Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Autor: Grégoire Vernaz, Milan Malinsky, Hannes Svardal, Mingliu Du, Alexandra M. Tyers, M. Emília Santos, Richard Durbin, Martin J. Genner, George F. Turner, Eric A. Miska

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-13 (2021)

The Lake Malawi cichlid fishes are an example of extreme vertebrate radiation; however, there is very little sequence divergence among the species. Here the authors present a comparative genome-wide methylome study to suggest DNA methylation played a

Externí odkaz: https://doaj.org/article/1a787f2ae63e44f3b0f679f4ecaa9219

Among-species rate variation produces false signals of introgression

Autor: Thore Koppetsch, Milan Malinsky, Michael Matschiner

The role of interspecific hybridization in the context of diversification dynamics has recently seen increasing attention. Genomic research has now made it abundantly clear that both hybridization and introgression – the exchange of genetic materia

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a98375624a4e45ac2595d3eb4b641443
https://doi.org/10.1101/2023.05.21.541635

Towards complete and error-free genome assemblies of all vertebrate species

Autor: Richard Hall, Tandy Warnow, Tanya M. Lama, Oliver A. Ryder, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Ivo Gut, Paul Flicek, Mark Chaisson, James Torrance, Guojie Zhang, Andrew J. Crawford, Federica Di Palma, Michael Hiller, Jennifer A. Marshall Graves, Sadye Paez, Sarah E. London, Mark Wilkinson, Kateryna D. Makova, Byung June Ko, Jimin George, Farooq O. Al-Ajli, Emma C. Teeling, George F. Turner, Robert H. S. Kraus, Sonja C. Vernes, Zev N. Kronenberg, Michelle Smith, Jonas Korlach, Daryl Eason, Jonathan Wood, Simona Secomandi, Claudio V. Mello, Arkarachai Fungtammasan, Arang Rhie, Tomas Marques-Bonet, Benedict Paten, Ekaterina Osipova, Richard Durbin, M. Thomas P. Gilbert, Beth Shapiro, Ivan Sović, Bruce C. Robertson, Richard E. Green, Eugene W. Myers, Leanne Haggerty, Sergey Koren, Martin Pippel, Bettina Haase, Patrick Masterson, Jay Ghurye, Maria Simbirsky, Samantha R. Friedrich, Chul Hee Lee, Luis R Nassar, Lindsey J. Cantin, Kerstin Howe, Erich D. Jarvis, Marlys L. Houck, Jason T. Howard, Jacquelyn Mountcastle, Mark Mooney, Paolo Franchini, Giulio Formenti, Siddarth Selvaraj, Robel E. Dagnew, Brett T. Hannigan, Brian P. Walenz, Alan Tracey, Heebal Kim, Constantina Theofanopoulou, Nicholas H. Putnam, Karen Clark, Iliana Bista, H. William Detrich, Dengfeng Guan, David Iorns, Andrew Digby, Trevor Pesout, Zemin Ning, Gregory Gedman, Woori Kwak, Maximilian Wagner, Joanna Collins, Harris A. Lewin, Hannes Svardal, Milan Malinsky, Byrappa Venkatesh, Françoise Thibaud-Nissen, Joana Damas, Andreas F. Kautt, Olivier Fedrigo, Christopher Dunn, William Chow, Warren E. Johnson, Yang Zhou, Adam M. Phillippy, Taylor Edwards, Paul Medvedev, Peter V. Lovell, Joyce V. Lee, Sylke Winkler, Stephen J. O'Brien, Wesley C. Warren, Alex Hastie, Marcela Uliano-Silva, Kevin L. Howe, Sarah B. Kingan, Fergal J. Martin, Christopher N. Balakrishnan, David F. Clayton, Ying Sims, Robert W. Murphy, Axel Meyer, Dave W Burt, Shane A. McCarthy, Sarah Pelan, Erik Garrison, Mark Diekhans, Frank Grützner, Gavin J. P. Naylor, Robert S. Harris, Hiram Clawson, Jinna Hoffman, Ann C Misuraca, J. H. Kim

Publikováno v: Nature, 592, 737-746
Nature
Rhie, A, McCarthy, S A, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, B J, Chaisson, M, Gedman, G L, Cantin, L J, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, S C, Lama, T M, Grutzner, F, Warren, W C, Balakrishnan, C N, Burt, D, George, J M, Biegler, M T, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, A F, Franchini, P, Detrich, H W, Svardal, H, Wagner, M, Naylor, G J P, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, B T, Pesout, T, Houck, M, Misuraca, A, Kingan, S B, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, R E, Putnam, N H, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, R E, Guan, D, London, S E, Clayton, D F, Mello, C V, Friedrich, S R, Lovell, P V, Osipova, E, Al-Ajli, F O, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, R S, Makova, K D, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, B P, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, R H S, Crawford, A J, Gilbert, M T P, Zhang, G, Venkatesh, B, Murphy, R W, Koepfli, K-P, Shapiro, B, Johnson, W E, Di Palma, F, Marques-Bonet, T, Teeling, E C, Warnow, T, Graves, J M, Ryder, O A, Haussler, D, O’Brien, S J, Korlach, J, Lewin, H A, Howe, K, Myers, E W, Durbin, R, Phillippy, A M & Jarvis, E D 2021, ' Towards complete and error-free genome assemblies of all vertebrate species ', Nature, vol. 592, no. 7856, pp. 737-746 . https://doi.org/10.1038/s41586-021-03451-0
Natureevents directory, 592(7856):737-746
Digital.CSIC. Repositorio Institucional del CSIC
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Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
Nature, 592, 7856, pp. 737-746

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d50f2a74ee7e66ef185d231bcebbd6ea
https://doi.org/10.1038/s41586-021-03451-0

Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation

Autor: Walter Salzburger, George F. Turner, Benjamin P. Ngatunga, Martin J. Genner, Richard Durbin, Eric A. Miska, Hannes Svardal, Fu Xiang Quah, Milan Malinsky

Publikováno v: Svardel, H, Quah, F X, Malinsky, M, Ngatunga, B P, Miska, E A, Salzburger, W, Genner, M J, Turner, G F & Durbin, R 2020, ' Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation ', Molecular Biology and Evolution, vol. 37, no. 4, pp. 1100-1113 . https://doi.org/10.1093/molbev/msz294
Molecular biology and evolution
Molecular Biology and Evolution

The adaptive radiation of cichlid fishes in East Afrian Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800 thousand years from a common founder population. It has been proposed that hybridisation between an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1c8ec12e09ef60f82c039800cb7c484
https://doi.org/10.1093/molbev/msz294

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of

Autor: A, Ciezarek, Antonia G P, Ford, Graham J, Etherington, Nasser, Kasozi, Milan, Malinsky, Tarang K, Mehta, Luca, Penso-Dolfin, Benjamin P, Ngatunga, Asilatu, Shechonge, Rashid, Tamatamah, Wilfried, Haerty, Federica, Di Palma, Martin J, Genner, George F, Turner

Publikováno v: Aquaculture (Amsterdam, Netherlands). 548

Cichlid fish of the genus

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::71204de9c51d116ba8b5e559a9958418
https://pubmed.ncbi.nlm.nih.gov/35177872