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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
...1 assembly. Independently, we predicted 23,249 genomic loci encoding StringTie2 transcripts assembled from ribodepleted RNA-seq data (Wang et al. 2022). These transcripts overlapped with (and thus confirmed) known or predicted N2 or AUGUSTUS protein-coding genes and with known N2 ncRNA genes (Table...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...-level using Pacific Biosciences (PacBio) HiFi long reads and high-throughput chromosome conformation capture (Hi-C) scaffolding (Wood et al. 2023; Bishop et al. 2023a,b, 2024).View larger version: In this window In a new window Figure 1. Comparative genomics of five chromosome-scale bryozoan s. (A...
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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
..., experimentally validated annotations are essential. To address this issue, de novo assembled contigs from RNA-seq data of poly(A)-enriched mRNA are useful. As mRNAs are devoid of introns, the resulting predictions are likely more accurate than predicting gene models from genomic sequences that are based...
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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
...for metazoan repeats) (Chen 2004). We mapped the RNA-seq reads to the repeat-masked using HISAT2 (version 2.2.1; hisat2-build for indexing and hisat2 with default options to map the RNA-seq reads to the corresponding ) (Kim et al. 2019b). RNA-mapping data were used to annotate genes using BRAKER (version 2...
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Research: Comparative genome analysis of programmed DNA elimination in nematodes
- Jianbin Wang,
- Shenghan Gao,
- Yulia Mostovoy,
- Yuanyuan Kang,
- Maxim Zagoskin,
- Yongqiao Sun,
- Bing Zhang,
- Laura K. White,
- Alice Easton,
- Thomas B. Nutman,
- Pui-Yan Kwok,
- Songnian Hu,
- Martin K. Nielsen,
- and Richard E. Davis
Genome Res. December 2017 27: 2001-2014; Published in Advance November 8, 2017, doi:10.1101/gr.225730.117
..., and comparative nematode and epi studies.Genome maintenance and stability are paramount for organisms. Major changes and instability can lead to abnormalities, disease, and lethality. While a variety of cellular processes have evolved to ensure stability, some organisms have developed processes that lead...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...during post-assembly analysis. Thus, we investigated the coverage of the transcript sequences. Reads from all the RNA-seq data in theOysterGenomeProjectwere assembled into contigs (RNA-contigs) using Trinity (Supplemental Methods; Grabherr et al. 2011).We thenmappedRNA-contigswhose lengths exceeded 500...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed...
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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
...be overlooked in traditional pairwise comparative analyses relying on a single reference per population or species.The nematode species pair Caenorhabditis briggsae and Caenorhabditis nigoni has emerged as a powerful model for dissecting the genetic and genomic bases of speciation. Although both species...
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Resource: The C. elegans 3′ UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3′-UTR biology, and miRNA targeting
- Hannah S. Steber,
- Christina Gallante,
- Shannon O'Brien,
- Po-Lin Chiu,
- and Marco Mangone
Genome Res. December 2019 29: 2104-2116; Published in Advance November 19, 2019, doi:10.1101/gr.254839.119
...nematode Caenorhabditis elegans is ideal to study these interactions because it possesses a well-defined 3′ UTRome. To improve its annotation, we have used a -wide bioinformatics approach to download raw transcriptome data for 1088 transcriptome data sets corresponding to the entire collection of C...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...of duplicated and de novo genes (Rödelsperger et al. 2019). One major prediction of this rapid turnover model is that the contribution of both categories of origin will depend on the evolutionary distance of the comparison. In this study, we explicitly test this model using genomic data of the nematode...

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