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

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...

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Bibliographic Details
Published in:American journal of botany 2019-03, Vol.106 (3), p.415-437
Main Authors: Morales‐Briones, Diego F., Tank, David C.
Format: Article
Language:English
Subjects:
Allopolyploidy
Biological evolution
Cell Nucleus - genetics
Chloroplasts
cpDNA
cytonuclear discordance
Deoxyribonucleic acid
Discordance
DNA
DNA sequencing
DNA, Chloroplast - analysis
DNA, Chloroplast - genetics
DNA, Ribosomal - analysis
DNA, Ribosomal - genetics
Enrichment
Evolution, Molecular
Genes, Plant
Genome, Plastid
Genomes
Genomics
haplotype inference
Hybridization
incomplete concerted evolution
Lachemilla
microfluidic PCR
multiple origins of polyploidy
Next-generation sequencing
nrDNA
Origins
Phylogeny
Plastids - genetics
Polymerase Chain Reaction
Polyploidy
Ribosomal DNA
ribotype clustering
Rosaceae
Rosaceae - genetics
Species
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Summary: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.
ISSN:0002-9122
1537-2197
DOI:10.1002/ajb2.1253