Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids

0573907 - ÚŽFG 2024 RIV GB eng J - Journal Article
Bartoš, Oldřich - Bohlen, Jörg - Bohlen Šlechtová, Vendula - Kočí, Jan - Röslein, Jan - Janko, Karel
Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids.
Molecular Ecology Resources. Roč. 23, č. 6 (2023), s. 1348-1360. ISSN 1755-098X. E-ISSN 1755-0998
R&D Projects: GA ČR(CZ) GA19-18453S; GA ČR(CZ) GA19-21552S; GA MŠMT EF15_003/0000460
Institutional support: RVO:67985904
Keywords : allelic drop-out * allopolyploids * Cobitis
OECD category: Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology
Impact factor: 7.7, year: 2022
Method of publishing: Open access
https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13806

As whole-genome sequencing has become pervasive, some have suggested that reduced genomic representation approaches, for example, sequence capture, are becoming obsolete. In the present study, we argue that these techniques still provide excellent tools in terms of price and quality of data as well as in their ability to provide markers with specific features, as required, for example, in phylogenomics. A potential drawback of the wide-scale application of reduced representation approaches could be their drop in efficiency with increasing phylogenetic distance from the reference species. While some studies have focused on the degree and performance of reduced representation techniques in such situations, to our knowledge, none of them evaluated their applicability to inter-specific hybrids and polyploids. This highlights a significant gap in current knowledge since there is increasing evidence for the frequent occurrence of natural hybrids and polyploids, as well as for the major importance of both phenomena in evolution. The main aim of the present study was to carry out a thorough validation of SEQcap applicability to (1) a set of non-model taxa with a wide range of phylogenetic relatedness and (2) inter-specific hybrids of various ploidies and genomic compositions. Considering the latter point, we especially focused on mechanisms causing allelic bias and consequent allelic dropout, as these could have confounding effects with respect to the evolutionary genomic dynamics of hybrids, especially in asexuals, which virtually reproduce as a frozen F1 generation.
Permanent Link: https://hdl.handle.net/11104/0344280