| 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. |
TATATATAGTCGTTGTTGTATGTATATGTTAGTTTGAGTTTGACATCAGA
ATTGTTGAAGTTAATAGTTTAAGGGGACATGTTGAGTTGTGAAAATGATA
GCTTCACCGAGAATGATGGGAATAGACGAGAAAATACATGTAACGTTGTT
GAAGAAGGAGCAGCAGCAGCAGTACAATCAGCACTTTTTTGTGGAGATTT
GAGCCTCCGTCTTTAAAGGGAAACTTCTCCGTACTCTTCCCTTTTTCTTC
TTCAAGTCTTTTACATTTTACCATTTTTGACTTCTTTCTCAAGCTTTAAA
CATAACCCCATCTCTTAATTTTGTTCAAGATTGAAAATTTATCTTCTGGG
CTGTTGGTGTTTTTACTGTTTGATTTCAAGAACCATCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCTCTCCCTCCCTCCCTCTCTCTCCCCCCTCTGTG
TATGGATGCATTGGATCGTGTGTTTGTTTGTTGTGATGAAGATTATTGGG
TTGACTAGCTAATTGGGGTTTTTAAGTTTGAGAGTCTTGTTTAGTGCTAG
ATTGATATAAACCAAAACAAAGAAAAAGAAAAGCTATACATGTTTTTGCC
ATAATACATAATCATACTATTACAAAGTTTGTATATATAGTAGTAGAAGG
GTATTCATCAAATTCCTTTAGAAATAATTTCAAGTTCCAGGGAAAATTTT
ATTCCTTTCTTGTTTCTTTTATTCTGACAATAGAAAAAGATTTTAACTTT
AAACAGCCCACCATTTTATTTTGGGATTTGGTAAATTTCACCTCTATTAG
TTGGGTAAAGTTTACATTTTCGATCTTTTAGAATTAATCAGGTACATTTA
CAGAAGAGAAGAAGAGTGATACACATTTTTTTGGGGGTTGGTATATGGTG
GATTGCAGTATTCTATGGGATTAGCTGATAGGGGTATACTGGATTTGATA
CAGAAAGTAGGATCTTGGATTAATTGGGGCAACGGTGATCAATATTTTTG
TTCGGGCGAATACAAAATGGATAAAATTTGCTGTGATTGCATGATGACTA
TTGCAGACTCTTGCATTAGTTATCATTGTCAAAGATGTGGTAGGATGTTG
TGTGACAATTGTGTGCAGTCAAATGGTTGTTTTGGAGGTGTTGCATTGGA
AGATTCTGATAACACATATGATGCTGGCGTAATTGGTTATTGCAAATTCT
GCTCTCATATGAGTAATAGGAAAAAAGTTGGAAAAAGGCTCATTGAAAAA
GTTCATCCTGCAGAGTCTCCACGACAAAGTTTTGAACCACCATCTCCTTG
TTTCAATGAGAGATGCGATGACTGTGCTAATCAGGATTTTGCTAGATGCA
GAACTCATTACTCTCCAAGCAGGAGTGATGGATATGATAGAGAGGATTCC
ACCAAAACCTTCTTCAGTTCATTTTTTGATGATACATCAGATATAGATTC
AAGTAGTATGAGCGCTAGACATGAGTTTTACAATAATAAGTCAGTTGGAT
CAAGTCCAATGGACAGTCCCTGTAGAATCCATAATTTTGATAAGACAGGG
CAATCTGCAGAGCAGGAGCAAGTTAGGACCGGAATGTCTCAGAATGATGG
CCCCTTCGATCAAGATACTTCAGCTGTACCAGAAAGGCCTGACACAGGTA
CCGAGGATATTGACCATACTTGTGAAAACGAGGATCTTTTATTGGCATTT
CAGGATCAACAGCACTTAAATTTGGAGAACAATGGTCTCATCTGGTTTCC
TCCTCCTGCTGTTGATGAAAATGATGAGAGAGAAGATAACTTTTTTGCTT
ATGAGGAAGATGAGGATGACATTGGGGAGGTAACTCCGATGTTGTCATCT
GGTGAATTGAATAGCATGCTACCTGAGAAGGAGAGAGATTGTGGCCAAAA
