Chloroplast omics of endive (Cichorium endivia L.): characterising genome structural variants and differential transcription in response to environment changes and stress.

Surveys on chloroplast (cp) genome diversity have been useful for phylogeny and marker-based DNA barcoding applicable to molecular breeding registration/legal protection of cultivars. Moreover, chloroplast functions in stress response have emerged by transcriptomic investigations. Smooth- and curly-leafed endives (C. endivia var. latifolia and var. crispa) are of nutritive and economic importance in the market segments of primary a minimally processed produce, and fall into breeding programs of public and private seed companies. So far, the endive cp genome sequence has not been released yet, hence we assembled and annotated that of the smooth-leafe cultivar 'Confiance' as reference, which was 152809 base pairs organized into the angiosperm-typical quadripartite structure harboring the inverted repeats IRA and IRB separated by the large- and short- single copy regions. The annotation included 137 genes, 91 coding regions, 37 tRNAs and 9 rRNAs. Starting from the notion that cp DNA is nearly fully transcribed, cp diversity of seven cultivars/genotypes was addressed by using RNA-se reads that covered over 70% of the reference cp genome. DNA and sequence diversity within 'Confiance' included variants in 40 genes a supported heteroplasmy and RNA editing phenomena. In addition, ca. variants among the cultivars included few genotype-specific polymorphysms and were effective to separate them in phylogenetic trees. transcriptome expression was assayed in smooth and curly cultivars th underwent short-term waterlog before harvest (due to rainfall exc versus those grown in normal regime. Overall, a eighteen gene set, whic included those encoding photosystem I and II proteins, was commonly down- regulated in all stressed genotypes, supporting events of photosynthesi impairment as observed also by the general drop of sugar levels.