118
...of the environment and to synchronize social activities. Although the circadian cycle is implicated in aging, it is unknown whether natural variation in its function contributes to differences in lifespan between populations and whether the circadian clock of specific tissues is key for longevity. We have sequenced...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...The population genomics of rhesus macaques (Macaca mulatta) based on whole- sequences Cheng Xue,1 Muthuswamy Raveendran,1 R. Alan Harris,1,2 Gloria L. Fawcett,1,19 Xiaoming Liu,3 Simon White,1 Mahmoud Dahdouli,1,20 David Rio Deiros,1 Jennifer E. Below,3 William Salerno,1 Laura Cox,4 Guoping Fan,5...
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Method: Single-cell genomics for dissection of complex malaria infections
- Shalini Nair,
- Standwell C. Nkhoma,
- David Serre,
- Peter A. Zimmerman,
- Karla Gorena,
- Benjamin J. Daniel,
- François Nosten,
- Timothy J.C. Anderson,
- and Ian H. Cheeseman
Genome Res. June 2014 24: 1028-1038; Published in Advance May 8, 2014, doi:10.1101/gr.168286.113
...was explored using infections from the same Thai clinics and which demonstrated that infections contain parasite s ranging in relatedness from full siblings to unrelated. The advent of large-scale population genomic data for P. vivax populations will allow similar analyses to be performed for this parasite...
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Research: Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
- Itai Sharon,
- Michael Kertesz,
- Laura A. Hug,
- Dmitry Pushkarev,
- Timothy A. Blauwkamp,
- Cindy J. Castelle,
- Mojgan Amirebrahimi,
- Brian C. Thomas,
- David Burstein,
- Susannah G. Tringe,
- Kenneth H. Williams,
- and Jillian F. Banfield
Genome Res. April 2015 25: 534-543; Published in Advance February 9, 2015, doi:10.1101/gr.183012.114
...present at very low abundance levels, and (4) evaluate levels of sequence variation and genomic content in populations of closely related species and strains. Results Sample collection and sequencing Sampleswere collected fromthree depths (4, 5, and6m) in an aquifer adjacent to theColoradoRiver, Rifle...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...different preferences. Transposable elements are a source of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Here, we perform genomic and transcriptomic analyses in six s of cactophilic species...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...function. The overall analysis shows that genic CNVs contribute more to population differentiation in mice than in humans and may promote and speed up population divergence.Studying genetic variation in natural populations is key to understanding the evolutionary processes that lead to divergence. Genomic...
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Article: Comparative genomics of protoploid Saccharomycetaceae
- The Génolevures Consortium,
- Jean-Luc Souciet,
- Bernard Dujon,
- Claude Gaillardin,
- Mark Johnston,
- Philippe V. Baret,
- Paul Cliften,
- David J. Sherman,
- Jean Weissenbach,
- Eric Westhof,
- Patrick Wincker,
- Claire Jubin,
- Julie Poulain,
- Valérie Barbe,
- Béatrice Ségurens,
- François Artiguenave,
- Véronique Anthouard,
- Benoit Vacherie,
- Marie-Eve Val,
- Robert S. Fulton,
- Patrick Minx,
- Richard Wilson,
- Pascal Durrens,
- Géraldine Jean,
- Christian Marck,
- Tiphaine Martin,
- Macha Nikolski,
- Thomas Rolland,
- Marie-Line Seret,
- Serge Casarégola,
- Laurence Despons,
- Cécile Fairhead,
- Gilles Fischer,
- Ingrid Lafontaine,
- Véronique Leh,
- Marc Lemaire,
- Jacky de Montigny,
- Cécile Neuvéglise,
- Agnès Thierry,
- Isabelle Blanc-Lenfle,
- Claudine Bleykasten,
- Julie Diffels,
- Emilie Fritsch,
- Lionel Frangeul,
- Adrien Goëffon,
- Nicolas Jauniaux,
- Rym Kachouri-Lafond,
- Célia Payen,
- Serge Potier,
- Lenka Pribylova,
- Christophe Ozanne,
- Guy-Franck Richard,
- Christine Sacerdot,
- Marie-Laure Straub,
- and Emmanuel Talla
Genome Res. October 2009 19: 1696-1709; Published in Advance June 12, 2009, doi:10.1101/gr.091546.109
...://www..org/cgi/doi/10.1101/gr.091546.109. Freely available online through the Genome Research Open Access option. 1696 Genome Research www..org 19:1696–1709 2009 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/09; www..org This offers a unique view on the population structure and reproductive preferences...
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Method: Detecting differential growth of microbial populations with Gaussian process regression
- Peter D. Tonner,
- Cynthia L. Darnell,
- Barbara E. Engelhardt,
- and Amy K. Schmid
Genome Res. February 2017 27: 320-333; Published in Advance November 18, 2016, doi:10.1101/gr.210286.116
....D. Tonner Schmid Amy K. AmyK Schmid Cynthia L, Darnell BE Engelhardt Engelhardt, BE PeterD Tonner 1549-5469 genome;gr.210286.116 1088-9051 10.1101/gr.210286.116 Detecting differential growth of microbial populations with Gaussian process regression Tonner et al. Microbial growth detection with Gaussian...
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