International Journal of Molecular Sciences Article Integrated Analysis of the Transcriptome and Metabolome of Cecropia obtusifolia: A Plant with High Chlorogenic Acid Content Traditionally Used to Treat Diabetes Mellitus Jorge David Cadena-Zamudio 1, Pilar Nicasio-Torres 2 , Juan Luis Monribot-Villanueva 1 , José Antonio Guerrero-Analco 1 and Enrique Ibarra-Laclette 1,* 1 Instituto de Ecología, A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAV), Xalapa 91073, Veracruz, Mexico;
[email protected] (J.D.C.-Z.);
[email protected] (J.L.M.-V.);
[email protected] (J.A.G.-A.) 2 Instituto Mexicano del Seguro Social (IMSS), Centro de Investigación Biomédica del Sur (CIBIS), Xochitepec 62790, Morelos, Mexico;
[email protected] * Correspondence:
[email protected]; Tel.: +52-(228)-842-1823 Received: 12 September 2020; Accepted: 9 October 2020; Published: 14 October 2020 Abstract: This investigation cultured Cecropia obtusifolia cells in suspension to evaluate the effect of nitrate deficiency on the growth and production of chlorogenic acid (CGA), a secondary metabolite with hypoglycemic and hypolipidemic activity that acts directly on type 2 diabetes mellitus. Using cell cultures in suspension, a kinetics time course was established with six time points and four total nitrate concentrations. The metabolites of interest were quantified by high-performance liquid chromatography (HPLC), and the metabolome was analyzed using directed and nondirected approaches. Finally, using RNA-seq methodology, the first transcript collection for C. obtusifolia was generated. HPLC analysis detected CGA at all sampling points, while metabolomic analysis confirmed the identity of CGA and of precursors involved in its biosynthesis. Transcriptome analysis identified differentially expressed genes and enzymes involved in the biosynthetic pathway of CGA.