Title

Progress Towards a Reference Genome for Sunflower

Authors

N. C. Kane, The University of British Columbia
Navdeep Gill, The University of British ColumbiaFollow
M. G. King, The University of British Columbia
J. E. Bowers, University of Georgia
H. Berges, Institut national de la recherche agronomique
J. Gouzy, Institut national de la recherche agronomique
E. Bachlava, Monsanto Vegetable Seeds
N. B. Langlade, Institut national de la recherche agronomique
Z. Lai, Center for Genomics and Bioinformatics
M. Stewart, The University of British Columbia
J. M. Burke, University of Georgia
C. Vincourt, Institut national de la recherche agronomique
S. J. Knapp, Monsanto Vegetable Seeds
L. H. Rieseberg, The University of British Columbia

Document Type

Article

Publication Date

8-3-2011

Publication Title

Botany

Keywords

Compositae, Helianthus annuus, next generation sequencing, physical map, reference genome, sunflower

ISSN

1916-2804

Volume

89

Issue/No.

7

First Page

429

Last Page

437

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.

NSUWorks Citation

Kane, N. C.; Navdeep Gill; M. G. King; J. E. Bowers; H. Berges; J. Gouzy; E. Bachlava; N. B. Langlade; Z. Lai; M. Stewart; J. M. Burke; C. Vincourt; S. J. Knapp; and L. H. Rieseberg. 2011. "Progress Towards a Reference Genome for Sunflower." Botany 89, (7): 429-437. doi:https://doi.org/10.1139/b11-032.

ORCID ID

http://orcid.org/0000-0003-3746-1866

DOI

https://doi.org/10.1139/b11-032