| 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. |
AGTTAGAGCCGAATTCCGGGTTGCACATAAAAAGACGAACACAAATAATG
ATTGCAATACATGTGTGTATATATAATATTTACTATTCCCTGTATCCAAG
AAGTCAGCAGGATATACATACATAAATACATATACACACAGCGGTAACCC
TAACTACCGACTAACAGATTTCTCTTCCAATCTGTTGATGCCTGCTGCTC
GACGACTTTTAGTTACGGCGTCGTTTAATTCACACCTGGTTTAGGATTTC
GGGATGTAAATTGTGCACAGAATGCACGATTTAATTGATTTTGTTTGGAG
ATACAGGCTTGTCAATTGTGATGCTTTGAGGATTTTGGTAGCACGATAAA
GGGTTGACATGGCTAGCGAGATGGTTATGGGTGAGGAAAATGTTAGTGTT
TCAGGAGAGGGAGGTTTAGTTGCGGATCGTGAATGTGGTGTTGAGAATTT
ATCAGTTTCAATGCAGTCATGTGAACCCTTTTGTACAGCTCAAGTTGACT
CCTTGGAGAGTTTCGTGGGTGCTTCTGATACAGTAGGGGCTAATGCTATT
TCCGGTGCCCTTGATAATATTAGTATAGCAGAGTCCTCAAGAGAAAAGCA
GGAGGAGAAAGATACTGTTGGTAGTCAGGATTTTGCTTCTGAGAGTACAG
TTCATGATGCTATTTGTTCGTCACTTCGTGCAAGAAATAGCACTATTAAT
GGGCCACTGTTGAAAACTGATACTGCAAGGCCTTTGAGAAAGTGCAAGAT
GATATCTAATAAAAAAGTTTTTCCGGGTATTGAGATATTAGAGCTTGCAA
GGAGGAGGAGGAGTTGTTTCTCCAATAGACCTCGTGTATCTGATTGGGGA
TCACTAGAAACTATTGGACACGTTTTTAATGTGTTTGAAGATGCTAATTT
GGATCAAATTGAGCAGAAAGAATCAAGAAAATGTAGTGGTAGTAAGGGAG
AGACTAAACGAAAGAATAATCGGAGACGCACAAATTCTCTCGGGACTAAA
AAAGAAATTCCTGCTTCAACTGGTGGCATCCGTTTGACAGTCACATTTGG
CGATATCATTCCCGGTGTTGTTGATGATCATAAAAGTTCTTCTGGTATGC
AGATTATATCTCCTAAATATAATAAAGATTTTGAGAAGAAGTTTGAGGAA
GGGACTTCTGGTACCCTTGATGGTCATGGCGGAATTGGTGCCCAGACACA
GGTTGGTCTATCGGAAGAAGCAGTAGGAAGCAGGTGCTTAGATCCTGGGA
CTTCACCTGATTCAGAAGTTATAAACCTAATTGCGGAGAGCCAAACTGAT
GAAAAAGTTGCCGAGGACGATATCTTAAACAAGAGATCTTGTGTTAGTGG
AGAGATCTCAAGTTTAAGTCTACCCAAAACATTTAGTAGGAAAGGAAAGA
AGAAAAATGAGCCCTCCCAGGATGATAAGGGAAGTGTTAATGATGAACCT
TCGAGTCCGGAAATTATAGACGATACTGGAGTAGCTGACCAACATAGGCA
CATGGAGAGGACAGATAACGGTTTCTCGACCAAAGATTCTGTGTCAATTA
CAACCGGTAATATAACTTCTAAAACTTCTAGTGCCGGTGTATGCTTTACG
GATACCCCCTTGCAACCATATGGAGTGTCCTCCTCTGGAGTCCTGCCAAA
AACATTTGAAGTTGAAAATTGTTTGGGAGGAGGCTTATGTTCTCCAGCAG
GGTTTCAACTTGAGACACTGGAGAAGTGTAATTCATTTACTGAACCAAGG
GATCATGAAAATAGCGAAAACTCAAGATCTCCCGGGAGCAGGTTGGAATT
CTCTGAAGCAAAGTCTCTAATAGGAAATTCCTATGTCCAGAAGGGAGACC