GGAATCTTTAAAAGCTCTCGTGCAGGGGCATTTTAGGGCGCTCGTGTTAC
AGCTCTTGCTTGGGGAGGGTATAAAGGTGGATAAAGAAAATAGTGAAGAC
AACTGGCTTGATGTAGTTACAGCAATATCCTGGCAAGCTGCAAACTTTGT
GAAACCAGACACTAGCAGTGGAGGCAGTATGGATCCTGTTGATTACATAA
AAGTTAAATGTATATCATCTGGAGTTCCTAGTGAAAGTAAATTCATTAAA
GGAGTAGTGTGTACCAAAAATATAAAACACAAGCGCATGATTTCGCAATT
TAGAAATGCCAGACTACTTATTTTGGAAGGAGCACTTGAGTACCAAAGAG
TTCCAAATGAGCTGGCATCTTTCGATATGCTCCTACAACAGGAAATTGAT
CATCTGAAGATGATTGTTTCAAGGATAGAGGCTCACCGCCCAAACGTGTT
ACTGGTTGAAAAAAGTGTATCTTCATATGCCCAAGAGTATCTGTTGGCAA
AGGAGATCTCCTTAGTGCTGAATGTTAAGAAGCCTCTGCTACAGAGAATA
GCTAGGTGTACTGGTGCTTCTGTAACTCCATCAATTGATAAATTGTCTAC
TGCACGTTTGGGACAGTGTGAACTCTTCCGCATAGAAAAAGTATCTGAAG
ACCTCGAACAAGCTAAACATCCCCAAAAGAAGCCATCTAAAACCTTAATG
TTCTTCGAAGGTTGTCCAAGGCGTTTAGGTTGCACGGTACTGCTAAAGGG
TTCCTCTCGTGAAGAACTAAAGAAAGTTAAGCATGTTGTTCAGTATGCAG
TTTTCGCAGCATATCATTTGTCCTTGGAAACTTCTTTCCTCGCAGATGAG
GGTGCTAGCTTACCTAAACCAACTTCAAGATCTTCATTTTCAATACTTGA
AAGGACAAGTATCGACAGTGCCATTTCTGTTGTCCCTACTCCAACCTCCT
ACTCGGAAATTGCTGATCTCCCAAGTTTTCATGAGGAGTCTGCAGGCCTC
AAGTTAGAACTTGAGGCAAGGGAGTCAGTAATTGAGCCTTTTAATTCTCA
ATTTATCTCTTCTCCTGCCTCTGTGAAGTATGGTGTAGAAACCTCTGATG
TACTTAATAATGGTTTACCAGCTACATTTATTTCGGAGGAATATAGGCCA
GGTGTAGTTTCTACCGGAAGTAGAAATTTTGATCGGGAGGATTCCCAGCT
GACCATAAACTATATGCAACCATCTGAACCCTTTAATCAGAAAAAACATG
AACAATTAAAAGATATTGATGGCTCTAGTGAATACAATTCAGCAGGTGAT
AGTCACCAGAGCATACTGGTATCTTTTTCAAGTCGCCGTGTCCTTGATGG
AACTGTCTGTGAACGTTCTCGACTCTTGCGCATTAAGTTCTATGGTTGTT
TTGATAAGCCACTTGGAAGGTATCTTCAAGAAGATCTGTTTGATCAGACT
TCCTGCTGTGAATCATGCAAAGAGCCGGCTGATGGCCACATAGTTTGCTA
TACTCACCAGCAGGGTAATCTAACAATAAGTGTTAGGAGACTACCCACGG
TGAGACTGCCTGGAGAACGAGATGGAAAAATTTGGATGTGGCACCGATGC
CTCAGATGTACACATGTAGATGGGGTTCCACCGGCAACCCGCAGGGTGGT
TATGTCTGATGCTGCTTGGGGTCTTTCTTTAGGAAAGTTCTTAGAACTTA
GTTTCTCAAACCATGCAACTGCTAATCGTGTTGCAAGTTGTGGTCATTCT
CTGCAAAGGGACTGTCTTCGGTACTACGGATTTGGGAGTATGGTAGCATT
CTTCCGCTATTCTCATATCGATATTTACTCGGTTTGTTTGCCCCCATTAG
CACTTGAGTTTATTCCCCATTCACAGCAGGATTGGATAAAGAAAGAGATG
GCAGAGATTTTGAACAAGCAAGAAGCTTTATACGAGGAAATATTGGGTTT
ACTTTATAAGATTGAACAGAGAAGTACATCTCTTGGACAAGAATCGTCTA
CGAGAAATGAGTTGCATAAACACATAATTGAGTTGAAAGACCAGCTCATA
