Media constantly refer of unscrupulous producers that adulterate, alter or replace premium products in food chains with the goal to maximize illegally profits. Food traceability is a central issue for the identification of improper labeling of processed food and feed and there are rules aimed to protect consumers and producers against fraudulent substitution of quality products in food chain, but the tools available are not always appropriate. DNA-based markers proved very effective for fresh and processed food molecular authentication. In this review, we illustrate potential and limits of different DNA markers focusing on low, medium and high-throughput markers, in order to monitor the genetic identity of food components in meat, fish and plants net-chains.

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The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, we generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing (RNA-seq), more than 90% of the reads (over one billion, derived from twelve dataset) were aligned to the tomato reference genome. We report a comprehensive analysis of the transcriptome, improved with 39,095 transcripts, which reveals previously unannotated novel transcripts, natural antisense transcripts, long non-coding RNAs and alternative splicing variants. In addition, we investigated the sequence variants between the cultivars under investigation to highlight their genetic difference. Our strand-specific analysis allowed us to expand the current tomato transcriptome annotation and it is the first to reveal the complexity of the poly-adenylated RNA world in tomato. Moreover, our work demonstrates the usefulness of strand specific RNA-seq approach for the transcriptome-based genome annotation and provides a resource valuable for further functional studies.

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Cucurbita pepo belongs to the Cucurbitaceae, the second-most large horticultural family of economic importance after Solanaceae. One major issue related to zucchini cultivation is the damage caused by aphids such as Aphis gossypii (Homoptera: Aphididae). The aim of this study is the identification of candidate genes involved in zucchini plant response to A. gossypii. In order to monitor the effect of zucchini-aphid interaction at transcriptomic level, zucchini plants (cv “San Pasquale”) were grown in controlled conditions in presence or absence of A. gossypii. Leaf material was collected at 24, 48 and 96 hours after aphid infestation. RNA extracted was sequenced using the Illumina HiSeq 2500 platform. The sequencing generated ~34 million of paired-end reads of 100 nucleotides in length per sample. High quality reads were de novo assembled into 71,648 transcripts. About 94% of the assembled transcripts contain coding sequences that could be translated into proteins. Over 60% of the transcripts were functionally annotated and assigned to one or more InterPro domains and Gene Ontology terms. A subset of 42,517 sequences of the C. pepo transcriptome was used for read mapping and differentially expressed genes (DEG) identification. Largest number of DEG were observed after 48 hours from aphid infestation. The transcriptome represents a high-quality reference for read alignment and DEG call. The understanding of the molecular response of infested plants will be essential to develop new tools for A. gossypii control.

The agri-food components of the Made in Italy are well known all over the world, therefore they may significantly contribute to the Italian economy. However, also owing to a large number of cases of improper labelling, the Italian agro-food industry faces an ever-increasing competition. For this reason, there is a decline of consumers’ confidence towards food production systems and safety controls. To prevent erroneous classification of products and to protect consumers from false instore information, it is important to develop and validate techniques that are able to detect mislabelling at any stage of the food-chain. This paper describes some examples of genetic traceability of primary products in some important plant food chains such as durum wheat, olive and tomato, based on DNA analysis both of raw material and of processed food (pasta, olive oil, and peeled tomato).

Cucurbita pepo belongs to the Cucurbitaceae, the second-most large horticultural family of economic importance after Solanaceae. One major issue related to zucchini cultivation is the damage caused by aphids such as Aphis gossypii (Homoptera: Aphididae). The aim of this study is the identification of candidate genes involved in zucchini plant response to A. gossypii. In order to monitor the effect of zucchini-aphid interaction at transcriptomic level, zucchini plants (cv "San Pasquale") were grown in controlled conditions in presence or absence of A. gossypii. Leaf material was collected at 24, 48 and 96 hours after aphid infestation. RNA extracted was sequenced using the Illumina HiSeq 2500 platform. The sequencing generated ~34 million of paired-end reads of 100 nucleotides in length per sample. High quality reads were de novo assembled into 71,648 transcripts. About 94% of the assembled transcripts contain coding sequences that could be translated into proteins. Over 60% of the transcripts were functionally annotated and assigned to one or more InterPro domains and Gene Ontology terms. A subset of 42,517 sequences of the C. pepo transcriptome was used for read mapping and differentially expressed genes (DEG) identification. Largest number of DEG were observed after 48 hours from aphid infestation. The transcriptome represents a high-quality reference for read alignment and DEG call. The understanding of the molecular response of infested plants will be essential to develop new tools for A. gossypii control.PeerJ PrePrints | https://doi.org/10.7287/peerj.preprints.1635v1 | CC-BY 4.0 Open Access |