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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
..., with a few notable systematic cases. These include a set of genes that are inverted on Chromosome 1 for OsLima at position 600,000–800,000 bp with respect to all other s. Similarly, there are two inversions on aus s (N22 and Natal Boro) around the center of Chromosome 1. Another notable case is present...
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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
...of CHROMOSOME_I and CHROMOSOME_III. For C. elegans to have a completely accurate reference , the N2 reference assembly needed to be replaced, but the VC2010 assembly could not fully replace it.View this table: In this window In a new window Table 1. Chromosome lengths and tandem repeat lengths of different C...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...Quadrupia provides a comprehensive catalog of G-quadruplexes across s from the tree of life Nikol Chantzi1,11, Akshatha Nayak1,11, Fotis A. Baltoumas2,3,11, Eleni Aplakidou2,3, Shiau Wei Liew4,5, Jesslyn Elvaretta Galuh4,5, Michail Patsakis1, Austin Montgomery1, Camille Moeckel1, Ioannis Mouratidis...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...long reads from C. elegans centromereEvaluation with RCA dataThe set of real data is a RCA-based ONT sequencing protocol from isocirc (Xin et al. 2021) that has been used to detect a catalog of full-length circular RNAs from 12 human tissues. We considered a subset of 101 sequences from prostate tissue...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...and atypical CNVs from family and population sequencing. Genome Res 21: 974–984. doi:10.1101/gr.114876.110 ↵Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. 2015. OMIM.org: online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res 43: D...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...for each read in question. After we have finished this process, we have the approximate copy numbers for each read. If the read-level k-mer functionality is enabled, motif-sized k-mers are computed for each read. If an SNV VCF catalog is provided: For each read, SNVs that differ from the reference...
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Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
- Junhai Qi,
- Zhidong Yang,
- Ting Yu,
- and Guojun Li
Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
...annotation of centromere with centroanno. bioRxiv doi: 10.1101/123456 .362 Ren J, Gu B, and Chaisson MJ. 2023. Vamos: variable-number tandem repeats annotation using efficient motif sets. Genome Biology 24: 175.363 Ting DT, Lipson D, Paul S, Brannigan BW, Akhavanfard S, Coffman EJ, Contino G, Deshpande V...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...Jellyfish (Marçais and Kingsford 2011). The left column of Figure 5 shows the k-mer distribution for HiFi reads for k = 17 (Fig. 5A1), k = 21 (Fig. 5B1), and k = 25 (Fig. 5C1). Odd integers in the range [17, 25] are typical choices for k to estimate size (see, e.g., Vurture et al. 2017; Ranallo-Benavidez et...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...al. 2012; Félix and Duveau 2012; Cook et al. 2017; Crombie et al. 2019, 2022; Lee et al. 2021). The C. elegans Natural Diversity Resource (CeNDR) catalogs and distributes thousands of wild strains, sequence data, and -wide variation data, including SNVs and short indels (Andersen et al. 2012; Cook et...
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Method: Multisample motif discovery and visualization for tandem repeats
- Yaran Zhang,
- Marc Hulsman,
- Alex Salazar,
- Niccolò Tesi,
- Lydian Knoop,
- Sven van der Lee,
- Sanduni Wijesekera,
- Jana Krizova,
- Erik-Jan Kamsteeg,
- and Henne Holstege
Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
...are ≤100 bp (Supplemental Fig. 1A). The motif sizes are also larger for the TRs in the vamos catalog compared to the PacBio catalog (Supplemental Fig. 1B). The PacBio catalog also showed reduced sequence complexity, as illustrated by the distinct k-mer (k = 10) counts observed in each repeat in the GRCh38...
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