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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Caenorhabditis briggsae and its sister species Caenorhabditis nigoni provide an ideal model system to address this question, as they exhibit extensive genomic divergence with limited gene flow from C. briggsae to C. nigoni. Despite previous comparative genomic studies, a comprehensive analysis of both...
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Resource: Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
- Nicolas J. Tourasse,
- Jonathan R.M. Millet,
- and Denis Dupuy
Genome Res. December 2017 27: 2120-2128; Published in Advance October 31, 2017, doi:10.1101/gr.224626.117
...of the complete Caenorhabditis elegans using transcriptome sequencing (RNA-seq) (Hillier et al. 2009; Ramani et al. 2011; Gerstein et al. 2014; Kuroyanagi et al. 2014; Ragle et al. 2015). Most of these analyses reported previously unannotated splice junctions, indicating that saturation has not yet been reached...
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Method: Scaffolding a Caenorhabditis nematode genome with RNA-seq
- Ali Mortazavi,
- Erich M. Schwarz,
- Brian Williams,
- Lorian Schaeffer,
- Igor Antoshechkin,
- Barbara J. Wold,
- and Paul W. Sternberg
Genome Res. December 2010 20: 1740-1747; Published in Advance October 27, 2010, doi:10.1101/gr.111021.110
...or genes lacking RNA-seq data were left untouched. While still fragmented, this assembly is sufficient to analyze genes and should also contain a substantial fraction of noncoding elements conserved between PS1010 and C. elegans. Assembly of the transcriptome and gene annotation To optimize our parameters...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
..., and RNA modification. However, reads derived from the current RNA-seq technologies are usually short and deprived of information on modification, compromising their potential in defining transcriptome complexity. Here, we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore...
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Resource: The time-resolved transcriptome of C. elegans
- Max E. Boeck,
- Chau Huynh,
- Lou Gevirtzman,
- Owen A. Thompson,
- Guilin Wang,
- Dionna M. Kasper,
- Valerie Reinke,
- LaDeana W. Hillier,
- and Robert H. Waterston
Genome Res. October 2016 26: 1441-1450; Published in Advance August 16, 2016, doi:10.1101/gr.202663.115
...University, New Haven, Connecticut 06520, USA Corresponding author: waterston@gs.washington.edu Abstract We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
...Adam D. Warner, Louis Gevirtzman, LaDeana W. Hillier, Brent Ewing and Robert H. Waterston Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA Corresponding author: watersto@uw.eduAbstractWe have used RNA-seq in Caenorhabditis elegans...
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Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- Yongbin Li,
- Xiao Liu,
- Peter Sarkies,
- and Zhongying Zhao
Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
...differences between bB2 and nB2 embryos may be explained, at least in part, by their different genomic compositions and subsequent difference in their transcriptome. We tested this hypothesis by examining the expression profiles of coding genes, TEs, and small RNAs by RNA sequencing (RNA-seq) analyses...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...and completeness of our chosen transcriptome assembly approach. We thus generated 74 million paired-end RNA-seq reads of 79-base length from a nonsynchronized C. elegans culture containing all developmental stages ranging from embryos to adult worms. The RNA-seq reads were quality controlled and either used...
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Research: Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression
- Runsheng Li,
- Xiaoliang Ren,
- Yu Bi,
- Vincy Wing Sze Ho,
- Chia-Ling Hsieh,
- Amanda Young,
- Zhihong Zhang,
- Tingting Lin,
- Yanmei Zhao,
- Long Miao,
- Peter Sarkies,
- and Zhongying Zhao
Genome Res. September 2016 26: 1219-1232; Published in Advance May 18, 2016, doi:10.1101/gr.204479.116
...C. briggsae sex-biased genes defined in recent studies using RNA-seq (Thomas et al. 2012; Figure 3. Expression profiling of coding genes in male hybrids and their parental males. (A) Venn diagrams showing shared numbers of up- or down-regulated genes between both hybrid males and C. nigoni. (B) The bootstrap...
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Research: Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
- Shuai Sun,
- Christian Rödelsperger,
- and Ralf J. Sommer
Genome Res. September 2021 31: 1590-1601; Published in Advance July 22, 2021, doi:10.1101/gr.275303.121
...were collected hourly or every 2 h in the molt or intermolt stage. (C) Schematic summary of the workflow for SWT. (D) RNA-seq read coverage is visualized at the self-1 locus using the Integrative Genomics Viewer (IGV) (Robinson et al. 2011) as one example for comparing SWT and standard RNA-seq (STD...

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