Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR‐based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics

Abstract

Premise of the Study Polyploidy has been long recognized as an important force in plant evolution. Previous studies had suggested widespread occurrence of polyploidy and the allopolyploid origin of several species in the diverse neotropical genus Lachemilla (Rosaceae). Nonetheless, this evidence has relied mostly on patterns of cytonuclear discordance, and direct evidence from nuclear allelic markers is still needed. Methods Here we used PCR target enrichment in combination with high throughput sequencing to obtain multiple copies of the nuclear ribosomal (nr) DNA cistron and 45 regions of the plastid genome (cpDNA) from 219 accessions representing 48 species of Lachemilla and to explore the allopolyploid origin of species in this group. Key Results We were able to identify multiple nrDNA ribotypes and establish clear evidence of allopolyploidy in 33 species of Lachemilla, showing that this condition is common and widespread in the genus. Additionally, we found evidence for three autopolyploid species. We also established multiple, independent origins of several allopolyploid species. Finally, based solely on the cpDNA phylogeny, we identified that the monotypic genus Farinopsis is the sister group of Lachemilla and allied genera within subtribe Fragariinae. Conclusions Our study demonstrates the utility of the nuclear ribosomal DNA cistron to detect allopolyploidy when concerted evolution of this region is not complete. Additionally, with a robust chloroplast phylogeny in place, the direction of hybridization events can be established, and multiple, independent origins of allopolyploid species can be identified.

Chloroplast primers for clade‐wide phylogenetic studies of Thalictrum

“…High‐throughput sequencing has facilitated the development of various approaches for collecting multiple regions or complete sequences of this genome (reviewed in Twyford and Ness, ). Furthermore, approaches based on PCR target enrichment in combination with high‐throughput sequencing (e.g., Uribe‐Convers et al., ) have proven to be a cost‐effective approach for sequencing multiple chloroplast regions simultaneously, and have been successfully applied in phylogenetic studies (e.g., Jacobs et al., ; Morales‐Briones and Tank, ).…”

Three new species of Lachemilla (Rosaceae) from South America

“…We used previously published datasets from Morales-Briones and Tank (2019b) from the nrDNA cistron and 45 regions of cpDNA for Lachemilla , and included 68 samples representing 48 species of Lachemilla , seven samples of the three new taxa, and four outgroups (Appendix 1). DNA extraction, amplification and sequencing were carried out as described in Morales-Briones and Tank (2019a). Molecular datasets from Morales-Briones and Tank (2019a) and data for the new taxa presented here were generated simultaneously.…”

“…DNA extraction, amplification and sequencing were carried out as described in Morales-Briones and Tank (2019a). Molecular datasets from Morales-Briones and Tank (2019a) and data for the new taxa presented here were generated simultaneously. Data processing and ribotype selection was performed as described in Morales-Briones and Tank (2019a).…”

“…Molecular datasets from Morales-Briones and Tank (2019a) and data for the new taxa presented here were generated simultaneously. Data processing and ribotype selection was performed as described in Morales-Briones and Tank (2019a). The three regions of the nrDNA (ETS, ITS1, and ITS2) were concatenated, and the 45 regions of the cpDNA were concatenated as well.…”

“…Finally, the Orbiculate clade encompasses species with a stoloniferous habit and palmately lobed leaves, and, it has been established that the Orbiculate clade is of ancient hybrid origin (Morales-Briones et al 2018b). Moreover, Morales-Briones and Tank (2019a), using copies (or ribotypes) of the nuclear ribosomal (nrDNA) cistron and multiple regions of the plastid genome (cpDNA), showed that at least 30 species of Lachemilla are allopolyploids, and that this condition is widespread among the four main clades of this group.…”