DNA Barcoding of the Solanaceae Family in Puerto Rico Including Endangered and Endemic Species

in Journal of the American Society for Horticultural Science

The Solanaceae family is one of the largest and well-distributed plant families in the world. It contains species of agricultural and economical importance, such as Solanum tuberosum, Solanum melongena, Solanum lycopersicum, Nicotiana tabacum, and Capsicum annuum. In Puerto Rico, there are ≈46 species of Solanaceae of which six are endemic: Brunfelsia densifolia, Brunfelsia lactea, Brunfelsia portoricensis, Goetzea elegans, Solanum ensifolium, and Solanum woodburyi. Our objective was to use DNA barcoding to identify the Solanaceae species in Puerto Rico, including the endemics, and to assess the species relationships between them. To accomplish our objective, two chloroplast regions (psbA-trnH and matK) and a nuclear region [internal transcribed spacer (ITS)] were assessed. Pairwise distance and phylogenetic analysis demonstrate that DNA barcoding can be used to discriminate at the species level among these taxa in Puerto Rico. For all three markers, the genus that showed the highest pairwise distance between represented species was Solanum, whereas the genus that displayed the least was Capsicum. Phylogenetic trees of single and concatenated regions were generated from sequences obtained in this study and from data downloaded from the National Center for Biotechnology Information database. Our results show that this technique can be used to identify species with one, two, or three combinations of DNA barcode markers depending on the taxon. In addition, this is the first study to include the endemic species S. woodburyi in a molecular phylogenetic analysis, and it was found to have a close relationship with S. ensifolium, also endemic to Puerto Rico, and to Solanum bahamense from the Bahamas and Greater Antilles. Therefore, we suggest that S. woodburyi might be part of the Bahamense clade.

Contributor Notes

The authors thank José A. Sustache (former Natural Resources employee) for all his help facilitating plant material, as well as Anastasio Gomez. We also thank Manuel Sepulveda (coordinator of the Jardin Botanico de Rio Piedras), Christian W. Torres Santana (former Director of Fundación Comunitaria Luis Muñoz Marin), Jose Rene Román (Guajataca Forest Management official), Hector Serrano (Cayey Forest Management), Miguel (Papo) Vives, and Henry E. Hernandez Rosario for their help collecting specimens. In addition, the authors thank Clinton Morse, Dr. Gregory J. Anderson, and their team from the Biodiversity Education and Research Greenhouse of the University of Connecticut for sending us plant material of Solanum ensifolium from Cayey, Puerto Rico. Special gratitude is extended to Jeanine Vélez, curator of the University of Puerto Rico Mayaguez-MAPR herbarium, for providing dried plant material. This project was supported by a grant to DS from the U.S. Department of Agriculture Hispanic Serving Institutions (HSI) program (2016-06469).

Corresponding author. E-mail: dimuth.siritunga@upr.edu.

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Article Figures

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    Phylogenetic neighbor joining analysis based on the matK barcode. Bootstraps scores are shown (100 replicates, ≥50%) for each branch. Samples with sequences obtained in this study are depicted with an asterisk (*). Discrimination at genus level can be observed using matK barcode.

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    Phylogenetic neighbor joining analysis based on the psbA-trnH barcode. Bootstraps scores are shown (100 replicates, ≥50%) for each branch. Samples with sequences obtained in this study are depicted with an asterisk (*). Discrimination at genus and species level can be observed using psbA-trnH barcode.

  • View in gallery

    Phylogenetic neighbor joining analysis based on the ITS (internal transcribed spacer) barcode. Bootstraps scores are shown (100 replicates, ≥50%) for each branch. Samples with sequences obtained in this study are depicted with an asterisk (*). Discrimination at species level was observed using ITS barcode.

  • View in gallery

    Neighbor joining analysis of the concatenated sequences of ITS + matK + psbA-trnH. Samples with sequences obtained in this study are depicted with an asterisk (*). A consensus of sequences was obtained for each species. Genera grouped by clades were designated with their respectively genus.

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    Neighbor joining analysis of the concatenated sequences of ITS + matK. Bootstraps scores are shown (100 replicates, ≥50%) for each branch.

  • View in gallery

    Neighbor joining analysis of the concatenated sequences of ITS + psbA-trnH. Bootstraps scores are shown (100 replicates, ≥50%) for each branch.

  • View in gallery

    Neighbor joining analysis of the concatenated sequences of matK+ psbA-trnH. Bootstraps scores are shown (100 replicates, ≥50%) for each branch.

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