The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny

Abstract

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.

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

“…DNA transposons were annotated with a custom pipeline that includes the 'gt tirvish' command, which is part of the GenomeTools suite 42 . The age of LTR-RTs was determined by obtaining a likelihood divergence estimate between the LTRs with baseml from PAML 43 16 , coffee 17 and lettuce 15 and with grape 18 as the outgroup. Identification of orthology and paralogy relationships, measurements of sequence divergence and estimation of divergence time through the level of synonymous substitutions were performed as detailed in Supplementary Note 3.1 on the basis of the methods described in ref.…”

“…Flowering time genes in A. thaliana were retrieved from a recently developed database, FLOR-ID 20 , which includes 295 protein-coding genes and 11 miRNA genes and describes their interactions. We built gene clusters for a set of seven species, namely H. annuus, A. thaliana, Cynara cardunculus, Oryza sativa, Hordeum vulgare, Brassica rapa and Populus trichocarpa, chosen to be consistent with a previous study that identified orthologues for more than 30 flowering-time genes in the sunflower 21 , adding the proteome of the recently sequenced member of Asterids II C. cardunculus 16 . To identify orthologues and in-paralogues (that is, paralogues post-dating speciation) of A. thaliana genes, we built and visually examined trees for the clusters defined above (Supplementary Note 6.2) and manually screened BLAST reports on the sunflower genome browser.…”

“…We identified orthologous genes between the sunflower and grape-coffeelettuce-artichoke as well as paralogous genes within the sunflower (Supplementary Data 2 and Supplementary Note 3.1), coffee and artichoke genomes. In addition to WGT-γ (common with grape, artichoke, lettuce, coffee and sunflower) we established that sunflower, lettuce and artichoke experienced a whole-genome triplication (WGT-1) 15,16 , which has recently been proposed as independent genome duplications that are close in time 6 . A minimum of 3 chromosomal fissions and 57 chromosomal fusions were necessary for the lettuce to reach its current structure of 9 chromosomes, and 14 fissions and 60 fusions for the artichoke to reach 17 modern chromosomes.…”

“…To assess the palaeohistory of the Asterid family, we performed a comparative genomic investigation of the sunflower with lettuce 15 and artichoke 16 as representatives of Asterids II, coffee as a representative of Asterids I (ref. 17) and grape 18 as an outgroup.…”

“…We used the pathway-tools software 51 to infer biochemical reactions and metabolic pathways from the protein annotations. The super pathway of sunflower oil metabolism was created on the basis of the main components of the known sunflower oil metabolism by merging 16 …”