A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.

Dariusz Grzebelus,Douglas Senalik,Emilia Morańska ,Shelby Ellison,Allen Van Deynze,Zhijun Zheng,Philipp W Simon ,Megan J Bowman ,Mehtap Yıldız ,Massimo Iorizzo,Walter Sanseverino,Pablo Federico Cavagnaro ,Alicja Macko-Podgórni,Ewa Grzebelus,Jiaying Huang,Marina Iovene,Peng Zeng,Hamid Ashrafi,Pimchanok Satapoomin,David M Spooner ,Shifeng Cheng

doi:10.1038/ng.3565

Abstract

We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.

Highlights

Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions[1]
We report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus
The high-quality carrot genome sequence described here, in combination with mapping and comparative transcriptome analysis, demonstrates that carotenoid accumulation in carrot is controlled at the regulatory level and that root de-etiolation leading to overexpression of the photosynthetic transcriptome cascade may have an important role in this regulatory mechanism

Summary

Introduction

Statistics; see URLs) through development of high-value products for fresh consumption, juices, and natural pigments and cultivars adapted to warmer production regions[1]. The first documented colors for domesticated carrot root were yellow and purple in Central Asia approximately 1,100 years ago[2,3], with orange carrots not reliably reported until the sixteenth century in Europe[4,5]. Lycopene and lutein in red and yellow carrots, respectively, are nutritionally important carotenoids, making carrot a model system to study storage root development and carotenoid accumulation. We report a high-quality genome assembly of a doubledhaploid orange carrot, characterization of the mechanism controlling carotenoid accumulation in storage roots, and the resequencing of 35 accessions spanning the genetic diversity of the Daucus genus. Our comprehensive genomic analyses provide insights into the evolution of the asterids and several gene families. These results will facilitate biological discovery and crop improvement in carrot and other crops

Methods

Results

Conclusion