Assembly and development of Cichorium endivia transcriptome to assess identity and traceability of endives and escaroles. Endives (Cichorium endivia var. crispum) and escaroles (C. e. latifolium) are widely consumed as fresh, minimally processed and cooked food. Italy is a major world consumer and producer. The project CISIA (www.ibba.mlib.cnr.it/Projects/Cisia/Project.html) has been developing markers (metabolic, transcriptional and allelic variants) used for identity, traceability and valorisation of curly- and broad- leafed cultivars in collaboration with the Enza Zaden Group. A de novo transcriptome was assembled (reference cultivar 'Domari') using RNA of several organs (from young and adult plants) and Illumina HiSeq2000 technology (100bp paired-end), which generated ca. 240M reads. The filtered reads were assembled into 91,784 contigs (77,360 unigenes) with an average length of ca. 1,202bp (N50 = 1,545bp). As for the unigenes, 68,858 (75.0%) showed significant similarity (E-value <1e-5) to proteins in public databases (NCBI, TAIR, SwissProt, TrEMBL); 64,870 (70.7%) were classified based on gene ontology criteria and 15,161 (16.5%) were mapped onto 130 KEGG pathways. The 'Domari' and 'Myrna' (curly-leaf type) and 'Confiance', and 'Flester' (broad -leaf type) cultivars were re-sequenced (ca. 20M of 50bp single-end reads) using edible leaves at harvest. Transcriptome expression variation of 'Domari' vs 'Myrna' and 'Confiance' vs 'Flester' were found and 906 and 1,873 genes, respectively, maintained the differential expression patterns through two production cycles (2011 and 2012), suggesting that they may be feebly dependent on the environment and intra-varietal potential markers. The SNPs were selected on RNA-seq data and validated by high resolution melting technology using genomic DNA. High-quality SNPs profiles were effective to fingerprint each cultivar from the other three. The genetic similarity was higher within the endive than the escarole group. These markers are envisaged to be used for genotype traceability and functional map enrichment for assisted breeding.
Assembly and development of Cichorium endivia transcriptome to assess identity and traceability of endives and escaroles
Testone G;Mele G;Di Giacomo E;Nicolodi C;Frugis G;Giannino D
2014
Abstract
Assembly and development of Cichorium endivia transcriptome to assess identity and traceability of endives and escaroles. Endives (Cichorium endivia var. crispum) and escaroles (C. e. latifolium) are widely consumed as fresh, minimally processed and cooked food. Italy is a major world consumer and producer. The project CISIA (www.ibba.mlib.cnr.it/Projects/Cisia/Project.html) has been developing markers (metabolic, transcriptional and allelic variants) used for identity, traceability and valorisation of curly- and broad- leafed cultivars in collaboration with the Enza Zaden Group. A de novo transcriptome was assembled (reference cultivar 'Domari') using RNA of several organs (from young and adult plants) and Illumina HiSeq2000 technology (100bp paired-end), which generated ca. 240M reads. The filtered reads were assembled into 91,784 contigs (77,360 unigenes) with an average length of ca. 1,202bp (N50 = 1,545bp). As for the unigenes, 68,858 (75.0%) showed significant similarity (E-value <1e-5) to proteins in public databases (NCBI, TAIR, SwissProt, TrEMBL); 64,870 (70.7%) were classified based on gene ontology criteria and 15,161 (16.5%) were mapped onto 130 KEGG pathways. The 'Domari' and 'Myrna' (curly-leaf type) and 'Confiance', and 'Flester' (broad -leaf type) cultivars were re-sequenced (ca. 20M of 50bp single-end reads) using edible leaves at harvest. Transcriptome expression variation of 'Domari' vs 'Myrna' and 'Confiance' vs 'Flester' were found and 906 and 1,873 genes, respectively, maintained the differential expression patterns through two production cycles (2011 and 2012), suggesting that they may be feebly dependent on the environment and intra-varietal potential markers. The SNPs were selected on RNA-seq data and validated by high resolution melting technology using genomic DNA. High-quality SNPs profiles were effective to fingerprint each cultivar from the other three. The genetic similarity was higher within the endive than the escarole group. These markers are envisaged to be used for genotype traceability and functional map enrichment for assisted breeding.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
