| Name | Description |
|---|---|
An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4. There are a few different naming schemes for this assembly. First there is the Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0 LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926. Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence. RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records. The NCBI Sequence report lists the correspondences between the various naming methods Link to the LNRQ01000000.1 master record at NCBI Raw Reads: Link to SRA accessions used for the genome assembly This genome is available in the CarrotOmics Blast Search | |
The RefSeq genome records for Daucus carota subsp. sativus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results. View the full report at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Daucus_carota_subsp._sativus/100/ Data from this analysis can be viewed in JBrowse here. |
ATGGCGCGGAGGAAACTTATGGCTAGGCTCCGGAGGAGCAATTTGTACAC
ATTTTCGCATATTAATCGCGCACATCATCAATCAGCTCAACAAGACATCA
TTGATTTTGGATATCCAAGAACGATATACTGCAACCAAATATTCCAACCA
TTTCAAAAGAGGAGCTTGATATATTGTGGCAATGATATATCTACCACAAA
ATATAGTGTTGCCACATTTTTACCAAAAGCCCTTCATGAGCAATTCAACC
GGGTGGCCAATATTTATTTTCTCATTGCGGCTGTCCTATCCACCACCCCC
TACGGTCCATTCTCGCCTTTTAGTGCAATTGCACCTTTAGCCTTTGTTGT
AGGGTTAAGTATGGTGAAAGAATTGATGGAAGATTGGCGGAGGTTCTTGC
AAGATCACAAGGTTAACATGCGCGATGCTGATGTGCATATTGGGGGTGGC
TTTTTTGGGATAAAACCTTGGAAAGAAGTGATGGTTGGAGATGTTATAAA
AGTTCATAAGGATCAGTTTTTTCCTGCTGATTTACTGCTACTGTCATCTG
TTTATGATGATGGGATGTGTTACGTGGAGACGATGAATTTAGATGGAGAG
ACAAATTTGAAGGCAAAAAGGGCTCTAGAGGCTACAATGGGGTTGGTTGA
GGATGGATATTTCAAAGATTTTAATGATGCTATTATTAGATGTGAAGATT
CGAATTCTAGTCTTTATACTTTTGTGGGAAATATTGAATATGATCATAAA
GTGTATAATCTTGATCCCAATCAAATTCTTCTACGTGATTCAAAGTTGAG
GAACACAGACTATGTCTATGGAGTTGTTATATATACAGGCCATGAAACAA
AAGTTATGCAAAATTCTACCAAGTCTCCTTCGAAGAGAAGCAGGATTGAG
AAGCAGATGGATAAAATTATTTACATTCTTTTTACACTCCTAATTTTGGT
ATCAGCTGTGAGCTCCATAGAATTTGCTTATATGACAAAATCAGATATGC
CTGACTGGTGGTACTTAAAAGCCCCTGATCGAAATCATTTGTATGATCCT
GATCAGCCCGTTACCTCAGGCGTTTACCATCTAATCACTGCACTGATTTT
GTATGGTTATCTGATTCCTATTTCTCTCTACGTTTCAATTGAGCTTGTGA
AAGTTTTGCAAGCAAGTTTCATTAATAAAGATGTGAATATGTATGATTAT
CAGACTTTAACTCCCGCACAAGCACGGACATCAAATTTGAATGAGGAGTT
AGGGCAAGTTGACACAATTCTGTCTGATAAAACAGGAACATTGACATGCA
ATCAGATGGAATTTCTCAAGTGTTCTATAGCTGGGATTGCATATGGAAAG
CGATCTAGTGAAGTTGAGCTGGCTGCTGCTAAGAAGATGGCTAAGGATCT
TGATGGAAATGACCCGGATTTCATGAGCTTTCAAGTTTCAAAATCCAATG
AAGTGGAATTGGAGTGTGTGATCACATCAAATGGTAATGAGAATAGTGAC
GATGCAACTGCAATAAGAGGATTTAGCTTTGAGGATGATCGTCTGATGAA
TGGGAATTGGTATAAAGAAAAATATGCTGATTTTCATTTATTATTTTTTC
GGATACTTGCAGTTTGTCACACTGCTATTCCGGAGTTAAATGATGAAACA
GGCGCATTAACTTATGAAGCAGAGTCACCTGATGAAGGATCTTTTCTTGT
TGCAGCCAGAGAATTCGGGTTTGAGTATTCTAGAAGAACTCATGCAAGCA
TCTTTGTACGTGAGATGGAGCCTTCAACTGGAGAAACTATCGAGAGGGAG
TTTAAGCTTCTCAATTTGTTGGATTTTACTAGCAAAAGAAAGCGAATGTC
TGTCATTGTGCGTGACGAGGAGGGGAAGATTTTCCTCTTATGCAAAGGTG
CAGACACAATTATCTTTGATAGATTATCAGAAGAGGGAAGAATGTTTCAA
GAATCTACAACAAAGCATCTTCATGATTATGGGGATGCAGGGTTGCGCAC
ACTTGTGTTTGCTTATAGAAAGTTAGAAGAGGCGGATTTTAATGCCTGGA
ATGATGAGTTCATGAATGCTAAGAATAACATGTCTAATGATAGGGATGAA
ACACTTGAACGTTTATCGGATGAAATGGAGAAGAATTTGATACTTGTTGG
TGCGACAGCTGTGGAGGACAAACTCCAGAAAGGAGTGCCTCAGTGTATAG
ACAAGCTTGCACAAGCTGGTCTCAAAATATGGGTTCTGACAGGTGATAAA
ATGGAAACAGCAATCAATATTGGATTTTCATGCAGTCTTCTCCGTCAAGG
GATGCAACAAATTTGCATAACTACGAATGATCAAGACACAATGCAAGGTA
TAAAATCAGATATTATGATGCAAATCACCAGTGGCACAAAAATGATAAAC
GTAGAGAAAGACCCTCATGCTGCATTTGCCTTGATCATTGATGGTAAAAC
GTTAACTTATGCTTTAGAGGATGAAGTGAAGCATCAGTTCTTGCACCTTG
CAGTCCATTGTGCATCTGTAATATGTTGTCGTGTGTCTCCTAAGCAAAAA
GCATTGGTAACAAGGTTGGTAAAAGAAGGGACGGGGAAGACAACACTGGC
TATTGGAGACGGAGCAAATGATGTAGGAATGATTCAAGAAGCTGATATCG
GTGTAGGCATTAGTGGAGTTGAAGGAATGCAAGCTGTAATGTCAAGTGAC
TTTGCGATAGCACAATTCAGATTTCTTGAGAGACTTCTTGTAGTTCATGG
ACATTGGTGCTACAAAAGAATTGCACAAATGATATGCTATTTCTTCTACA
AGAACGTGGCTTTTGGCCTTACAATCTTCTATTATGAAGCCTGCACAGGT
TTCTCAGGTAGCTCCATATATGACGACTGGTACATGATTCTATACAACGT
TGCTGTTACATCTTTGCCGGTGATTTCACTTGGTGTGTTTGAACAAGATG
TCACGTCCGAAATCTGCTTACAGTTTCCAGCACTCTACCAACAAGGCCCT
CAAAACTTGTTTTTTGGATGGTATCGAATCATCGGCTGGATCTGCAATGG
AGTGTATACATCCCTAGCCATATTTTTTCTCAATATTATAGCCTTCACTT
ATGACCCTTTTCGCTCAGATGGTCAAACAACTGATATGAGCATTGTTGGA
GCAGGAATGTTCACTACAATTGTTTGTGCGGTAAATGTTCAAATAGCTCT
TGCATTGAGTCACTTCACTTGGATACAACACATTCTTATATTGGGCAGCG
TTATAGTTTGGTTTGTGTTTCTTGTAATCTACGGGGGAATGCCCCCAGAA
TATTCACACAGTGCCTTCCATGTCTTTGTGGAGACATTAGCCCCTTCACC
GATATTCTGGATAATCTCGGTTTTAGTAGTGGTGGCATGTAACTTCCCAT
ACTTCATACATATTGCTTTCCAGAGATCGTTTCATCCGATGGATCATCAC
GTTATTCAGGAGATGGTGTACTACAACAAACACGTCGAAGATCATCAAAT
GTGGAAAAGAGAAAGAAGAAAAGGAAGAAGAAAGGCTAAATTTGGATTCA
CTGCAAGAGTTGATGAAAAGATTAGGCAATTAAAACATAAGCTCCATGGG
AGACCCTCTACTCTCACTTTGGACAGTCCGCAGCATGTATAGTTCCATAG
TGTAACCAAAATTTCACCATAGGACAATTCTTTAAGTAATTGTAATTAAG
TTTATTAAGACACAGAAAGTCATTAAAACAAAATTCTT
MARRKLMARLRRSNLYTFSHINRAHHQSAQQDIIDFGYPRTIYCNQIFQP
FQKRSLIYCGNDISTTKYSVATFLPKALHEQFNRVANIYFLIAAVLSTTP
YGPFSPFSAIAPLAFVVGLSMVKELMEDWRRFLQDHKVNMRDADVHIGGG
FFGIKPWKEVMVGDVIKVHKDQFFPADLLLLSSVYDDGMCYVETMNLDGE
TNLKAKRALEATMGLVEDGYFKDFNDAIIRCEDSNSSLYTFVGNIEYDHK
VYNLDPNQILLRDSKLRNTDYVYGVVIYTGHETKVMQNSTKSPSKRSRIE
KQMDKIIYILFTLLILVSAVSSIEFAYMTKSDMPDWWYLKAPDRNHLYDP
DQPVTSGVYHLITALILYGYLIPISLYVSIELVKVLQASFINKDVNMYDY
QTLTPAQARTSNLNEELGQVDTILSDKTGTLTCNQMEFLKCSIAGIAYGK
RSSEVELAAAKKMAKDLDGNDPDFMSFQVSKSNEVELECVITSNGNENSD
DATAIRGFSFEDDRLMNGNWYKEKYADFHLLFFRILAVCHTAIPELNDET
GALTYEAESPDEGSFLVAAREFGFEYSRRTHASIFVREMEPSTGETIERE
FKLLNLLDFTSKRKRMSVIVRDEEGKIFLLCKGADTIIFDRLSEEGRMFQ
ESTTKHLHDYGDAGLRTLVFAYRKLEEADFNAWNDEFMNAKNNMSNDRDE
TLERLSDEMEKNLILVGATAVEDKLQKGVPQCIDKLAQAGLKIWVLTGDK
METAINIGFSCSLLRQGMQQICITTNDQDTMQGIKSDIMMQITSGTKMIN
VEKDPHAAFALIIDGKTLTYALEDEVKHQFLHLAVHCASVICCRVSPKQK
ALVTRLVKEGTGKTTLAIGDGANDVGMIQEADIGVGISGVEGMQAVMSSD
FAIAQFRFLERLLVVHGHWCYKRIAQMICYFFYKNVAFGLTIFYYEACTG
FSGSSIYDDWYMILYNVAVTSLPVISLGVFEQDVTSEICLQFPALYQQGP
QNLFFGWYRIIGWICNGVYTSLAIFFLNIIAFTYDPFRSDGQTTDMSIVG
AGMFTTIVCAVNVQIALALSHFTWIQHILILGSVIVWFVFLVIYGGMPPE
YSHSAFHVFVETLAPSPIFWIISVLVVVACNFPYFIHIAFQRSFHPMDHH
VIQEMVYYNKHVEDHQMWKRERRKGRRKAKFGFTARVDEKIRQLKHKLHG
RPSTLTLDSPQHV
| Relationships |
|---|
| The mRNA, XM_017387046.1, is a part of gene, LOC108214834. |
| The polypeptide, XM_017387046.1, derives from mRNA, XM_017387046.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |