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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...transcriptase activity. (C) The amino acid sequence alignment of L1-32_DR ORF1p and exon L of the American alligator's Lyosin protein. (D) Protein structures of human L1 ORF1p (PDB: AF_AFQ9UN81F1) and the Lyosin protein predicted by AlphaFold2 (Jumper et al. 2021) implemented in ColabFold (Mirdita et al. 2022...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
.... By aligning the sequencing data of L. oculatus and A. spatula to Chromosome 3 of A. spatula, we found that, at the fusion region, the sequencing depth of a 2-kb fragment in L. oculatus was zero, whereas A. spatula showed a relatively high sequencing depth in the fusion region. Further genomic feature analysis...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...sequence alignment, interactive sequence choice and visualization. Brief Bioinform 20: 1160–1166. doi:10.1093/bib/bbx108 ↵Kent WJ. 2002. BLAT—the BLAST-like alignment tool. Genome Res 12: 656–664. doi:10.1101/gr.229202 ↵Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. 2011. Adaptive seeds tame genomic...
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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
...the assembly's accuracy.We first assembled HiFi reads into 80 contigs (Supplemental Table S2A) with HiCanu (Nurk et al. 2020) and purge_dups (Guan et al. 2020) and further reduced them to 61 nonredundant contigs by manually inspecting their order after aligning them to the VC2010 assembly (Supplemental Fig. S1...
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Method: Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
- Ilya B. Slizovskiy,
- Nathalie Bonin,
- Jonathan E. Bravo,
- Peter M. Ferm,
- Jacob Singer,
- Christina Boucher,
- and Noelle R. Noyes
Genome Res. November 2024 34: 2048-2060; Published in Advance November 5, 2024, doi:10.1101/gr.279226.124
...to Figure 5.View larger version: In this window In a new window Figure 6. Heatmap of alignments to GT-ARGs (y-axis), by replicate (x-axis). Replicates are grouped by enrichment protocol and probe set (x-axis), and each GT-ARG is listed along with the bacterial species from which it originated (y-axis). Gray...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...DNA assemblies for other Oryza species. Although mitochondrial sequence composition is highly conserved across the genus, structural variations such as recombination or lineage-specific rearrangements may result in undetected NUMTs. Alignment-based methods like BLAST are particularly susceptible to missing NUMTs...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
....1.4.1 (Kassambara 2023) R packages.Breakpoint analysisWe identified approximate breakpoint regions by aligning each haplotype sequence to the H1 sequence using BLAST (Basic Local Alignment Search Tool) (Altschul et al. 1990). We mapped the approximate breakpoint region in the T2T-CHM13 v2.0 by BLAT (Kent 2002...
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Methods: MAVID: Constrained Ancestral Alignment of Multiple Sequences
- Nicolas Bray and
- Lior Pachter
Genome Res. April 2004 14: 693-699; doi:10.1101/gr.1960404
...approach to multiple alignment. Bioinformatics 17 : 803 -820. ↵ Kent, W.J. 2002 . BLAT—The BLAST-like alignment tool. Genome Res. 12 : 656 -664. ↵ Korber, B.T.M., Brander, C., Haynes, B.F., Koup, R., Kuiken, C., Moore, J.P., Walker, B.D., and Watkins, D.I. (Ed.) 2001 . In HIV molecular immunology , pp. 02...
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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
.... 2021). To produce more accurate annotations, transcripts aligned to s with BLAT (Kent 2002) version 36 were used as “hints.” In cases in which an assembled transcriptome was not available, data from related individuals were used. In particular, the transcriptome assembly generated by Wang et al. (2015...
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Methods: Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
- Michael Brudno,
- Alexander Poliakov,
- Asaf Salamov,
- Gregory M. Cooper,
- Arend Sidow,
- Edward M. Rubin,
- Victor Solovyev,
- Serafim Batzoglou,
- and Inna Dubchak
Genome Res. April 2004 14: 685-692; doi:10.1101/gr.2067704
...database project. Nucleic Acids Res. 30 : 38 -41. ↵ Kellis, M., Patterson, N., Endrizzi, M., Birren, B. and Lander, E.S. 2003 . Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423 : 241 -254. ↵ Kent, W.J. 2002 . BLAT—The BLAST-like alignment tool. Genome Res. 12...

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