Widespread false gene gains caused by duplication errors in genome assemblies

Autor: Byung June Ko, Chul Lee, Juwan Kim, Arang Rhie, Dong Ahn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis, Heebal Kim

Publikováno v: Genome Biology, Vol 23, Iss 1, Pp 1-26 (2022)

Abstract Background False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna’s Hummingbird, and their new counter

Externí odkaz: https://doaj.org/article/b5cc7d4f8b024cf2b6ddd59c199ba656

Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

Autor: Aravind Prasad, Nisha E. Pillai, Byrappa Venkatesh, Vydianathan Ravi, Prashant Shingate, Aoife McLysaght, Yoichiro Nakatani

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)
Nature Communications

Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4301e83d4304dc2896285101a4561b80
https://doaj.org/article/64fac8c9d8854c38b8d9129a075fb842

Avian blood parasite richness decreases with major histocompatibility complex class I loci number

Autor: Mathieu Giraudeau, Orsolya Vincze, Claire Loiseau

Publikováno v: Biology Letters
Biology Letters, Royal Society, The, 2021, 17 (8), ⟨10.1098/rsbl.2021.0253⟩
Biol Lett
Biology Letters, 2021, 17 (8), ⟨10.1098/rsbl.2021.0253⟩

Major histocompatibility complex (MHC) genes are among the most polymorphic in the vertebrate genome. The high allele diversity is believed to be maintained primarily by sexual and pathogen-mediated balancing selection. The number of MHC loci also va

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ab03c303dbf3d256b39db0a88fd9a3b8
https://doi.org/10.1098/rsbl.2021.0253

Origins and evolutionary consequences of ancient endogenous retroviruses

Autor: Welkin E. Johnson

Publikováno v: Nature Reviews Microbiology. 17:355-370

Retroviruses infect a broad range of vertebrate hosts that includes amphibians, reptiles, fish, birds and mammals. In addition, a typical vertebrate genome contains thousands of loci composed of ancient retroviral sequences known as endogenous retrov

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3fa15de79fdf9f4aedf9469246fc6607
https://doi.org/10.1038/s41579-019-0189-2

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Autor: Alden Deran, Benedict Paten, Jeremy A. Johnson, Qi Fang, Jessica Alföldi, David Haussler, Ian T. Fiddes, Robert S. Harris, Elinor K. Karlsson, Duo Xie, Erich D. Jarvis, Mark Diekhans, Voichita D. Marinescu, Kerstin Lindblad-Toh, Glenn Hickey, Josefin Stiller, Joel Armstrong, Adam M. Novak, Diane P. Genereux, Guojie Zhang, Shaohong Feng

Publikováno v: Nature, vol 587, iss 7833
Nature
Armstrong, J, Hickey, G, Diekhans, M, Fiddes, I T, Novak, A M, Deran, A, Fang, Q, Xie, D, Feng, S, Stiller, J, Genereux, D, Johnson, J, Marinescu, V D, Alföldi, J, Harris, R S, Lindblad-Toh, K, Haussler, D, Karlsson, E, Jarvis, E D, Zhang, G & Paten, B 2020, ' Progressive Cactus is a multiple-genome aligner for the thousand-genome era ', Nature, vol. 587, no. 7833, pp. 246-251 . https://doi.org/10.1038/s41586-020-2871-y

New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1–3. For example, the number of vertebrate genome assemblies currently in the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8cbc58ed970cfc0abce8743d2e2976dc
https://escholarship.org/uc/item/94h1f1zn