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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
...be relatively recent. Indeed, most of the import of livestock, particularly cattle, into the Americas occurred from the seventeenth to the nineteenth century by Portuguese and Spanish colonists and during the Victorian Age by British settlers (McTavish et al. 2013; Ficek 2019).Our genomic results are consistent...
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PERSPECTIVE: Advances in livestock genomics: Opening the barn door
- James E. Womack
Genome Res. December 2005 15: 1699-1705; doi:10.1101/gr.3809105
...of highly conserved genomic elements other than coding sequences ( Margulies et al. 2003 ; Thomas et al. 2003 ). The power of this approach has been enhanced by the availability of whole- sequence from the livestock species. An exciting harvest from comparative genomics will come when multiple species from...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses reveal significant variation in gene content and structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly...
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Research: A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
- Xuelei Dai,
- Peipei Bian,
- Dexiang Hu,
- Funong Luo,
- Yongzhen Huang,
- Shaohua Jiao,
- Xihong Wang,
- Mian Gong,
- Ran Li,
- Yudong Cai,
- Jiayue Wen,
- Qimeng Yang,
- Weidong Deng,
- Hojjat Asadollahpour Nanaei,
- Yu Wang,
- Fei Wang,
- Zijing Zhang,
- Benjamin D. Rosen,
- Rasmus Heller,
- and Yu Jiang
Genome Res. August 2023 33: 1284-1298; Published in Advance September 15, 2023, doi:10.1101/gr.277481.122
..., China; 5Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA; 6Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; 7Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China ↵8 These authors contributed equally...
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Method: Inferring the mode and strength of ongoing selection
- Gustavo V. Barroso and
- Kirk E. Lohmueller
Genome Res. April 2023 33: 632-643; Published in Advance April 13, 2023, doi:10.1101/gr.276386.121
...constraint. These improvements come at the cost of targeting inference at the average s rather than a DFE (when using multiple SNPs) and requiring sample sizes of the order of tens of thousands of trios. Fortunately, extravagantly large genomic data sets are becoming commonplace, and we anticipate that TIDES...
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Resource: Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)
- Sanjida H. Rangwala,
- Anatoliy Kuznetsov,
- Victor Ananiev,
- Andrea Asztalos,
- Evgeny Borodin,
- Vladislav Evgeniev,
- Victor Joukov,
- Vadim Lotov,
- Ravinder Pannu,
- Dmitry Rudnev,
- Andrew Shkeda,
- Eric M. Weitz,
- and Valerie A. Schneider
Genome Res. January 2021 31: 159-169; Published in Advance November 25, 2020, doi:10.1101/gr.266932.120
...access to a wide range and large volume of biological sequence data and literature. Staff scientists at NCBI analyze user-submitted data in the archive, producing gene and SNP annotation and generating sequence alignment tools. NCBI's flagship browser, Genome Data Viewer (GDV), displays our in-house Ref...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...650223, China; 12Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; 13Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia; 14Guy Harvey Oceanographic Center, Halmos College...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...is necessary to detect historical recombination events, a downward bias in these rate estimates is often present in regions of the under selection (O'Reilly et al. 2008), an area of particular interest in the study of domestication and selective breeding of livestock.The horse is a unique species for which...
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Research: Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system
- Dan Sun,
- Donna L. Maney,
- Thomas S. Layman,
- Paramita Chatterjee,
- and Soojin V. Yi
Genome Res. October 2019 29: 1673-1684; Published in Advance September 23, 2019, doi:10.1101/gr.248641.119
...was evaluated using Mann–Whitney U tests. (***) P < 0.001, (NS) not significant.DiscussionMuch of our current knowledge about the epigenetic regulation of gene expression and dosage compensation comes from studies of male heterogametic mammalian systems. By comparison, information about these processes...
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Research: Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
- Mirte Bosse,
- Hendrik-Jan Megens,
- Ole Madsen,
- Richard P.M.A. Crooijmans,
- Oliver A. Ryder,
- Frédéric Austerlitz,
- Martien A.M. Groenen,
- and M. Angeles R. de Cara
Genome Res. July 2015 25: 970-981; Published in Advance June 10, 2015, doi:10.1101/gr.187039.114
...the commercial Pietrain breed to study the effect of management on selection signals. Genomic tools are increasingly important in livestock conservation and selection (Lenstra et al. 2012). Pietrain is under strong management regarding pig performance; therefore, clear selection signals are present...

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