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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...of human diseases. Although the macaque major histocompatibility complex (MHC) region shares most features with the human leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class I genes. Although a chimera of two rhesus macaque MHC haplotypes was first published in 2004...
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LETTER: Genetic Divergence of the Rhesus Macaque Major Histocompatibility Complex
- Riza Daza-Vamenta,
- Gustavo Glusman,
- Lee Rowen,
- Brandon Guthrie,
- and Daniel E. Geraghty
Genome Res. August 2004 14: 1501-1515; doi:10.1101/gr.2134504
...nucleotide substitutions were responsible for inactivating some of the class I genes. View larger version: In this window In a new window Figure 1 Linear representation of the rhesus macaque major histocompatibility complex (MHC) with telomeric end to the left and centromeric to the right . The following...
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LETTER: The Genomic Sequence and Comparative Analysis of the Rat Major Histocompatibility Complex
- Peter Hurt,
- Lutz Walter,
- Ralf Sudbrak,
- Sven Klages,
- Ines Müller,
- Takashi Shiina,
- Hidetoshi Inoko,
- Hans Lehrach,
- Eberhard Günther,
- Richard Reinhardt,
- and Heinz Himmelbauer
Genome Res. April 2004 14: 631-639; doi:10.1101/gr.1987704
...., Evans, G.A., and Fischer Lindahl, K. 2003 . Species-specific class I gene expansions formed the telomeric 1 Mb of the mouse major histocompatibility complex. Genome Res. 13 : 589 -600. ↵ Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994 . CLUSTAL W: Improving the sensitivity of progressive multiple...
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LETTER: Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region
- Naoya Yuhki,
- Thomas Beck,
- Robert M. Stephens,
- Yoko Nishigaki,
- Kymberly Newmann,
- and Stephen J. O'Brien
Genome Res. June 2003 13: 1169-1179; Published in Advance May 12, 2003, doi:10.1101/gr.976103
...: 1311 –1319. ↵ Takada, T., Kumánovics, A., Amadou, C., Yoshino, M., Jones, E.P., Athanasiou, M., Evans, G.A., and Fischer-Lindahl, K. 2003 . Species-specific class I gene expansions formed the telomeric 1 mb of the mouse major histocompatibility complex. Genome Res. 13 : 589 –600. ↵ Takahashi, K...
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ARTICLE: Gene copy number variation spanning 60 million years of human and primate evolution
- Laura Dumas,
- Young H. Kim,
- Anis Karimpour-Fard,
- Michael Cox,
- Janet Hopkins,
- Jonathan R. Pollack,
- and James M. Sikela
Genome Res. September 2007 17: 1266-1277; Published in Advance July 31, 2007, doi:10.1101/gr.6557307
...Tables S7, S8), and a few are highlighted here. Genes on chr 6 that encode the histocompatibility antigen Class I (HLA-I) proteins are known to be increased in copy number in macaque relative to humans and great apes ( Daza-Vamenta et al. 2004 ; Macaque Genome Sequencing and Analysis Consortium 2007...
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LETTER: Differential Expansion of Zinc-Finger Transcription Factor Loci in Homologous Human and Mouse Gene Clusters
- Mark Shannon,
- Aaron T. Hamilton,
- Laurie Gordon,
- Elbert Branscomb,
- and Lisa Stubbs
Genome Res. June 2003 13: 1097-1110; Published in Advance May 12, 2003, doi:10.1101/gr.963903
...evolutionary time. Since KRAB-ZNF proteins are predicted to function as transcriptional regulators, the elaboration of new lineage-specific genes in this and other clustered ZNF families is likely to have had a significant impact on species-specific aspects of biology. Mammalian s contain a large number...
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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
...with significant support, but no transcript ORF (see Ashurst and Wilming 2002 for definitions of the different annotation classes of genes used in this study). In addition, a further 95 pseudogenes were identified. The features, including gene annotation of the region, are summarized in Figure 1 . The annotated...
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Article: Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes
- Paul J. Norman,
- Laurent Abi-Rached,
- Ketevan Gendzekhadze,
- John A. Hammond,
- Achim K. Moesta,
- Deepti Sharma,
- Thorsten Graef,
- Karina L. McQueen,
- Lisbeth A. Guethlein,
- Christine V.F. Carrington,
- Dasdayanee Chandanayingyong,
- Yih-Hsin Chang,
- Catalina Crespí,
- Güher Saruhan-Direskeneli,
- Kamran Hameed,
- Giorgi Kamkamidze,
- Kwadwo A. Koram,
- Zulay Layrisse,
- Nuria Matamoros,
- Joan Milà,
- Myoung Hee Park,
- Ramasamy M. Pitchappan,
- D. Dan Ramdath,
- Ming-Yuh Shiau,
- Henry A.F. Stephens,
- Siske Struik,
- Dolly Tyan,
- David H. Verity,
- Robert W. Vaughan,
- Ronald W. Davis,
- Patricia A. Fraser,
- Eleanor M. Riley,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2009 19: 757-769; doi:10.1101/gr.085738.108
...affiliations appears at the end of the paper before the Acknowledgments section.] Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
...for cattle (Supplemental Methods; Supplemental Table S11). However, the increased heterozygosity in these hybrid offspring challenges DV's capabilities with genotype class imbalance (Supplemental Table S4). Therefore, phase 4 strategically uses these data after exhausting standard cattle and bison trios...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...more homeobox genes than does H. symbiolongicarpus, with expansions in the CERS, LIM, POU, and PRD classes (Supplemental Table S26). Four unclassified homeobox genes are unique to H. echinata. It is possible that some of these expansions in H. echinata may be duplicates from different alleles...
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