Using Reference -assisted chromosome assemblies to study chromosome structures and evolution in vertebrates

  • Larkin, Denis Mikhailovich (PI)

Project: Externally funded research

Project Details

StatusFinished
Effective start/end date06 Sept 2012 → 05 Sept 2015

Funding

  • Biotechnology and Biological Sciences Research Council (Funder reference unknown): £241,531.72

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  • Fourth Report on Chicken Genes and Chromosomes 2022

    Smith, J., Alfieri, J. M., Anthony, N., Arensburger, P., Athrey, G. N., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., Blackmon, H., Borodin, P. M., Carroll, R., Casono, M. C., Charles, M., Cheng, H., Chiodi, M., Cigan, L., Coghill, L. M. & Crooijmans, R. & 104 others, Das, N., Davey, S., Davidian, A., Degalez, F., Dekkers, J. M., Derks, M., Diack, A. B., Djikeng, A., Drechsler, Y., Dyomin, A., Fedrigo, O., Fiddaman, S. R., Formenti, G., Frantz, L. A. F., Fulton, J. E., Gaginskaya, E., Galkina, S., Gallardo, R. A., Geibel, J., Gheyas, A. A., Godinez, C. J. P., Goodell, A., Graves, J. A. M., Griffin, D. K., Haase, B., Han, J.-L., Hanotte, O., Henderson, L. J., Hou, Z.-C., Howe, K., Huynh, L., Ilatsia, E., Jarvis, E. D., Johnson, S. M., Kaufman, J., Kelly, T., Kemp, S., Kern, C., Keroack, J. H., Klopp, C., Lagarrigue, S., Lamont, S. J., Lange, M., Lanke, A., Larkin, D. M., Larson, G., Layos, J. K. N., Lebrasseur, O., Malinovskaya, L. P., Martin, R. J., Martin Cerezo, M. L., Mason, A. S., McCarthy, F. M., McGrew, M. J., Mountcastle, J., Muhonja, C. K., Muir, W., Muret, K., Murphy, T. D., Ng’ang’a, I., Nishibori, M., O’Connor, R. E., Ogugo, M., Okimoto, R., Ouko, O., Patel, H. R., Perini, F., Pigozzi, M. I., Potter, K. C., Price, P. D., Reimer, C., Rice, E. S., Rocos, N., Rogers, T. F., Saelao, P., Schauer, J., Schnabel, R. D., Schneider, V. A., Simianer, H., Smith, A., Stevens, M. P., Stiers, K., Tiambo, C. K., Tixier-Boichard, M., Torgasheva, A. A., Tracey, A., Tregaskes, C. A., Vervelde, L., Wang, Y., Warren, W. C., Waters, P. D., Webb, D., Weigend, S., Wolc, A., Wright, A. E., Wright, D., Wu, Z., Yamagata, M., Yang, C., Yin, Z.-T., Young, M. C., Zhang, G., Zhao, B. & Zhou, H., 30 Jan 2023, In: Cytogenetic and Genome Research. 162, 8-9, p. 405-528

    Research output: Contribution to journal › Article › peer-review

    Open Access
    19 Citations (Scopus)

  • Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

    Farré, M., Kim, J., Proskuryakova, A. A., Zhang, Y., Kulemzina, A. I., Li, Q., Zhou, Y., Xiong, Y., Johnson, J. L., Perelman, P. L., Johnson, W. E., Warren, W. C., Kukekova, A. V., Zhang, G., O'Brien, S. J., Ryder, O. A., Graphodatsky, A. S., Ma, J., Lewin, H. A. & Larkin, D. M., Apr 2019, In: Genome Research. 29, 4, p. 576-589 14 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    35 Citations (Scopus)
    150 Downloads (Pure)

  • Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes

    O'Connor, R. E., Farré, M., Joseph, S., Damas, J., Kiazim, L., Jennings, R., Bennett, S., Slack, E. A., Allanson, E., Larkin, D. M. & Griffin, D. K., 24 Oct 2018, In: Genome Biology. 19, 1, 171.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    49 Citations (Scopus)
    139 Downloads (Pure)

  • Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

    Joseph, S., O’Connor, R., Al Mutery, A., Watson, M., Larkin, D. & Griffin, D., 18 Oct 2018, In: Diversity. 10, 4, 113.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    26 Citations (Scopus)

  • Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly

    Rando, H. M., Farré, M., Robson, M. P., Won, N. B., Johnson, J. L., Buch, R., Bastounes, E. R., Xiang, X., Feng, S., Liu, S., Xiong, Z., Kim, J., Zhang, G., Trut, L. N., Larkin, D. M. & Kukekova, A. V., 20 Jun 2018, In: Genes. 9, 6, 308.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    10 Citations (Scopus)
    141 Downloads (Pure)

  • Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes

    Damas, J., Kim, J., Farré, M., Griffin, D. K. & Larkin, D. M., 05 Oct 2018, In: Genome Biology. 19, 1, 155.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    42 Citations (Scopus)
    149 Downloads (Pure)

  • Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs

    O'Connor, R. E., Romanov, M. N., Kiazim, L. G., Barrett, P. M., Farré, M., Damas, J., Ferguson-Smith, M., Valenzuela, N., Larkin, D. M. & Griffin, D. K., 21 May 2018, In: Nature Communications. 9, 1883.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    56 Citations (Scopus)
    147 Downloads (Pure)

  • Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

    Damas, J., O'Connor, R., Farré, M., Lenis, V., Martell, H., Mandawala, A., Fowler, K., Joseph, S., Swain, M., Griffin, D. & Larkin, D. M., 01 May 2017, In: Genome Research. 27, 5, p. 875-884 10 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    74 Citations (Scopus)
    172 Downloads (Pure)

  • Novel insights into chromosome evolution in birds, archosaurs, and reptiles

    Farré, M., Narayan, J., Slavov, G., Damas, J., Auvil, L., Li, C., Jarvis, E. D., Burt, D. W., Griffin, D. K. & Larkin, D. M., 25 Aug 2016, In: Genome Biology and Evolution. 8, 8, p. 2442-2451 10 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    53 Citations (Scopus)
    152 Downloads (Pure)

  • Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

    Beynon, S. E., Slavov, G. T., Farré-Belmonte, M., Sunduimijid, B., Waddams, K., Davies, B., Haresign, W., Kijas, J., Macleod, I. M., Newbold, C. J., Davies, L. & Larkin, D. M., 20 Jun 2015, In: BMC Genetics. 16, 1, 65.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    59 Citations (Scopus)
    306 Downloads (Pure)

  • Comparative genomics reveals insights into avian genome evolution and adaptation

    Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., Ödeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H. & Yang, W. & 85 others, Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., da Fonseca, R. R., Alfaro-Núñez, A., Schubert, M., Orlando, L., Mourier, T., Howard, J. T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M. V., Hara, E., Smith, J., Farré-Belmonte, M., Narayan, J., Slavov, G., Romanov, M. N., Borges, R., Machado, J. P., Khan, I., Springer, M. S., Gatesy, J., Hoffmann, F. G., Opazo, J. C., Håstad, O., Sawyer, R. H., Kim, H., Kim, K.-W., Kim, H. J., Cho, S., Li, N., Huang, Y., Bruford, M. W., Zhan, X., Dixon, A., Bertelsen, M. F., Derryberry, E., Warren, W., Wilson, R. K., Li, S., Ray, D. A., Green, R. E., O'Brien, S. J., Griffin, D., Johnson, W. E., Haussler, D., Ryder, O. A., Willerslev, E., Graves, G. R., Alstrom, P., Fjeldsa, J., Mindell, D. P., Edwards, S. V., Braun, E. L., Rahbek, C., Burt, D. W., Houde, P., Zhang, Y., Yang, H., Wang, J., Jarvis, E. D., Gilbert, M. T. P. & Wang, J., 12 Dec 2014, In: Science. 346, 6215, p. 1311-1320 10 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File
    751 Citations (Scopus)
    197 Downloads (Pure)
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