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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...duplicated segments containing the *03 allele displayed almost identical sequences even beyond the V gene exon (Fig. 6B), which suggests that some multicopy IGHV3-23/D haplotypes will require long reads (>50 kb) to correctly resolve CNV. However, designation of these duplication blocks to those harboring...
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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...across homologous chromosomes. This information is required to discover compound heterozygous variants, which occur when both homologous copies of a gene contain variants at different positions with a potentially deleterious impact on the function of both gene copies and which play a key role in numerous...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...genes are often designated redα (or exo) and redβ (or bet). Consequently, λ grows on recA and recBCD mutant hosts. λ also encodes an inhibitor of RecBCD called Gam. λ red gam double mutants fail to grow on recA mutants because of the lack of both host- and phage-promoted recombination. They do grow...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...end of the Y (MSY). Sequence divergence between X and Y in the segment is on average five times higher than in the proximal part in agreement with reduced recombination. The MSY is enriched for repeats and transposons but does not differ in the content of coding genes from the X, indicating that genic...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
....8 Mbp to 5.1 Mbp. The MHC region is known to have significant polymorphism, inter-gene sequence similarity, and long-range haplotype structures (Dilthey 2021). We used Minigraph (v0.20-r559) (Li et al. 2020) to build an acyclic pan graph using the 60 MHC haplotypes. The graph construction algorithm...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...into haplotype 2. All IGHJ and constant gene segments were present in the expected order. A block of IGHD gene segments was missing from each haplotype; haplotype 1 was missing D3-3 through D2-8, and haplotype 2 was missing D6-6 through D5-1.View larger version: In this window In a new window Figure 2. A donor...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...the presence of full-length PRDM9 genes in the s of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...) and haplotype 2 (D).Assembly quality and completenessUsing the HiFi reads, we estimate that our haplotypes 1 and 2 assemblies have a high base accuracy with a consensus quality value (QV) of 60.46 and 60.24, indicating only one error per megabase. To assess gene completeness, we first used compleasm (Huang...
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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
...involved in the CNV. The recombination locus was scrutinized for its precise coordinates, elucidating the genes and repetitive elements involved.In addition, we were able to infer the crossover site by long-range PCR and subsequent long-read PacBio sequencing in one index patient (AB004, Fig. 2B...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...of ancestrally low male recombination. Population genetic data showed high rates of sex-reversed XY-type females, and recombination between the X and Y Chromosomes in these individuals helps maintain the integrity of sequence and gene expression on the Y Chromosome. Finally, we revealed modest sexualization...

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