Globe artichoke (Cynara cardunculus var. scolymus) is an out-crossing, perennial, multi-use crop species that is grown worldwide and belongs to the Compositae, one of the most successful Angiosperm families. We describe the first genome sequence of globe artichoke. The assembly, comprising of 13,588 scaffolds covering 725 of the 1,084 Mb genome, was generated using ~133-fold Illumina sequencing data and encodes 26,889 predicted genes. Re-sequencing (30×) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1×) genotyping-by-sequencing of 163 F1 individuals resulted in 73% of the assembled genome being anchored in 2,178 genetic bins ordered along 17 chromosomal pseudomolecules. This was achieved using a novel pipeline, SOILoCo (Scaffold Ordering by Imputation with Low Coverage), to detect heterozygous regions and assign parental haplotypes with low sequencing read depth and of unknown phase. SOILoCo provides a powerful tool for de novo genome analysis of outcrossing species. Our data will enable genome-scale analyses of evolutionary processes among crops, weeds, and wild species within and beyond the Compositae, and will facilitate the identification of economically important genes from related species.

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The influence of the holoparasite branched broomrape on the vegetative growth, leaf chlorophyll content, photosynthetic rate, and chlorophyll fluorescence of tomato was studied over two growing seasons on plants grown in a commercial greenhouse. The presence of the parasite strongly reduced the aerial biomass by acting as a competing sink for assimilate, but more importantly, by compromising the efficiency of carbon assimilation via a reduction in leaf chlorophyll content and photosynthetic rate. The chlorophyll fluorescence parameters F0, Fm, Fv, and Fv/Fm were all altered in parasitized plants, indicating that branched broomrape–infected plants are more susceptible to photoinhibition. The degree of damage to the host was not dependent on either the number or the biomass of parasitic plants per host plant. We suggest that the ability to maintain a high photosynthetic rate, leaf chlorophyll content, or both and the ability to minimize photoinhibition can be developed as indirect assays for improved tolerance to branched broomrape.

Tomato cultivation in the Mediterranean region is susceptible to infestation by the parasitic weed branched broomrape (Orobanche ramosa), and severe yield losses can result. The effectiveness of solarization, a soil disinfection technique that uses passive solar heating, to control the incidence of broomrape under greenhouse conditions was studied over two growing seasons. Solarization was accomplished by the application of clear polyethylene sheets to moist soil for 58 to 61 d during the hot season. The treatment increased maximum soil temperature by around 10 C, and at 5 cm below the soil surface, a temperature of more than 45 C was reached for 34 to 58 d, whereas this temperature was not reached at all in the first season and not for 20 d (second season) in unmulched soil. In solarized soil, no broomrape shoots emerged, and neither haustoria nor underground tubercles of the parasite were found on tomato roots. The treatment killed about 95% of buried viable seed, and induced secondary dormancy in the remaining 5%. In nonsolarized plots, broomrape shoots were present at a high density, decreasing plant growth and fruit production. Fruit yield was 133 to 258% higher in the solarized as compared with the nonsolarized treatment. Based on these results, we suggest that soil solarization, which precludes chemical contamination and is suitable for organic farming, is an appropriate technology where the risk of branched broomrape infestation is high.