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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets Jeanlin Jourdain,1,2 Harmonie Barasc,3 Thomas Faraut,3 Anne Calgaro,3 Nathalie Bonnet,3 Camille Marcuzzo,4 Amandine Suin,4 Anne Barbat,2 Chris Hozé,1...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...or get fixed) (Maynard Smith and Haigh 1974; Cutter and Payseur 2013). Although -wide estimates of recombination rate and large-scale variation have been characterized for many species, detailed recombination maps are still mainly limited to model organisms and domesticated species, although little...
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Research: Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia
- Xiao Gou,
- Zhen Wang,
- Ning Li,
- Feng Qiu,
- Ze Xu,
- Dawei Yan,
- Shuli Yang,
- Jia Jia,
- Xiaoyan Kong,
- Zehui Wei,
- Shaoxiong Lu,
- Linsheng Lian,
- Changxin Wu,
- Xueyan Wang,
- Guozhi Li,
- Teng Ma,
- Qiang Jiang,
- Xue Zhao,
- Jiaqiang Yang,
- Baohong Liu,
- Dongkai Wei,
- Hong Li,
- Jianfa Yang,
- Yulin Yan,
- Guiying Zhao,
- Xinxing Dong,
- Mingli Li,
- Weidong Deng,
- Jing Leng,
- Chaochun Wei,
- Chuan Wang,
- Huaming Mao,
- Hao Zhang,
- Guohui Ding,
- and Yixue Li
Genome Res. August 2014 24: 1308-1315; Published in Advance April 10, 2014, doi:10.1101/gr.171876.113
...and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402. Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, Liberg O, Arnemo JM, Hedhammar A, Lindblad-Toh K. 2013. The genomic signature of dog domestication reveals adaptation...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...variation. This indicates trait selection in dogs is likely a balancing act between preserving essential gene functions and maximizing regulatory variation to drive phenotypic extremes.The s of domestic species hold immense promise for the discovery of novel genotype–phenotype associations (Andersson...
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12 Drosophila Genomes/Letter: Genomic regulatory blocks underlie extensive microsynteny conservation in insects
- Pär G. Engström,
- Shannan J. Ho Sui,
- Øyvind Drivenes,
- Thomas S. Becker,
- and Boris Lenhard
Genome Res. December 2007 17: 1898-1908; Published in Advance November 7, 2007, doi:10.1101/gr.6669607
...and their interpretation, including an informed choice of core promoter type for enhancer trap constructs. Methods Sequences and annotations We used the following assemblies: Dmel release 4 (Berkeley Drosophila Genome Project); Dpse release 1.03 (Baylor HGSC); Dana , Dvir , and Dmoj Aug. 2005 (Agencourt); Agam MOZ2 (The...
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LETTER: Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database
- Li Li,
- Brian P. Brunk,
- Jessica C. Kissinger,
- Deana Pape,
- Keliang Tang,
- Robert H. Cole,
- John Martin,
- Todd Wylie,
- Mike Dante,
- Steven J. Fogarty,
- Daniel K. Howe,
- Paul Liberator,
- Carmen Diaz,
- Jennifer Anderson,
- Michael White,
- Maria E. Jerome,
- Emily A. Johnson,
- Jay A. Radke,
- Christian J. Stoeckert, Jr.,
- Robert H. Waterston,
- Sandra W. Clifton,
- David S. Roos,
- and L. David Sibley
Genome Res. March 1, 2003 13: 443-454; doi:10.1101/gr.693203
...rapid analysis of gene function, thus greatly facilitating traditional research approaches. To further the process of gene discovery in protozoan parasites, we have undertaken large-scale EST sequencing projects for several apicomplexan parasites. The Apicomplexa is an ancient phylum of ∼5000 species...
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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
...and pan graphs improved sequence read mapping and removed biases in variant discovery (Crysnanto and Pausch 2020). Despite these improvements, the unique genetic diversity and SVs of Chinese indicine cattle are not reflected in any high-quality genomic resources currently available, despite the fact...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...genomic variation in their graph representations. To date, several tools have been developed for visualizing pan graphs. Among them, Bandage (Wick et al. 2015), GfaViz (Gonnella et al. 2019), and gfaestus (https://github.com/chfi/gfaestus) focus more on large-scale graph topology, whereas Sequence...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...cardiovascular disease (Ference et al. 2017), and some networks underlying polar bear adaptation have been implicated in high-fat dietary adaptations in humans (Fumagalli et al. 2015). Thus, comparative genomic studies of diet offer novel insights for medical advancement. Large-scale comparative genomic...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...unresolved genomic regions? With T2T s around the corner for domestic and wild cat species, we anticipate exciting discoveries when the complete set of genetic variation is interrogated in -wide screens for disease and signatures of natural selection.Of great importance to future feline genomic advances...

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