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Carrot Genome Sequenced

NEW YORK (GenomeWeb) – An international team has sequenced and begun an analysis of the genome of the carrot, Daucus carota.

The new, high-quality genome assembly, which the researchers established for an orange doubled-haploid carrot, contains more than 32,000 predicted protein-coding genes. As the researchers reported today in Nature Genetics, they were able to track down a candidate gene involved in orange carrot pigmentation and gained insight into the evolution of plants in the euasterid II lineage, which contains carrots, lettuce, sunflower, celery, and parsley.

"The motivation was to get as complete a genome for carrot as we could … for basic knowledge reasons and from the standpoint of crop improvement," senior author Philipp Simon, a horticulture researcher affiliated with the University of Wisconsin at Madison and the US Department of Agriculture's Agricultural Research Service, told GenomeWeb. "It gives us a better handle on genomic regions to track when we're in the plant breeding process, and to get a better handle on the process of gene expression in both basic and applied applications."

He also noted that the results are generating interest amongst carrot breeders in the public sector, at academic institutions, and seed companies.

Domesticated yellow and purple carrots have existed for more than 1,000 years, Simon and his co-authors wrote. And in the past four decades or so, production of the more familiar orange carrot has increased roughly four-fold. Alongside its growing popularity, the plant's nutritional value has been enhanced as well, with rising levels of alpha- and beta-carotene pigments rich in vitamin A.

To delve into carrot traits and the history of the euasterid II clade, the researchers performed Illumina paired-end sequencing on libraries with a range of insert sizes on an orange, doubled-haploid, Nantes-type carrot called DH1, which has an estimated genome size of 473 million bases. The sequence data was then combined with bacterial artificial chromosome end reads and linkage map data.

They also sequenced RNA from 20 DH1 carrot tissues and did genome re-sequencing on representatives from 35 carrot accessions spanning several D. carota sub-species or outgroups.

The reference genome assembly spanned 421.5 million bases, with nearly half of assembled sequences stemming from transposable elements and other repetitive sequences. The team's annotation efforts uncovered 32,113 predicted protein-coding genes — including thousands of suspected regulatory genes — along with almost 250 microRNAs, and more than 1,000 more non-coding RNAs.

"It's a relatively small genome," Simon said, "and that certainly played into our ability to be able to say that … it's one of the most complete [plant genomes] in coverage and contiguity."

From the re-sequencing data, the researchers identified almost 1.4 million high-quality SNPs, which they used to cluster the carrot accessions into groups coinciding with plant geography, origins in Central Asia, and cultivation history.

The researchers also compared the carrot genome to sequences from more than a dozen other plants ranging from potato and tomato plants in the euasterid I clade — which diverged from carrot ancestors around 90.5 million years ago — to more distantly related grape and kiwi plants. They saw evidence of two past whole-genome duplications in the carrot lineage, one taking place roughly 70 million years ago, with a more recent duplication occurring an estimated 43 million years ago.

Meanwhile, the researchers' fine mapping search for genes related to key carrot traits led them to a candidate gene called DCAR_032551 on chromosome 5 that appears to influence the accumulation of the carotenoid pigment, turning otherwise white carrots orange. That pigment is mainly found in domestic carrots, Simon explained, and was not documented prior to the 16th century when it first appeared in Europe.

The team is now following up on this and other leads from the study, including genes that may contribute to the production of anthocyanin, lycopene, and lutein pigments that lend some carrots their purple, red, and yellow coloring, respectively. Simon noted that the researchers are also investigating genes involved in resistance to plant disease or pests such as nematodes, and genes that mediate key plant growth features or response to abiotic stressors such as drought.