ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language [version 3; peer review: 1 approved, 2 approved with reservations]

Autor: Alex Mas-Sandoval, Chenyu Jin, Marco Fracassetti, Matteo Fumagalli

Publikováno v: F1000Research, Vol 11 (2023)

A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest. Sequencing and mapping errors coupled with low and variable coverage hamper the identification of genotypes and variants and the

Externí odkaz: https://doaj.org/article/ca8368bea07c4a84bf23025c5924035f

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

Autor: Christian Brochmann, Rimjhim Roy Choudhury, Loren H. Rieseberg, Anne K. Brysting, Tanja Slotte, Christian Parisod, Abel Gizaw, Siri Birkeland, Terezie Mandáková, Marco Fracassetti, Audun Schrøder-Nielsen, Martin A. Lysak, Anna Lovisa S Gustafsson, Xinyi Guo, Michael D. Nowak

Publikováno v: Molecular Ecology Resources
Nowak, Michael D.; Birkeland, Siri; Mandakova, Terezie; Choudhury, Rimjhim Roy; Guo, Xinyi; Gustafsson, Anna Lovisa S.; Gizaw, Abel; Schroder-Nielsen, Audun; Fracassetti, Marco; Brysting, Anne K.; Rieseberg, Loren; Slotte, Tanja; Parisod, Christian; Lysak, Martin A.; Brochmann, Christian (2021). The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Molecular ecology resources, 21(3), pp. 661-676. Wiley 10.1111/1755-0998.13280

The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome‐scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2bc27969f2a08660558f324c47ce556f
http://europepmc.org/articles/PMC7983928

Validation of Pooled Whole-Genome Re-Sequencing in Arabidopsis lyrata.

Autor: Marco Fracassetti, Philippa C Griffin, Yvonne Willi

Publikováno v: PLoS ONE, Vol 10, Iss 10, p e0140462 (2015)

Sequencing pooled DNA of multiple individuals from a population instead of sequencing individuals separately has become popular due to its cost-effectiveness and simple wet-lab protocol, although some criticism of this approach remains. Here we valid

Externí odkaz: https://doaj.org/article/2e83b07b74be4570a0cac4e5713e333e

Demographic Processes Linked to Genetic Diversity and Positive Selection across a Species' Range

Autor: Yvonne Willi, Josh Van Buskirk, Marco Fracassetti, Olivier Bachmann

Publikováno v: Plant Communications

Demography determines the strength of genetic drift, which generally reduces genetic variation and the efficacy of selection. Here, we disentangled the importance of demographic processes at a local scale (census size and mating system) and at a spec

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe1a0f336e6a013d481e82402bb4f82c
http://europepmc.org/articles/PMC7747977

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

Autor: Sivan Yair, Filip Kolář, Benjamin Laenen, Jakub Vlček, Marco Fracassetti, Veronika Konečná, Tanja Slotte, Magdalena Bohutínská

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::943b5808fb3954b3e5c301e8cd5bff8b