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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
...follow the original strand choice of the C. elegans N2 assembly (The C. elegans Sequencing Consortium 1998). We drew dot plots between sequences of two chromosomes or chromosome sets with GenomeMatcher 3.0.6 (Ohtsubo et al. 2008) using the NUCmer program in MUMmer 4.0.0rc1 (Kurtz et al. 2004); we drew...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
.... 2020; Glinos et al. 2022; Veiga et al. 2022; Zhang et al. 2022), and represents a data source of great value for the de novo annotation of the Earth BioGenome Project (Lawniczak et al. 2022). Despite its strengths, LRS presents several shortcomings. The quality of long-read RNA sequencing (lr...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...of bioinformatics tools and resources to interrogate s for evolutionary patterns and features of biomedical interest. But even as s became available for other model organisms such as mouse (Mus musculus) (Mouse Genome Sequencing Consortium et al. 2002) and rhesus macaque (Macaca mulatta) (Rhesus Macaque Genome...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...Genome Structural Variant Consortium (Ebert et al. 2021), and RD cohorts such as the Genomic Answers for Kids project (Cohen et al. 2022). Additionally, a data set of 1019 samples from the 1000 Genomes Project sequenced at intermediate coverage (16.9×) by ONT LRS suitable for SV analysis (Schloissnig et...
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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
.... 2021), is an outgroup belonging to the freshwater class Phylactolaemata (Taylor and Waeschenbach 2015). Four of the five assemblies were generated and made openly accessible by the Darwin Tree of Life (DToL) project (The Darwin Tree of Life Project Consortium et al. 2022), sequenced to chromosome...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...are the gold standard for high-throughput transcriptome profiling (Wang et al. 2009). RNA-sequencing (RNA-seq) has been used to investigate gene expression (The ENCODE Project Consortium 2012), canonical and alternative mRNA splicing (Wright et al. 2022a), noncoding RNAs, and post-transcriptional modifications...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...sequence that is assigned to the four genomic contexts.Active CREs in tissues and cells are associated with increased chromatin accessibility (Keene et al. 1981; McGhee et al. 1981; Buenrostro et al. 2013). Thus, to study the contribution of TEs to the salmon CRE landscape, we integrated our TE annotation...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...sequencing data (Supplemental Table S1). The resulting assembly was then used as input for the second HiRise scaffolding using Hi-C sequencing data (Fig. 1A; Supplemental Table S1).View larger version: In this window In a new window Figure 1. Genome assemblies. (A) Methodological workflow for the generation...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...hundreds of millions of years ago (Fig. 7; Drosophila 12 Genomes Consortium 2007; Hane et al. 2011; Albertin et al. 2022; Damas et al. 2022). The phylogeny we estimated suggests that the three lineages (KUM + OKI, AOM + OSA, BAR + BER) may correspond to three distinct cryptic species, which...
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Resource: Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
...of the highest possible quality. For Caenorhabditis elegans, such an assembly for the wild-type strain N2 has existed for 20 yr (The C. elegans Sequencing Consortium 1998). However, this assembly was generated with sequence data from N2 and CB1392 [nuc-1(e1392)] populations of uncertain lineage grown in at least...
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