AAAGAAAGAGATGATTCTCAGTGCATATATCAGCAATTTAGCAAAGATAG
TTCAGAACTAGTCCCAGCGACAATGGATGTTTTTGACCTTAATCAATTGA
GACAATCACTCCTGATTGTTTCACATGATTGGGAGCACCGGCTTAGTTCA
TTAGATTCTCTCATTAGCTCCAATGCAGGGTTACAAGATTTGAGAAGTGT
TTCGTGTATTAATGATATTAGTCTTTCCTGTGACCGTGATAATGATGGTG
TCTCTGATCTGGTTTTGAAATTGCCAGATTTCCTCCAGAAAGATATACCG
TACACACAAGACAGAGAGCCTGAAAAATCCCTGGTTGATTCTGGTGTTCC
TAAAGTTAACATGCCGATGTCATGCAAGACTAAGAATGAGACATTGACAC
ACTTGGATGGGGAACCTACAGTCAACAAGACGCTCTTGGATCGTGCTCCC
TCAGCTGCATCTGAATTGTCTGATAAAATTGATTCTGTATGGAATGGTAC
AGCAGACAGTCCGTTGAAATTGCCTTCTTGGAGATTGCTATCACCAGCAA
GAGTTCAATCCATTGATTCTGCTATAAGTATCCAAGAAAAGCTAATGAAA
GGATTACCGCCCTCATCATTTCATTTATTAGCAATTAGATCTTCTCACGC
CTCTGGGGACTATGCAAACATGTCTAGAGATCCCTTACTTAATGTACAGA
GGACTTATTCTCAAATGTCACCTCTTGAGGCCCAGAAGTTTAACCTTTGG
AACACCTCACACTCATTTAACTCGTCTGCATCTCTTTTGCCTGAAGGGGC
ACGATTGGTACGTCGGCAAGATGGCCAGACAGATTTGACCATTGTTGTTT
ATGACAATGAACCAACTAGCGTGATTTCATATGCTCTCAGTTCCAAAGAG
CATAAAGACTGGATAGCTGATGAGCCTTGTGAATTTGAAGAAGCCTGGAA
TGCTGCTCAACTGAAGCGAGAGAATTCTGTGGCTTCAACCATTCCAGCCT
GGCAGTCTTTTGGTTCTGTGGACTTGGATTATATCCACTATGGAAGTTAT
GGTTCTGAAGACGTTTCAACAACCATTAGTACTATGCTTACAGATACAAC
CAATAGCAGTTCCCATTTTAAAATTGCTTTTGAGGATGATAACCCCAGTG
CTGGAGGAAGGGTAAAGTTTTCTGTTACCTGTTATTTTCCAAAGCAATTT
GACGTGCTCAGAAAGAAATGTAGCTGTAGCCAAATAGATCTTGTACGTTC
TTTGAGCCGCTGCAAGAGGTGGAGTGCACAAGGTGGAAAAAGCAATGTGT
ACTTTGCAAAGTCTTTGGATGAAAGGTTTATTATAAAGCAAGTCACGAAG
ACTGAATTAGAATCTTTTGAAGAGTTTGCACCTGAGTACTTTAATTATAT
GAAAGATTCCCTCGACTCCAGAAGTCCAACATGTCTCGCGAAAATTCTGG
GGATATTCCAGGTAACCGTCAAACACTTGAAGGGTGGAAAGGAAACAAAA
ATGGATCTGATGGTGATGGAAAATCTATTTTTCAGAAGAAATATTTCAAG
AATCTATGATCTTAAGGGCTCTTTACGATCTCGTTACAATTCAGATACTA
CCGGAGTGAACAAGGTGTTGCTTGACATGAATCTCTTGGAAGCATTGCGA
ACAAATCCTATGTTTCTTGGAAGTAAGGCCAAGAGAAGCTTGGAAAGAGC
AATTTGGAATGACACATCCTTTTTAGCGTCTGTAGACGTTATGGATTATT
CTTTGCTGGTCGGAGTAGATGAAGAAAAGAAAGAGCTGGTGGTTGGGATA
ATCGATTACATGAGACAATATACATGGGATAAGCACCTGGAGACATGGGT
GAAGAGCTCTGGAATACTAGGAGGTCCAAAGAATGCTGCCCCAACTATCG
TGTCGCCGAAACAATACAAAAAAAGATTTAGAAAAGCAATGACAGCTTAT
TTTCTAACAGTACCTGATCAGTGGTCAGCATAAAGTTTCATTAGTTGATT
