Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A ...

@article{1838237,
   author = {Šlenker, Marek and Kantor, Adam and Marhold, Karol and Schmickl, Roswitha and Malík Mandáková, Terezie and Lysák, Martin and Perný, Marián and Caboňová, Michaela and Slovák, Marek and ZozomováandLihová, Judita},
   article_location = {Lausanne},
   article_number = {April},
   doi = {http://dx.doi.org/10.3389/fpls.2021.659275},
   keywords = {allopolyploidy; Balkan endemism; genomic in situ hybridization; Hyb-Seq; nrDNA; Pindhos Mts; read-backed phasing; target enrichment},
   language = {eng},
   issn = {1664-462X},
   journal = {Frontiers in Plant Science},
   title = {Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides},
   url = {https://www.frontiersin.org/articles/10.3389/fpls.2021.659275/full},
   volume = {12},
   year = {2021}
}

TY  - JOUR
ID  - 1838237
AU  - Šlenker, Marek - Kantor, Adam - Marhold, Karol - Schmickl, Roswitha - Malík Mandáková, Terezie - Lysák, Martin - Perný, Marián - Caboňová, Michaela - Slovák, Marek - Zozomová-Lihová, Judita
PY  - 2021
TI  - Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides
JF  - Frontiers in Plant Science
VL  - 12
IS  - April
SP  - "659275"
EP  - "659275"
PB  - Frontiers Media SA
SN  - 1664462X
KW  - allopolyploidy
KW  - Balkan endemism
KW  - genomic in situ hybridization
KW  - Hyb-Seq
KW  - nrDNA
KW  - Pindhos Mts
KW  - read-backed phasing
KW  - target enrichment
UR  - https://www.frontiersin.org/articles/10.3389/fpls.2021.659275/full
N2  - Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of Cardamine (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic in situ hybridization (GISH), to resolve the origin of tetraploid Cardamine barbaraeoides endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for C. barbaraeoides, which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.
ER  - 

ŠLENKER, Marek, Adam KANTOR, Karol MARHOLD, Roswitha SCHMICKL, Terezie MALÍK MANDÁKOVÁ, Martin LYSÁK, Marián PERNÝ, Michaela CABOŇOVÁ, Marek SLOVÁK a Judita ZOZOMOVÁ-LIHOVÁ. Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides. \textit{Frontiers in Plant Science}. Lausanne: Frontiers Media SA, 2021, roč.~12, April, s.~''659275'', 22 s. ISSN~1664-462X. Dostupné z: https://dx.doi.org/10.3389/fpls.2021.659275.