AGTTTAACCTCAAAGCCAGGGAAACATCTGATCCTGTTCAGGCTGTACAT
ATGATCGACAATTATTCAAAAACAGGAAGTCACACATTTACTTATCACGG
AGAACTCAAAACTGGATGCAGCATAACTCCAGATACAACTAGCTTAAAAA
TGAATGGGGTAGGAGATGAACAATCACCACCACGGAATGCTTGGGTGAGT
TGTGACAATTGCTATAAATGGAGGCGTATTCCAGCTCTGCTTGCAGATTC
CATTGAAGACACAAAAAGTAGTTGGACCTGTAAGGACAACGTGGATGAAG
AATTTTCTGATTGCTCAATTCCCCAAGAGAAATCAAATGCAGAAATCAAT
GCAGAGTTGGACTTATCCGATGCATCTTGTGAAGATGAGGCTGGTGCTTC
CCTCCATAAGCCCAGTGGACCGGAGAAAAAGAAATTAACAGCTTCTAAAC
AGTCGACTTGGAAGCTTATCAGATTGAACCATTTCCTGCATCGTGCCCGT
AGAACACAAACAATAGATGAGATAATGGTTTGTCACTGCAAAGCACCTGT
AGGAGGTCGAATGGGCTGTGGAAATGGATGCCTGAATCGGATGCTTAACA
TTGAATGTGTAAAAGGAACGTGTCCATGTGGTGAACTTTGTTCAAACAAC
CAATTCCAGAAAAGGAAGTATGCAAAACTGAAGTGCTTTCGAAGTGGAAA
GAAGGGCTACGGGCTTCAGTTATTAGAAGACATTCATGAGGGGCAGTTTC
TTATTGAATATGTTGGAGAGGTGCTTGATATGCATGCTTATGAGGATCGG
CAAAAGGAGTATGCTTTGGATGGGCATAAGCATTTTTACTTCATGACATT
GAATGGCAGTGAGGTAATAGATGCATGCGCCAAAGGGAATTTGGGTCGTT
TTATTAACCATAGCTGTGAACCAAATTGCCGTACAGAGAAGTGGATGGTG
AATGGGGAAGTTTGTGTTGGACTCTTTGCACTGAAAGATATTAAAAAGGG
TGAAGAGGTGACATTTGATTATAATTACGTACGGGTTTTTGGAGCTGCTG
CCAAAAAATGTGTGTGTGGTTCATCTCTGTGTCGGGGCTATATAGGTGGT
GATCCTTCAAGTGGTGAGATTATTGTCCAAGATGATTCAGATGAAGAAAA
TCTGGAATCAGTTATTGTCTGTGAAGATAGTGATGATTATTTGGACGCTA
CGGTTTCTGCAAGCAGTTTTGTTGAAGTTACAGATACACGTATTGCTGAG
AAAGATGTACTTGGCAACAATGCAAGGGCTATTGAGCATTCGGAGGGTAC
AGAAAAGATGCATGCTTCGTATAGTTTATCAAAGCAAAGGAAAGAAACCA
ATGTTGACAACAGTGCTGCTGGATGTATGGTGATGTCCTCTAGCATTGAA
GAATCTACACAAGAAACTTCTTCTGGTGACACGGATCTTAAAAGTGTTGC
AGAAATGGATGGCATGATAAGATTACCGGCATCCGTGCAAGCTATGGATA
CTTTCATGCAACTGGCTGATAGAAAAAAAAAGATCTTAGCTGTAGCTCCA
CCAGAGCCCTGTCTAGCTGAAGAAGAATCAAGCAAATCTTTAAGCACCAC
ACAGAGCTTTGAGTTATCAACAACAAAATTGAGCAGATCGTCAGTTGATA
AATCTAGTAGTCGGAGGAAGCTAAAGGATGATCTCAGGGAAGACAGGAGT
GTAATTACAGCTTCACATCCCAATGCAAAAACTTCTCACACAACATCTTC
TCTTAAAAAAGTAAAACCTCGAAAGAGTGACTTGCTTTCAAAAAATTCTG
CAGAGAGGGGAAATAAATTACATCCGTTACCTTACAGATCAAGAAAGACT
GTAGACAGTTCCTCAAGCGATCCATTTGAAGCAGTTCAGGTGAAGCTTAA
TGAGCTGTTAGATTCTGAAGGGGGAATAAGCAAAAGGAAAGATGCATCAA
GGGGGTACCTGAAGCTTCTTTTCTTAACTGCTGCTTCTGGAGGTAGTGGC
AATGGAGAAGCAATCCAAAGCAACCGAGATCTGTCTATGATTCTTGATGC
ACTGTTGAAAACAAAGTCTCGAACTGTTTTGGCTGATGTAATCAACAAAA
ATGGTTTGCAGATGTTGCACAACATAATGAAGCGGTGCAGAAAAGAGTTT
CATAAGATCCCAATTCTCAGAAAGCTTCTTAAGGTCCTGCAGTACCTGGC
TCTGAGGGAGATACTTACCCCAGAACATATCACTAGTGGTCCACATTGTG
CTGGGGTGGAGAGTTTTAGGGAGTCAATATTGTCATTGACGGAGCATGAT
GACAAACAGGTCCATCAAATTACACGCAATTTTCGAGATAGGTGGATCCC
GCGTCCAATTAGGAAGAACAGTTACATGGACAGAGACAGTGGTAAGCTGG
ATTTTAATAGGGTGGCCTCAAACTCCAGCAGGTTATCACCACTACAAAGT
CAGTCATCTGATTCAGGCGCAAGACATCCTGAATCAGTAGAATGCATCAA
GCAACCAAGAAGCTCAAATATTAATCGTGAAAATACAGACGGCTGCTCTG
CTTTATGTAGTAGTGAATTTGTTGCTGATGGAGCAAGAGTCCAAAAACGT
AGAAGTCGATGGAATGAGGCAGAAGACTCAAACCGTGGTAAATATGCTCC
CCTGCATAAAGAACCAAGGATTCATTCTGAATCTGTACAAGTTTCACATA
TTAGCCTGCTTTATGGGAATAGTGGAGTGCCATCTGACCAGGCTGCTATT
ATAAATGAGGAAAAGCATAACAATCTATATGTAAATCGTTCCCCCAATAG
GATGACTATTAAATATCTAGATAACAACGAGCAAAGCATTGATGAGGATG
TACCTCCTGGTTTTTCTCCTCCTCATAAAGCTTCTTTTGTGCCATCTAGT
GCTTCTTCAACTGCCTCAACTTTTTGCCAAGAGAAGTGCTTGTTCCCAGA
GTACCCTTTTGAAGTGACGGTGGGCCATCCACAGGAGAGATTTGTTTCAA
GGTCCCCTGTTTCATTTGGGATTCCAATGCATGCGGTGGAGCATTTTGGT
AGACAAGGTGAAATAGCTGAGAATTGGTTTGTAGCAGCTGGGATTCCTTT
CCACCCTTATCCACCACTACCTCCGTATCCCCGTGATAGGCGAGGCCCTG
CACCTGCTTTAAGTTCTATGATATTGAACTCTGTTCCAGTAATTGGGGAG
GGTTTTCAAAATAATGCCACTTATCAATCGGATCAGATTACTTTCAGCAC
ATCTGCTTCTTGCATGCCGGATTTGGAACTTTCAGCTCCCGTGAAGCAGC
ACCATTTTCAAGGAACAGGGGGTGCCTCTAATAGGTTGGAAAGGAGATAC
TTCAGGCAGCAAAAGTGGATCAATACAAAATCAAGGCCTCCCTGGGTCCG
GGGTGAAGCTGGTAGGGGAAACTTTGGGAACATTTAAAGATATGGATTCA
GTTTTGTAGGCATATGAACCGGAGCAAACGTTCTGAAAAGTCCATCTATC
CCAAATCAGATACATATGGGAGTAGGGCGTTGTGGGAATATATTTTAGCA
ACATCTGCAGCACCAAAATTTGCCTTTAACTATTAAACTCTAGATACATC
CTCTCCATTTTCTGTTTGTACTTCCTATTCTTTATTTATTACTCAAACTG
GAATCTACGGTACAATGCGGTACTGCCTTGAGTCCCAGCATTCTATAGGT
TGGGAAAGCAATTATTCTGATTATGTTGTGTCATGGGCTGGACTTTCATA
CATGATACCTCAAAGAGGTAAGCAATATGTTGTTTTTTTTAAAAAAATTT
