Carrot Genome Resources

Carrot genome resources

• Link to the carrot genome publication at Nature Genetics http://www.nature.com/ng/journal/v48/n6/full/ng.3565.html
• The carrot genome assembled sequences and annotations may be obtained from the following online resources:
  • At GenBank under the accession LNRQ00000000
  • At Phytozome https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Dcarota
  • At CarrotOmics https://carrotomics.org/bio_data/79609
• The version described in the publication is version LNRQ01000000.
• All raw reads have been deposited at the Sequence Read Archive (SRA) under umbrella project PRJNA285926, accessions SRP062070, SRP062113, and SRP062159.
• List of resequenced biosamples.
• Variants described in the publication have been submitted to dbSNP, however dbSNP has dropped support for plant genomes, so the a copy of the vcf file submitted to dbSNP is here:
  58.pubsnpavLNRQ.vcf.gz and checksum file 58.pubsnpavLNRQ.vcf.gz.md5.txt
  And dbSNP has archived the data at
  ftp://ftp.ncbi.nih.gov/snp/organisms/archive/carrot_79200/
  (Former dbSNP links, now non-functional: Search, FTP)
• Custom programs referenced by the materials and methods.
• Short URL to this page http://vcru.wisc.edu/cgr

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Frequently asked questions about the carrot genome

What important discoveries come from sequencing the carrot genome?

The discovery of a candidate gene for the Y locus, which conditions the accumulation of carotenoid pigments in carrot roots. In previous work we were able to map the trait and also genes in the carotenoid biosynthetic pathway, but none of those genes involved in carotenoid biosynthesis mapped with the Y locus. With a well-characterized genome available, we discovered a candidate for that important gene. The Y locus is one of the two genes responsible for converting white carrots (ancestral wild type) to orange.

A better understanding of plant evolution. Genomes in the Euasterid II branch of the plant phylogenetic tree that includes crops like carrot, celery, lettuce, and sunflower had not been sequenced, or were unpublished, before the sequencing of the carrot genome. Carrot diverged from grape ~113 million years ago, from kiwi ~101 million years ago, and from potato and tomato ~90.5 million years ago. With the release of the carrot genome sequence, the evolution of this group of plants is better understood.

Who will use the carrot genome sequence?

The immediate users of the whole genome sequence will be public and private plant breeders who will use it for marker-assisted selection they have underway for carrot disease resistance and seed production traits. There are also several laboratories that conduct fundamental research on carrot pigments, biotic and abiotic stress response, growth, reproduction, and evolution that will find the genome sequence useful.

How might knowledge about the carrot genome have application in improving dietary nutrients we get from plants in our diet?

There are several possibilities. The identification of a candidate for the Y gene in carrot may provide insights to identify similar mutations in sequenced genomes of other crops, or to generate similar mutations with genome editing technologies. This could be applicable in other root crops such as cassava. Similar mutations are known to influence pigment accumulation in fruit crops, so there may be application beyond root crops.

How might the carrot genome be useful in studying other traits in carrot?

The genome will contribute to our understanding of genes and biosynthetic pathways for other carrot traits, including genes influencing accumulation of carotenoids, anthocyanins, carbohydrates and flavor terpenoids; pest and disease resistance; abiotic stress responses; plant reproduction and growth. In turn, a better understanding of the carrot genome will help make plant breeding efforts more efficient and effective for carrot and related crops.

Has the full genome sequence been published for other vegetables?

Yes, to date over 100 plant genomes have been sequenced including the genomes of about 11 vegetable crops (e.g. potato, tomato, cucumber, pepper).

More information about completed plant genomes can be found at the following websites:
https://genomevolution.org/wiki/index.php/Sequenced_plant_genomes
https://phytozome.jgi.doe.gov/pz/portal.html
http://www.ncbi.nlm.nih.gov/genome/browse/