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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...) and was subsequently confirmed to play a role in desiccation tolerance in animals such as nematodes (Browne et al. 2002). The LEA proteins eliminate the aggregation of water-soluble proteins in cells caused by desiccation which increases cytoplasmic viscosity. It also participates in repairing desiccation-induced DNA...
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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
...its genetics and genomics fully reproducible by C. elegans laboratories over many years. CGC1 is available at the Caenorhabditis Genetics Center stock center (https://cgc.umn.edu/strain/CGC1).Genome sequencing and assemblyWe harvested genomic DNA (gDNA) from CGC1 and sequenced it in two sets apiece...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...and assemble, and therefore, they are underrepresented or absent even in the best assemblies (for review, see Miga 2015; Lower et al. 2018). However, with the improvement of long-read sequencing technology, especially the Oxford Nanopore platform, it has recently been demonstrated that genomic loci made of satDNAs...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...-strandedness, which is most pronounced at transcript end sites, is dependent on high AT content and symmetrically positioned nucleosomes. We propose that sharp transitions in sequence composition at functional genomic elements constitute a common regulatory code and that DNA structure and propagation of torsional...
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Methods: Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
- Antoine Barrière,
- Shiaw-Pyng Yang,
- Elizabeth Pekarek,
- Cristel G. Thomas,
- Eric S. Haag,
- and Ilya Ruvinsky
Genome Res. March 2009 19: 470-480; Published in Advance February 9, 2009, doi:10.1101/gr.081851.108
...have continued to change after strains were sequenced. Our results highlight the impact of mating systems on sequencing projects. Whereas originally large s were sequenced using minimal tiling paths of genomic DNA clones ( C. elegans Sequencing Consortium 1998 ), more recently the whole- shotgun (WGS...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C...
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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
...assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig...
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LETTER: Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants
- James H. Thomas
Genome Res. August 2006 16: 1017-1030; Published in Advance July 6, 2006, doi:10.1101/gr.5089806
...appear thus far to be nematode-specific. About 80 members of the F-box-FTH family share an additional ∼50-amino-acid domain N-terminal to their F-box domain. This unnamed domain is distantly related to the DNA-binding domain of mariner transposes (Fig. 2 ; data not shown). View larger version...
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Resource: GAGE: A critical evaluation of genome assemblies and assembly algorithms
- Steven L. Salzberg,
- Adam M. Phillippy,
- Aleksey Zimin,
- Daniela Puiu,
- Tanja Magoc,
- Sergey Koren,
- Todd J. Treangen,
- Michael C. Schatz,
- Arthur L. Delcher,
- Michael Roberts,
- Guillaume Marçais,
- Mihai Pop,
- and James A. Yorke
Genome Res. March 2012 22: 557-567; Published in Advance December 6, 2011, doi:10.1101/gr.131383.111
...coverage of most species, including mammals, in just a few days. The sequence data generated by one of these projects consist of millions or billions of short DNA sequences (reads) that range from 50 to 150 nt in length. These sequences must then be assembled de novo before most genome analyses can begin...
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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
...to have a tendency to occur in tandemarrays (Meyers et al. 2003; Kohler et al. 2008). Interestingly, proteins containing LRR and TIR domains were under-represented among Salicoid duplicates, while the categories most enriched for Salicoids—RING fingers and DNA-dependent transcriptional regulators...

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