Molecular identification of the economically important Solanum subgenus Leptostemonum (Solanaceae) using DNA barcodes

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.

Automated summary

This study investigates the feasibility of using standard DNA barcoding markers for molecular identification in Solanum subgenus Leptostemonum. The study finds that the nrITS region is the most variable and can provide high resolution in species discrimination, especially for closely related species. However, the universality and amplification success rate of nrITS are limited. Therefore, it is recommended to supplement the standard matK coding region barcode with nrITS in the Leptostemonum group.