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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...variant had a unique set of substitutions and insertions (Fig. 4B). In contrast, in the CHROMOSOME_V array, the most frequent 10 variants match the reference by ≤92%, and they lacked unique substitutions or deletions that would allow individual variants to be unambiguously distinguished (Supplemental Fig...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...with splicing QTLsPrevious studies, such as those conducted by the Gene-Tissue Expression (GTEx) consortium, have identified numerous SNVs associated with splicing variation in human populations (splicing quantitative trait loci [sQTLs]) (The GTEx Consortium 2020). However, whether these sQTLs represent causal...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...of specific isolated muscle resident cell populations (Fukada et al. 2007; Cho and Doles 2017; Liu et al. 2019) has generated insights into targeted cell subpopulations, but these studies are necessarily biased toward specific cell types.Here, we employ single-nucleus RNA-sequencing (snRNA-seq), ATAC-seq (sn...
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Research: A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize
- Mélisande Blein-Nicolas,
- Sandra Sylvia Negro,
- Thierry Balliau,
- Claude Welcker,
- Llorenç Cabrera-Bosquet,
- Stéphane Dimitri Nicolas,
- Alain Charcosset,
- and Michel Zivy
Genome Res. November 2020 30: 1593-1604; Published in Advance October 15, 2020, doi:10.1101/gr.255224.119
...of upstream molecular traits such as transcript expression (eQTLs) or protein abundance (pQTLs). Until recently, this approach had been mostly applied in human and mice (Moreno-Moral and Petretto 2016). In plants, systems genetics studies have been carried out in a few species including wheat (Munkvold et al...
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Research: A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
...are significantly enriched among expressed genes associated with plant architectural traits (Fig. 5A). In contrast, natural variation linked to disease and metabolic traits maps preferentially near TFs underlying PC3. A breakdown into individual architectural traits shows that different PC1-correlated TF families...
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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
...differences in aging and lifespan across natural populations (Mackay 2002; Geiger-Thornsberry and Mackay 2004; Durham et al. 2014; Carbone et al. 2016), the short generation time and ease of maintenance has allowed the laboratory evolution of strains that diverge in aging traits from the parental population...
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Method: MultiBLUP: improved SNP-based prediction for complex traits
- Doug Speed and
- David J. Balding
Genome Res. September 2014 24: 1550-1557; Published in Advance June 24, 2014, doi:10.1101/gr.169375.113
..., while BLUP and genetic risk scores fare better for the more polygenic traits BD and HT. In contrast, BSLMM,whosemodel allows for both sparsity and shrinkage, performs well regardless of the genetic architecture of the trait and overall is the best of the current methods. As a first demonstration...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...traits (Flint and Mackay 2009; Mackay et al. 2009). Efforts to utilize naturally occurring genetic variation in D. melanogaster to add to our understanding of functional DNA elements have been greatly expedited by the Drosophila Genetic Reference Panel (DGRP), a publicly available population of 205...
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Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
- Eli Rodgers-Melnick,
- Shrinivasrao P. Mane,
- Palitha Dharmawardhana,
- Gancho T. Slavov,
- Oswald R. Crasta,
- Steven H. Strauss,
- Amy M. Brunner,
- and Stephen P. DiFazio
Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
...Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus Eli Rodgers-Melnick 1 , Shrinivasrao P. Mane 2 , 3 , Palitha Dharmawardhana 4 , Gancho T. Slavov 1 , 5 , Oswald R. Crasta 2 , 6...
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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
...size. Among the genes annotated as singleton genes in the reference , Sfi1 showed unexpectedly high variation and population divergence (one-way ANOVA, F(2,21) = 53.57, P < 0.0001 after FDR).Extended analysis of Cwc22, Hjurp, and Sfi1To study the polymorphism of extreme outlier loci in more depth, we...
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