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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...Biol Evol 37: 18–30. doi:10.1093/molbev/msz176 ↵Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, et al. 2016. Long-read sequence assembly of the gorilla . Science 352: aae0344. doi:10.1126/science.aae0344 ↵Grochowski CM, Krepischi ACV...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...of these genes, 4068, have novel sequences compared with the current Immuno Polymorphism Database (IPD). These novel gene sequences are represented by 2664 distinct alleles, some of which contained nonsynonymous variations, resulting in 92 novel protein sequences. We demonstrate the complex haplotype structures...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...family Felidae but show high transcript diversity, copy number variation, and structural rearrangement. Our analysis of ampliconic gene evolution unveils a complex pattern of long-term gene content stability despite extensive structural variation on a nonrecombining background.Advances in DNA sequencing...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...cell lines, including two chimpanzees (Pan troglodytes), two gorillas (Gorilla gorilla), two orangutans (Pongo pygmaeus), and three macaques (two M. mulatta and one M. fascicularis); we used marmoset (Callithrix jacchus) as outgroup when necessary (Fig. 2A; Supplemental Table S5).View larger version...
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Method: A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
- Marta Tomaszkiewicz,
- Samarth Rangavittal,
- Monika Cechova,
- Rebeca Campos Sanchez,
- Howard W. Fescemyer,
- Robert Harris,
- Danling Ye,
- Patricia C.M. O'Brien,
- Rayan Chikhi,
- Oliver A. Ryder,
- Malcolm A. Ferguson-Smith,
- Paul Medvedev,
- and Kateryna D. Makova
Genome Res. April 2016 26: 530-540; Published in Advance March 2, 2016, doi:10.1101/gr.199448.115
.... Tomaszkiewicz et al. 532 Genome Research www..org Because the gorilla lineage diverged prior to the human–chimpanzee split (Scally et al. 2012), we expected a similar sequence identity for the gorilla–human and gorilla–chimpanzee pairwise alignments. Indeed, at the nucleotide level, we observed highly similar...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...in the current study), which were identified as inverted across at least one of six different species (chimpanzee, bonobo, gorilla, orangutan, gibbon, and macaque) compared with human using Strand-seq (current study and previous literature) (Maggiolini et al. 2020; Porubsky et al. 2020a). For each inversion pair...
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LETTER: A genome-wide survey of structural variation between human and chimpanzee
- Tera L. Newman,
- Eray Tuzun,
- V. Anne Morrison,
- Karen E. Hayden,
- Mario Ventura,
- Sean D. McGrath,
- Mariano Rocchi,
- and Evan E. Eichler
Genome Res. October 2005 15: 1344-1356; Published in Advance September 16, 2005, doi:10.1101/gr.4338005
...were designed based on flanking conserved sequences adjacent to the chimpanzee deletion such that PCR amplification would readily amplify the deleted variant ( Fig. 2E ). Human, chimpanzee, bonobo, gorilla, orangutan, baboon, and macaque were then tested by PCR. Five assays verified the putative...
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Research: Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
- Elodie Gazave,
- Fleur Darré,
- Carlos Morcillo-Suarez,
- Natalia Petit-Marty,
- Angel Carreño,
- Urko M. Marigorta,
- Oliver A. Ryder,
- Antoine Blancher,
- Mariano Rocchi,
- Elena Bosch,
- Carl Baker,
- Tomàs Marquès-Bonet,
- Evan E. Eichler,
- and Arcadi Navarro
Genome Res. October 2011 21: 1626-1639; Published in Advance August 8, 2011, doi:10.1101/gr.117242.110
...polymorphism, for they only document human-specific losses and gains, while most intraspecific studies, such as that by Perry et al. (2008) in chimpanzees, have so far focused on single species. We studied genomic regions of structural polymorphism in all the great apes (bonobo, chimpanzee, gorilla...
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Research: Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
- Jennifer F. Hughes,
- Helen Skaletsky,
- Tatyana Pyntikova,
- Natalia Koutseva,
- Terje Raudsepp,
- Laura G. Brown,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Shannon Dugan-Rocha,
- Ziad Khan,
- Colin Kremitzki,
- Catrina Fronick,
- Tina A. Graves-Lindsay,
- Lucinda Fulton,
- Wesley C. Warren,
- Richard K. Wilson,
- Elaine Owens,
- James E. Womack,
- William J. Murphy,
- Donna M. Muzny,
- Kim C. Worley,
- Bhanu P. Chowdhary,
- Richard A. Gibbs,
- and David C. Page
Genome Res. December 2020 30: 1716-1726; Published in Advance November 18, 2020, doi:10.1101/gr.269902.120
...that massive lineage-specific MSY amplification of testis-specific gene families is not a peculiarity of the mouse lineage, but is widely distributed among mammals. More limited sequencing surveys of additional mammalian MSYs (including pig, gorilla, cat, and horse) show evidence for large-scale amplification...
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LETTER: Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16
- Violaine Goidts,
- Justyna M. Szamalek,
- Pieter J. de Jong,
- David N. Cooper,
- Nadia Chuzhanova,
- Horst Hameister,
- and Hildegard Kehrer-Sawatzki
Genome Res. September 2005 15: 1232-1242; doi:10.1101/gr.3732505
...16q. Thus, the most parsimonious interpretation is that the gorilla and chimpanzee homologs exhibit similar but nonidentical derived pericentric inversions, whereas HSA 16 represents the ancestral form among hominoids. Footnotes [Supplemental material is available online at www.genome...

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