| 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. |
ATAAATATTGTATGTTTTTCCGCACACCTTTTGTCTTAAAGTGTAGTACA
TTAACAAGTGTTGTCAAGTGTATAGAATAGAGAGAGAGAGAGAGAGAGAG
AGAGATGGAGAGAGGAGGTCAAGTAAGAATTGGCAGTGATGATGAAGATG
ATGTTGTTGTGTTTGCAGTAAATGGAAAAAGATACGAGGTTTCAGTACAC
CCCTCTACCACTCTTCTTGATTTCTTGCGTTCTTCTACCCCTTTCAAGGG
TGTCAAGCTCAGCTGTGGTGAAGGTGGTTGTGGTGCTTGTGTTGTTTTAC
TGTCTAATTACGACCCTTTGCTAAAGAAAGTAAAAAGTTACACTGTGAGT
TCATGTCTTACACTTGTTCATAGTGTAAATTATTGCTCAATTACAACAAC
TGAAGGACTTGGAAATAGCAGAGATGGTTTTCACCCAATCCATGAAAGAT
TTTCTGGTTTTCATGCTTCTCAATGTGGTTTCTGTACGCCCGGAATGTGC
ATTTCGCTGTTCTCAGCGCTGGTCAATGCCGAAGAGAAGCAGAGGCCGGA
CCCCCCTACAGGATTCTCCAAACTCACTGTTTCAGAAGCTGAAAAGGCTA
TATCAGGGAATCTGTGTAGATGTACTGGATATCGACCCATTGCAGATGCC
TGTAAAAGTTTTGCTGCTGATGTTGATCTGGAGGATTTGGGAATGAATTC
CTTCTGGAGAAAGGGAGAGAGTAATGAAGATAAACTAAGTAAATTACCTT
CTTATAATCCGAAAGATGATGTTTGTACATATCCTGAATTCTTAAAAAGA
GAATTGGAGTCTACAATGTATTTGAGCCCTCATAAAAAGTCTTGGTACAG
TCCTCGCACTCTTGAGGAGCTCCGAACTTTCACTGACCCAAAATTGTCTA
CAACTCGAACTAAGTTAGTTGCTGGTAACACAGGAATTGGTTATTACAAG
GACCTTGATCAATATGAGAGATACATCAACTTGAGGAATGTCTCTGAGCT
TTCATCAATTAGTAGAAACGAGACAGGGATGGTAATTGGAGCAACTGTCA
CAATATCTAAAGCTATCTCAGCATTGAAAGAAAAAGTAGGTGGCGTCGTA
TGTTCAGATTGGGAATTGATATTCACCAAAATTGCTGAGCATATGGAGAA
GATTGCTTCAGAGCCTGTTCGTAACTTAGCTAGTGTAGGGGGGAATGTGG
TTATGGCACAAAGACATTGTTTCCCATCAGACATTGTCACAGTACTTCTT
GCTGTGAGTTCTACAGTTGATTTAATAATCAATACAAAACGTGAAAATCT
TACATTGGAGGACTATCTGTCAAAGCCACCATTGGATAATAGAGGGGTTC
TATTGAGTATCCAAATTCCTTTCTCGACCTCATTTACAAGTAACTTCTCT
ACCAAAACTAGTAAGTTGGTGTTTGAAACTTATCGCGCTGCTCCAAGGCC
ACTTGGAAATGCACTCCCTTACCTAAATGCTGCTTTTTTAGCCATTATTT
CACCAAGTAAAATGGGATTTGTGATAAATAAGATTAAGTTAGCTTTTGGT
GCTTTTGGAGCTAAACATGCCATGAGAGCAAGGGAGGCTGAAGAATACTT
GGCTGGTAAGCCTATAAGTTTGAATGTTCTCTATGAAGCTATTAACATAG
TTCGAGCCACTGTGATTTCCAAAGATGGAACTTCAGATGCTACTTATAAA
TCAAGCTTGGTTGTCAGTTATCTTTTTAAGTTTCTTTATCCCTTGTCTGA
TGGCGTTGTTTCGGTTTCCAATGGTTTATCTACTCATAATTCTGCTAACA
ACTTTAAAGATGGAGACAACCTGTCAAATGATGCTAAAAAGCCTTCACTA
TTGTCATCTGGAAAGCAGCTGGTGGAAACAAGCAGAGAGTACTATCCGGT
TGGTCAACCAATTGTTAAATCCGGTGCTTCTATTCAAGCTTCTGGCGAAG
