Abstract
Solanum is the largest and most diverse genus of the Solanaceae family. The genus includes around 1,400 species, and almost a third belong to subgenus Leptostemonum. The species in this subgenus are commonly known as the spiny solanums, and include economically important species such as brinjal eggplant, naranjilla/lulo, and cocona. This study investigates the feasibility of using standard DNA barcoding markers for molecular identification in this subgenus, using sequence similarity (barcoding gap and best close match) and tree‐based (maximum likelihood tree) methods. The molecular framework uses 189 matK, 112 trnH-psbA and 222 nrITS sequences, corresponding to 37, 29 and 51 species, respectively. From them, 164 sequences were newly generated for this study and 359 were obtained from NCBI GenBank. Sequence divergence analysis shows that nrITS is the most variable region with the greatest nucleotide divergence between species, followed by trnH-psbA and matK. Using tree‐based methods nrITS region discriminates 69% of the 51 included species, matK discriminates 76% of 37 species. Discrimination of the closely related species S. quitoense—S. pseudolulo—S. candidum was possible with nrITS, whereas this was not possible using matK or trnH-psbA. The main drawback of nrITS was primer universality and amplification success with a sequencing rate of only 51%. Subgenus specific universal primers for nrITS could overcome this limitation, and make this a high resolution molecular identifier for the Leptostemonum group. In conclusion this study recommends that the standard matK coding region barcode is supplemented with nrITS in Solanum subgenus Leptostemonum, especially when matK has limited discriminatory power.
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Abbreviations
- matK :
-
Maturase K
- nrITS:
-
Internal transcribed spacer of the nuclear ribosomal DNA
- trnH-psbA :
-
Intergenenic spacer of trnH and psbA gene
- trnH :
-
Histidine-accepting tRNA
- psbA :
-
Photosystem II
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Acknowledgements
The members of the Research Group on Molecular Systematics, Universidad Nacional de Colombia, are thanked for their help in the collection of specimens. Jorge Mario Vélez at the MEDEL Herbarium, Universidad Nacional de Colombia, is thanked for identifying the plant material used in this study.
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ICC: Conception and design, acquisition, analysis and interpretation of study data and paper writing. CEG: Conception and design, acquisition of study data and critical revision of the article. NB: Application of computational techniques analysis and interpretation of study data and in critical revision of the article. MAG: Conception and design, analysis and interpretation of study data and critical revision of the article. SIUS: Conception and design, analysis and interpretation of study data and acquisition of the financial support for the project, project supervision and paper writing. HJBB: Analysis and interpretation of study data, acquisition of the financial support and critical revision of the article. All the authors read and approved the manuscript.
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Collection of plant material was done in accordance with Colombian decree no. 1376, which regulates the permission to collect specimens of wild species of biological diversity for non-commercial research. In addition, the Universidad Nacional de Colombia, Medellín campus regulations for field research were followed. The institution that granted permission for the research was the Autoridad Nacional de Licencias Ambientales (ANLA).
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13562_2022_773_MOESM1_ESM.tiff
Figure. S1. Variability distribution along the region alignment by using Entropy graphs. A. matK. B. trnH-psbA. C. nrITS (TIFF 4025 kb)
13562_2022_773_MOESM2_ESM.tif
Figure. S2. Maximum likelihood phylogenetic reconstruction based in matK + nrITS+ trnH-psbA regions combined. Values above the nodes are bootstrap support of the analysis. The scale at the bottom of the figure represents the number of substitutions per site. (TIF 532 kb)
13562_2022_773_MOESM3_ESM.tif
Figure. S3. Maximum likelihood phylogenetic reconstruction based in matK + nrITS regions combined. Values above the nodes are bootstrap support of the analysis. The scale at the bottom of the figure represents the number of substitutions per site. (TIF 590 kb)
13562_2022_773_MOESM4_ESM.tif
Figure. S4. Maximum likelihood phylogenetic reconstruction based in nrITS+ trnH-psbA regions combined. Values above the nodes are bootstrap support of the analysis. The scale at the bottom of the figure represents the number of substitutions per site. (TIF 544 kb)
13562_2022_773_MOESM5_ESM.tif
Figure. S5. Maximum likelihood phylogenetic reconstruction based in matK + trnH-psbA regions combined. Values above the nodes are bootstrap support of the analysis. The scale at the bottom of the figure represents the number of substitutions per site. (TIF 729 kb)
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Cadavid, I.C., Giraldo, C.E., Balbinott, N. et al. Molecular identification of the economically important Solanum subgenus Leptostemonum (Solanaceae) using DNA barcodes. J. Plant Biochem. Biotechnol. 31, 938–952 (2022). https://doi.org/10.1007/s13562-022-00773-6
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DOI: https://doi.org/10.1007/s13562-022-00773-6