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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...in the next paragraph. The contig location was defined by the mRNA-coding gene in the ARS-UCD1.2 assembly.The potential of the novel sequence identified in the pan to represent parts of expressed genes was evaluated by determining if transcriptome sequence data that fail to map to the reference assembly might...
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Resource: Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)
- Sanjida H. Rangwala,
- Anatoliy Kuznetsov,
- Victor Ananiev,
- Andrea Asztalos,
- Evgeny Borodin,
- Vladislav Evgeniev,
- Victor Joukov,
- Vadim Lotov,
- Ravinder Pannu,
- Dmitry Rudnev,
- Andrew Shkeda,
- Eric M. Weitz,
- and Valerie A. Schneider
Genome Res. January 2021 31: 159-169; Published in Advance November 25, 2020, doi:10.1101/gr.266932.120
...).GDV is composed of an embedded instance of SV that displays sequence and track data, along with additional page elements that allow a user to search within an entire assembly and efficiently narrow in on their chromosome, sequence, region, or gene of interest. GDV replaced the NCBI Map Viewer (Dombrowski...
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RESOURCE: A Cattle–Human Comparative Map Built with Cattle BAC-Ends and Human Genome Sequence
- Denis M. Larkin,
- Annelie Everts-van der Wind,
- Mark Rebeiz,
- Peter A. Schweitzer,
- Sharon Bachman,
- Cheryl Green,
- Chris L. Wright,
- Edhilvia J. Campos,
- Leslie D. Benson,
- Jennifer Edwards,
- Lei Liu,
- Kazutoyo Osoegawa,
- James E. Womack,
- Pieter J. de Jong,
- and Harris A. Lewin
Genome Res. August 2003 13: 1966-1972; doi:10.1101/gr.1560203
...maps for cattle. These maps and accompanying BAC resources will enable robust assembly of the cattle sequence. Furthermore, comparatively anchored BESs provide a powerful tool for evolutionary studies of vertebrate organization and an important new resource for positional cloning of genes affecting...
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Commentary: Every genome sequence needs a good map
- Harris A. Lewin,
- Denis M. Larkin,
- Joan Pontius,
- and Stephen J. O'Brien
Genome Res. November 2009 19: 1925-1928; Published in Advance July 13, 2009, doi:10.1101/gr.094557.109
...) Project. Science 306: 636–640. Everts-van der Wind A, Kata SR, Band MR, Rebeiz M, Larkin DM, Everts RE, Green CA, Liu L, Natarajan S, Goldammer T, et al. 2004. A 1463 gene cattle-human comparative map with anchor points defined by human sequence coordinates. Genome Res 14: 1424–1437. Everts-van derWind A...
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LETTER: An Ordered Comparative Map of the Cattle and Human Genomes
- Mark R. Band,
- Joshua H. Larson,
- Mark Rebeiz,
- Cheryl A. Green,
- D. Wayne Heyen,
- Jena Donovan,
- Ryan Windish,
- Chad Steining,
- Prapti Mahyuddin,
- James E. Womack,
- and Harris A. Lewin
Genome Res. September 1, 2000 10: 1359-1368; doi:10.1101/gr.145900
...radiation hybrid (RH) mapping in conjunction with EST sequencing, database mining for unmapped cattle genes, and a predictive bioinformatics approach (COMPASS) for targeting specific homologous regions. A total of 768 genes were placed on the RH map in addition to 319 microsatellites used as anchor markers...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...verification, and physical mapping to chromosomes. Multi-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian s. As proof of principle, we assembled s of the pigeon (Columbia livia...
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LETTER: A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping
- William J. Murphy,
- Shan Sun,
- Zhang-qun Chen,
- Naoya Yuhki,
- Deborah Hirschmann,
- Marilyn Menotti-Raymond,
- and Stephen J. O'Brien
Genome Res. May 1, 2000 10: 691-702; doi:10.1101/gr.10.5.691
...L.A. , McKenzie L. , O'Brien S.J. ( 1999 ) A human map of comparative anchor tagged sequences. J. Hered. 90 : 477 – 484 . ↵ Cho K.W. , Okuda M. , Endo Y. , Satoh H. , Kang C.B. , Watari T. , Tsujimoto H. , Hasegawa A. ( 1997a ) Assignment of the cat p53 tumor suppressor gene (TP53) to cat chromosome...
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LETTER: Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle
- Miri Cohen-Zinder,
- Eyal Seroussi,
- Denis M. Larkin,
- Juan J. Loor,
- Annelie Everts-van der Wind,
- Jun-Heon Lee,
- James K. Drackley,
- Mark R. Band,
- A.G. Hernandez,
- Moshe Shani,
- Harris A. Lewin,
- Joel I. Weller,
- and Micha Ron
Genome Res. July 2005 15: 936-944; doi:10.1101/gr.3806705
...: The role of the human ABC transporter ABCG2. Review. Curr. Protein Pept. Sci. 3 : 503 -511. ↵ Everts-van der Wind, A., Kata, S.R., Band, M.R., Rebeiz, M., Larkin, D.M., Everts, R.E., Green, C.A., Liu, L., Natarajan, S., Goldammer, T., et al. 2004 . A 1463-gene cattle–human comparative map with anchor...
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Resource: Breakpoint graphs and ancestral genome reconstructions
- Max A. Alekseyev and
- Pavel A. Pevzner
Genome Res. May 2009 19: 943-957; Published in Advance February 13, 2009, doi:10.1101/gr.082784.108
...completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee...
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Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
- Florent Murat,
- Jian-Hong Xu,
- Eric Tannier,
- Michael Abrouk,
- Nicolas Guilhot,
- Caroline Pont,
- Joachim Messing,
- and Jérôme Salse
Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
...comparative analysis (i.e., establishment of orthologous and paralogous gene pair repertory) of two (rice, sorghum) whole- sequences and three high-density EST-based genetic maps (wheat, barley, maize) has permitted us to use synteny blocks to model an AGK based on gene order and content. We defined two new...

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