CTGTTTATGTAGATGACATTCCTTCACCATCAAACTGCCTTCACGGTGCA
TTTATATATAGCACAAAGCCACTGGCAAGGGTGAAGAATGTCCGATTCAA
GACCAAGTCACTACCAGATGGAGTAACTGCTGTTATAACCTACAATGATA
TTCCAAATGGAGGGGAGAACATAGGTTCTAAGACCATATTTGGTACAGAA
CCACTGTTTGCTGACGAAATTACCAGGTGTGCTGGCCAGTGTCTTGCTTT
TGTGGCTGCAGATACACAGAAGCTTGCAGATAGGGGTGCATCTCTGTCCC
TAATTGATTATGATACTGATGATTTAGAGCCACCTATATTAACTCTTGAA
GAGGCTGTTGAGAAATCAAGTTTCTTCGAAGTTCCTTCCTTCTTATATCC
GGCCCCGATTGGGGACTTCTCGAAAGGCATGGCTGAAGCTGATCACAGGA
TTAACTCTGAGATCAAACTTGGTTCCCAATATTATTTTTATATGGAAACA
CAAACTGCCCTTGCTATACCAGATGAAGACAATTGCATGGTGGTGTATAG
TTCTATTCAGTGTCCAGAGTATGTACACACAGTTATTGCAAGATGTCTTG
GTATACCTGAACATAATGTTCGAGTTATCACGAGAAGGGTTGGAGGAGGT
TTTGGTGGAAAGGCAATAAGGGCCATGCCTGTAGCAACAGCATGTGCACT
TGCAGCATACAAATTGCGGCGTCCTGTACGAATGTATCTTAATCGTAAGA
CTGACATGATAATGGTGGGAGGAAGGCATCCCATGAAGATAACTTATGAT
GTTGGGTTCAAATCCGATGGAAAGATTACAGCCCTACACCTATGTATTTT
GATCAATGCAGGGATGTCTGCAGATATAAGCCCTATTATGCCAAATAACA
TGTTGGGGGTGCTTAAGAAGTATAATTGGGGAGCCTTATCTTTTGACATT
AAGGTATGCAAAACAAACCATTCCAATAAATCTGCAATGCGAGCCCCTGG
GGAGGTGCAGCCATCTTTTATTGCAGAAGCTGTAATGGAACATGTTGCCT
CTATGCTTTTCATGGAAGTAGATTCTGTTAGACACAGGAACCTTCACACA
TTTGATAGCCTCAATTTATTCTATAAGCATAGCGCAGGAGAACTTGTGGA
GTATACTTTGCCATCTATCTGGGACAAATTACAGGTAACATCGAATTTTA
GCCAAAGAACTGAAATGATACAACAGTTTAATCAAAAGAATTTATGGAAG
AAAAGGGGAATTTCTCGAGTTCCCATTGTGCATGAAGTAACCGTGAGACC
TACCCCGGGGAAAGTAAGCATTCTTTCAGATGGGTCCGTTGCTGTAGAAG
TTGGTGGGATTGAACTTGGGCAGGGGCTGTGGACGAAGGTCAAACAAATG
ACTGCATATGCACTTGGTACGATTCAATGTGATGGAACTGCAAACCTTGT
GGATAAGGTACGGATTGTACAAGCAGATACATTGAGCTTAATTCAAGGCG
GGTTTACAGCTGGAAGCACGACTTCTGAATCAAGCTGCGAAGCAGTTAGA
ATTTGCTGTAACATTTTGATCGAACGACTCTCCCCTTTAAAGGAAAAGTT
GCAGGCTCAAATGGCTTCTTTGACCTGGGATACTTTAGTTCTCCAGGCAC
ACAGGCAAGCTGTGAACATGTCAGCAAGTTCGTATTTTGTGCCCGACTTC
GGTTCCATGCAATACTTGAATTATGGCGCTGCAGTAAGTGAGGTGGAGAT
AAATACTCTGACCGGAGAAACTACAATTCTTCGCTCGGATATCATTTATG
ATTGCGGACAGAGCTTGAACCCTGCTGTAGATTTGGGACAGATTGAAGGT
GCTTTTGTTCAAGGAATTGGATTCTTCATGTCTGAAGAGTACCTTACTAA
TTCAGATGGACTAATGGTTGCGGATAGCACATGGACATACAAGATACCGA
CTATTGATACAATTCCAAAGCAGCTTAATGTTGAGGTACTTAATAGCGAA