ATTTAATAAATTTGTCAATCTTT
MASEMVMGEENVSVSGEGGLVADRECGVENLSVSMQSCEPFCTAQVDSLE
SFVGASDTVGANAISGALDNISIAESSREKQEEKDTVGSQDFASESTVHD
AICSSLRARNSTINGPLLKTDTARPLRKCKMISNKKVFPGIEILELARRR
RSCFSNRPRVSDWGSLETIGHVFNVFEDANLDQIEQKESRKCSGSKGETK
RKNNRRRTNSLGTKKEIPASTGGIRLTVTFGDIIPGVVDDHKSSSGMQII
SPKYNKDFEKKFEEGTSGTLDGHGGIGAQTQVGLSEEAVGSRCLDPGTSP
DSEVINLIAESQTDEKVAEDDILNKRSCVSGEISSLSLPKTFSRKGKKKN
EPSQDDKGSVNDEPSSPEIIDDTGVADQHRHMERTDNGFSTKDSVSITTG
NITSKTSSAGVCFTDTPLQPYGVSSSGVLPKTFEVENCLGGGLCSPAGFQ
LETLEKCNSFTEPRDHENSENSRSPGSRLEFSEAKSLIGNSYVQKGDQFN
LKARETSDPVQAVHMIDNYSKTGSHTFTYHGELKTGCSITPDTTSLKMNG
VGDEQSPPRNAWVSCDNCYKWRRIPALLADSIEDTKSSWTCKDNVDEEFS
DCSIPQEKSNAEINAELDLSDASCEDEAGASLHKPSGPEKKKLTASKQST
WKLIRLNHFLHRARRTQTIDEIMVCHCKAPVGGRMGCGNGCLNRMLNIEC
VKGTCPCGELCSNNQFQKRKYAKLKCFRSGKKGYGLQLLEDIHEGQFLIE
YVGEVLDMHAYEDRQKEYALDGHKHFYFMTLNGSEVIDACAKGNLGRFIN
HSCEPNCRTEKWMVNGEVCVGLFALKDIKKGEEVTFDYNYVRVFGAAAKK
CVCGSSLCRGYIGGDPSSGEIIVQDDSDEENLESVIVCEDSDDYLDATVS
ASSFVEVTDTRIAEKDVLGNNARAIEHSEGTEKMHASYSLSKQRKETNVD
NSAAGCMVMSSSIEESTQETSSGDTDLKSVAEMDGMIRLPASVQAMDTFM
QLADRKKKILAVAPPEPCLAEEESSKSLSTTQSFELSTTKLSRSSVDKSS
SRRKLKDDLREDRSVITASHPNAKTSHTTSSLKKVKPRKSDLLSKNSAER
GNKLHPLPYRSRKTVDSSSSDPFEAVQVKLNELLDSEGGISKRKDASRGY
LKLLFLTAASGGSGNGEAIQSNRDLSMILDALLKTKSRTVLADVINKNGL
QMLHNIMKRCRKEFHKIPILRKLLKVLQYLALREILTPEHITSGPHCAGV
ESFRESILSLTEHDDKQVHQITRNFRDRWIPRPIRKNSYMDRDSGKLDFN
RVASNSSRLSPLQSQSSDSGARHPESVECIKQPRSSNINRENTDGCSALC
SSEFVADGARVQKRRSRWNEAEDSNRGKYAPLHKEPRIHSESVQVSHISL
LYGNSGVPSDQAAIINEEKHNNLYVNRSPNRMTIKYLDNNEQSIDEDVPP
GFSPPHKASFVPSSASSTASTFCQEKCLFPEYPFEVTVGHPQERFVSRSP
VSFGIPMHAVEHFGRQGEIAENWFVAAGIPFHPYPPLPPYPRDRRGPAPA
LSSMILNSVPVIGEGFQNNATYQSDQITFSTSASCMPDLELSAPVKQHHF
QGTGGASNRLERRYFRQQKWINTKSRPPWVRGEAGRGNFGNI
| Relationships |
|---|
| The mRNA, XM_017396674.1, is a part of gene, LOC108222772. |
| The polypeptide, XM_017396674.1, derives from mRNA, XM_017396674.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |