The plastome of the Yerba Mate tree

CASCALES J.; BRACCO M.; POGGIO L.; GOTTLIEB AM

San Carlos de Bariloche

Congreso; V Argentinian Conference on Bioinformatics and Computational Biology; 2014

The plastome of the Yerba Mate tree  Jimena Cascales1,2, Mariana Bracco1, Lidia Poggio1,2, Alexandra M Gottlieb1,2 1Laboratorio de Citogenética y Evolución, Departamento de Ecología, Genética y Evolución, IEGEBA (UBA-CONICET), FCEyN, UBA. Int. Güiraldes 2620, Ciudad Universitaria, Pab. II, 4to piso, Laboratorio 61-62. (C1428EHA), CABA, Argentina. 2CONICET. jcascales@ege.fcen.uba.ar Background The "yerba mate" tree (Ilex paraguariensis) is a perennial native to subtropical South America. Its economic value relies on the usage of the leaves and twigs, to prepare a popular  infusion. The custom of drinking ?mate? is a legacy of the Guaraní culture strongly rooted in our society. Several medicinal properties are attributed to the high concentrations of various secondary metabolites, minerals and vitamins. In Argentina the production of "yerba mate" is restricted to Misiones and Corrientes, due to the climate and soil requirements of the crop. Phytochemical studies on this species abound in the literature[1,2]; notably, the information about basic genetics is very limited. To contribute to its genetic knowledge, we faced the sequencing of the chloroplastgenome, analyzing its structure and gene content. Materials and methods First, intact chloroplasts were isolated from fresh materials using the Chloroplast Isolation Kit (Sigma). The plastidic DNA was extracted adapting protocols [3,4]. The samples were sequenced using 454 GSFLX+Roche at the INDEAR (Rosario, Santa Fe). There, a preliminary contig assembly was attempted. We used bioinformatic tools to verify and assemble a definite plastome. A consensus sequence was obtained with Sequencher v4.1.4 (GeneCodes Corporation); the annotation was carried-out with CpGAVAS[5]. Specific PCR primers were designed with Primer3Plus[6] and Primer-BLAST[7], to check the junctions between the large (LSC) and small (SSC) single-copy segments and the two inverted repeats (IRs). The reading frameworks were adjusted using sequences of Ilex cornuta as references, with the NCBI-BLAST[8] algorithms and the MSWAT[9] web server. The number and location of repeats were assessed using REPuter[10]. Plastidic microsatellite loci and the corresponding primer pairs were detected using the WebSat[11] server. Results As the sequencing result, 492,515bp were generated (in 56 contigs from 4 individuals). A consensus sequence of 157.6bp was obtained for the complete plastome. It shows the typical quadripartite structure, having a LSC of 87,148bp; two IRs of 26,076bp each, and a SSC of 18,310bp. In total, 114 unique genes were detected; 80 are coding sequences, 30 tRNAs and 4 rRNAs. Fourty-nine repeats were identified, 27 palindromic and 22 forward. Thirty-five potential mononucleotidic and one dinucleotidic microsatellite loci were detected, their utility as markers remains to be evaluated. Conclusions The data presented herein constitutes a novel contribution, and a useful information platform that will enhance the generation of new "yerba mate" varieties, the improvement of the crop´s genetic background, and the devise of original transgenesis experiments. These, in turn, will directly benefit the "yerba mate" industry, one of our most profitable economic activities.