Progress towards a reference genome for sunflower

Abstract

The Compositae is one of the largest and most economically important families of flowering plants and includes a diverse array of food crops, horticultural crops, medicinals, and noxious weeds. Despite its size and economic importance, there is no reference genome sequence for the Compositae, which impedes research and improvement efforts. We report on progress toward sequencing the 3.5 Gb genome of cultivated sunflower ( Helianthus annuus ), the most important crop in the family. Our sequencing strategy combines whole-genome shotgun sequencing using the Solexa and 454 platforms with the generation of high-density genetic and physical maps that serve as scaffolds for the linear assembly of whole-genome shotgun sequences. The performance of this approach is enhanced by the construction of a sequence-based physical map, which provides unique sequence-based tags every 5–6 kb across the genome. Thus far, our physical map covers ∼85% of the sunflower genome, and we have generated ∼80× genome coverage with Solexa reads and 15.5× with 454 reads. Preliminary analyses indicated that ∼78% of the sunflower genome consists of repetitive sequences. Nonetheless, ∼76% of contigs >5 kb in size can be assigned to either the physical or genetic map or to both, suggesting that our approach is likely to deliver a highly accurate and contiguous reference genome for sunflower.

Genomic islands of divergence are not affected by geography of speciation in sunflowers

“…For example, empirical studies of genomic divergence often report higher levels in regions of low recombination 25 . Recombination rates across the sunflower genome were inferred by comparing our high-density genetic map to a physical map recently developed for H. annuus 23,26 ( Supplementary Figs S5 and S6). We found that overall, recombination rates were negatively correlated with F ST (r 2 ¼ 0.14, Pearson correlation coefficient test, P-value o2.2e À 16, Supplementary Fig.…”

Changes in sunflower breeding over the last fifty years

“…However, the genes actually involved in the character are known only in a few cases. A new step forward for sunflower in 2010 was the International sequencing initiative, led by Rieseberg at British Columbia University, Canada (a return of Canada to the sunflower research scene), together with American, French and Argentinean collaboration (Kane et al, 2011). Using the Illumina/454 technique, the sequence of the USDA inbred line HA412OL should be available very soon, together with those of two French lines (XRQ and PSC8), sequenced by INRA using the new technique PacBio.…”

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

“…This higher alignment percentage stresses the importance of the genome because oil palm has a complete genome sequence (Singh et al 2013) while the current assembly of the sunflower genome represents only 85 % of the complete genome. Although the draft genome of sunflower is not complete, the assembled genome is highly accurate and contiguous because most (more than 76 %) of the contigs larger than 5 kb were assigned to the physical and/or genetic map (Kane et al 2011). The present study implemented the GBS approach for SNP discovery in sunflower.…”