CATCACAGAAACCGTGTTCTCTCATCTAAAGCTTCTGGTGAACCGCCTTT
ACTTTTGGCAGTTTCAGTACACTGTGCAACAAGGGCTGCCATAAAGGAAG
CTCGAAAACAACTTCATTCTTGGAAAAATTCATCAGACCAGTCTAACGTT
TCATTCCAATTAGATGTCCCCGCTACCATGCCTGTTGTGAAGCGACTTTG
TGGAATGGATTATGTGGAGTCCTATTTGCAGAACTTGTTATCTTGTCAAG
GAAGAAAACAGGCTTAATGTTTTTCTTTCCGCATGTCTGATGAGAACTGA
TATTATACACACTTCACTTGGAATAATATTGGGGTGGAGCTAAAAATTTA
TCTTGAGAATTTTTTTCCTTTTTTCTATAAATTTCTTTGATATATTTTAT
CCAA
MERGGQVRIGSDDEDDVVVFAVNGKRYEVSVHPSTTLLDFLRSSTPFKGV
KLSCGEGGCGACVVLLSNYDPLLKKVKSYTVSSCLTLVHSVNYCSITTTE
GLGNSRDGFHPIHERFSGFHASQCGFCTPGMCISLFSALVNAEEKQRPDP
PTGFSKLTVSEAEKAISGNLCRCTGYRPIADACKSFAADVDLEDLGMNSF
WRKGESNEDKLSKLPSYNPKDDVCTYPEFLKRELESTMYLSPHKKSWYSP
RTLEELRTFTDPKLSTTRTKLVAGNTGIGYYKDLDQYERYINLRNVSELS
SISRNETGMVIGATVTISKAISALKEKVGGVVCSDWELIFTKIAEHMEKI
ASEPVRNLASVGGNVVMAQRHCFPSDIVTVLLAVSSTVDLIINTKRENLT
LEDYLSKPPLDNRGVLLSIQIPFSTSFTSNFSTKTSKLVFETYRAAPRPL
GNALPYLNAAFLAIISPSKMGFVINKIKLAFGAFGAKHAMRAREAEEYLA
GKPISLNVLYEAINIVRATVISKDGTSDATYKSSLVVSYLFKFLYPLSDG
VVSVSNGLSTHNSANNFKDGDNLSNDAKKPSLLSSGKQLVETSREYYPVG
QPIVKSGASIQASGEAVYVDDIPSPSNCLHGAFIYSTKPLARVKNVRFKT
KSLPDGVTAVITYNDIPNGGENIGSKTIFGTEPLFADEITRCAGQCLAFV
AADTQKLADRGASLSLIDYDTDDLEPPILTLEEAVEKSSFFEVPSFLYPA
PIGDFSKGMAEADHRINSEIKLGSQYYFYMETQTALAIPDEDNCMVVYSS
IQCPEYVHTVIARCLGIPEHNVRVITRRVGGGFGGKAIRAMPVATACALA
AYKLRRPVRMYLNRKTDMIMVGGRHPMKITYDVGFKSDGKITALHLCILI
NAGMSADISPIMPNNMLGVLKKYNWGALSFDIKVCKTNHSNKSAMRAPGE
VQPSFIAEAVMEHVASMLFMEVDSVRHRNLHTFDSLNLFYKHSAGELVEY
TLPSIWDKLQVTSNFSQRTEMIQQFNQKNLWKKRGISRVPIVHEVTVRPT
PGKVSILSDGSVAVEVGGIELGQGLWTKVKQMTAYALGTIQCDGTANLVD
KVRIVQADTLSLIQGGFTAGSTTSESSCEAVRICCNILIERLSPLKEKLQ
AQMASLTWDTLVLQAHRQAVNMSASSYFVPDFGSMQYLNYGAAVSEVEIN
TLTGETTILRSDIIYDCGQSLNPAVDLGQIEGAFVQGIGFFMSEEYLTNS
DGLMVADSTWTYKIPTIDTIPKQLNVEVLNSEHHRNRVLSSKASGEPPLL
LAVSVHCATRAAIKEARKQLHSWKNSSDQSNVSFQLDVPATMPVVKRLCG
MDYVESYLQNLLSCQGRKQA
| Relationships |
|---|
| The mRNA, XM_017402475.1, is a part of gene, LOC108227368. |
| The polypeptide, XM_017402475.1, derives from mRNA, XM_017402475.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |