Over the past years metagenomics approaches have opened novel doors for exploring the sanitary status and the genetic diversity within and between plant species in a high-throughput and cost-effective manner. From the applicative point of view metagenomics may help in carrying out a fine characterization and valorisation of the autochthonous plant Germplasm. Autochthonous varieties of plants were selected since hundreds years to obtain plant population with specific resilience to biotic and abiotic stresses in local environments.
Within the project SaveGraINPuglia (http://savegrainpuglia.ibbr.cnr.it/) led by IBBR-CNR, we have one activity aiming mainly to evaluate the sanitary status of black and red Chickpea of “Cassano delle Murge” to either analyse known viruses by means of a reference-guided approach or to discover novel viruses using a de novo-based strategy. Metagenomics approaches are currently used for a fine molecular characterization of those varieties with a particular attention to the functionality of small non-coding RNAs and to the degradation products of mRNAs.