TAGGATTTGAGGTGATAATTCATGTTACATGTACATTATATCTAATCTTT
TGCACAACATAATTGAAATAACCAAAGATTACTATTGGTTGATTATTACT
TATTA
MGLADRGILDLIQKVGSWINWGNGDQYFCSGEYKMDKICCDCMMTIADSC
ISYHCQRCGRMLCDNCVQSNGCFGGVALEDSDNTYDAGVIGYCKFCSHMS
NRKKVGKRLIEKVHPAESPRQSFEPPSPCFNERCDDCANQDFARCRTHYS
PSRSDGYDREDSTKTFFSSFFDDTSDIDSSSMSARHEFYNNKSVGSSPMD
SPCRIHNFDKTGQSAEQEQVRTGMSQNDGPFDQDTSAVPERPDTGTEDID
HTCENEDLLLAFQDQQHLNLENNGLIWFPPPAVDENDEREDNFFAYEEDE
DDIGEVTPMLSSGELNSMLPEKERDCGQKESLKALVQGHFRALVLQLLLG
EGIKVDKENSEDNWLDVVTAISWQAANFVKPDTSSGGSMDPVDYIKVKCI
SSGVPSESKFIKGVVCTKNIKHKRMISQFRNARLLILEGALEYQRVPNEL
ASFDMLLQQEIDHLKMIVSRIEAHRPNVLLVEKSVSSYAQEYLLAKEISL
VLNVKKPLLQRIARCTGASVTPSIDKLSTARLGQCELFRIEKVSEDLEQA
KHPQKKPSKTLMFFEGCPRRLGCTVLLKGSSREELKKVKHVVQYAVFAAY
HLSLETSFLADEGASLPKPTSRSSFSILERTSIDSAISVVPTPTSYSEIA
DLPSFHEESAGLKLELEARESVIEPFNSQFISSPASVKYGVETSDVLNNG
LPATFISEEYRPGVVSTGSRNFDREDSQLTINYMQPSEPFNQKKHEQLKD
IDGSSEYNSAGDSHQSILVSFSSRRVLDGTVCERSRLLRIKFYGCFDKPL
GRYLQEDLFDQTSCCESCKEPADGHIVCYTHQQGNLTISVRRLPTVRLPG
ERDGKIWMWHRCLRCTHVDGVPPATRRVVMSDAAWGLSLGKFLELSFSNH
ATANRVASCGHSLQRDCLRYYGFGSMVAFFRYSHIDIYSVCLPPLALEFI
PHSQQDWIKKEMAEILNKQEALYEEILGLLYKIEQRSTSLGQESSTRNEL
HKHIIELKDQLIKERDDSQCIYQQFSKDSSELVPATMDVFDLNQLRQSLL
IVSHDWEHRLSSLDSLISSNAGLQDLRSVSCINDISLSCDRDNDGVSDLV
LKLPDFLQKDIPYTQDREPEKSLVDSGVPKVNMPMSCKTKNETLTHLDGE
PTVNKTLLDRAPSAASELSDKIDSVWNGTADSPLKLPSWRLLSPARVQSI
DSAISIQEKLMKGLPPSSFHLLAIRSSHASGDYANMSRDPLLNVQRTYSQ
MSPLEAQKFNLWNTSHSFNSSASLLPEGARLVRRQDGQTDLTIVVYDNEP
TSVISYALSSKEHKDWIADEPCEFEEAWNAAQLKRENSVASTIPAWQSFG
SVDLDYIHYGSYGSEDVSTTISTMLTDTTNSSSHFKIAFEDDNPSAGGRV
KFSVTCYFPKQFDVLRKKCSCSQIDLVRSLSRCKRWSAQGGKSNVYFAKS
LDERFIIKQVTKTELESFEEFAPEYFNYMKDSLDSRSPTCLAKILGIFQV
TVKHLKGGKETKMDLMVMENLFFRRNISRIYDLKGSLRSRYNSDTTGVNK
VLLDMNLLEALRTNPMFLGSKAKRSLERAIWNDTSFLASVDVMDYSLLVG
VDEEKKELVVGIIDYMRQYTWDKHLETWVKSSGILGGPKNAAPTIVSPKQ
YKKRFRKAMTAYFLTVPDQWSA
| Relationships |
|---|
| The mRNA, XM_017363032.1, is a part of gene, LOC108195990. |
| The polypeptide, XM_017363032.1, derives from mRNA, XM_017363032.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |