| 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. |
CCCATATATAAAACTGTGGAGCTGAGAACTAGAGAACTAGGGTTTATCTC
AAATTCTCAATCAAGCAACCTCACTCTCCATTTCAATGGCATCCAAAAAC
AAGAGAAAAAAGGCCAAGAACAAGAATCAAAACAATCTGCAAGGCGAGAG
TAAACCTCATTGTTTGCCGCCAAAACAAGATCATATAATTAAGACGGAGA
CAGAGAAGTTGTTTGAGAGGGTCAAGGCTAAAGTTGAGGCCCTCAAAGCT
GCTATATCCACTAATGCTGGTAGTATCCCTTTCCATGATACGTCTGCCTC
TACACCCGAGAAGGCAGAATCACTTGAAAAGAAAATTGAAAATGGAGGGC
CTGACGACCTTCATGATTTACCAAATGTTTCTGAAAGAGCGGAAGTGACA
GCTGACACCGACCCACTCCTTGTTAGTGACAAGGTACAGAACTTGGCAAA
TATCAAGGTCCCCCAGCCCGTGTCAAATTCTGGATCTGATCCTAAAATTT
TAAAGCGTGAGAATGACGACAATACTGGTTTAAAACCGAAGAAAAAGATG
AAGAAAAAGGCCTCAAACATTAAGATTCAGACACTTCTCAAACAATCCGA
CGATTCTTCCCCGATTGTCGGACTTGGTCCAGCCAGTATCGATCCAGTTA
AGGAATCTTCAGCTCAAGAACTGCCTGAGTGCGAGGTCCCCCAACCGGTG
TCAAATTCTGGATCTAATCCTAGAATTTTCAGCTCTAAGAATGAGGGCAG
TACTGTTTTGAAACCGAAGAAGGTGACAATGAAGAAAAAGAAGAAAAAAA
CAACAAATATCAAGATTGAGACACTTCTTGAAAACTCCTCCAACATTTCC
CCGATTGTTGGATGCGATCCATCCAGTTTTAATCCCGTTAAGGAATCTTT
AGATCAAGACTTGCCTGACTGCGAGGTCCCCCAGCCCGTGTCAAATTCTG
GATCTATTCCTAAAATTTTGAATTGTGAGAATAACACCACAAATATTAAG
ATGCAGACACTTCTTGAACAATCTGCCAACACTTCCACGGTTGTTGGATG
TGGTCCAGCTAGTATCGACCCAGTAAAGGAATCATTAGTTCAAGATTTGC
CTGAGTGCGAGGTCCCCCACCCCATGTCAAATTCTGGATCTAATCCTAAA
ATTTTGATTAGCGAGAATGACAACAGTACTGCTCTGAAACCGAAGAAAAA
GACTACAGATGTCAATATTCAGACTCGTCTTGAACAATCCGCCAACACTT
CCCCGATTGTCGGATTCGGTCCAGCCAGTTTCGATCCAGTTACGGAATCT
TTAGATCAAGAATTGCCTGAGTGCAAGGTCCCCCAGCCAGTGTCAACTTC
TGGATGTGATCCTAGAATTTCGAAATGTGAGAATGACGACAGTACTGTTT
TGAAACCAAACCAAAAGACCACAGATATCAAGATTCAAAAAAATATTGAA
CAATCTGCCACCGCTTCCCCGGTTGTTGCATTCGGTCGAGGCATTTTTGA
TCCAGTTGAGGAATCTTTAGTTCAAGAATTGCCTGAGTGCGAGGTCCCCC
AGCCAGTGTCAACTTCTGGATGTGATCCTAGAATTTCGAAATGTGAGAAT
GACGACAGTACTGTTTTGAAACCAAACCAAAAGACCACAGATAACAAGAT
TCAAACAAATATTGAACAATCTGCCACCACTTCCCCGGTTGTTGCATTCG
GTCGAGGCATTTTCGATCCAGTTGAGGAATCTGTAGTTCAAGAATTGCCT
GAGTGCGAGGTCCCCCAGCCCGTGTCAGATTCTGGATCTGATCCTAAAAT
TTTAAGTTGTGAGAATGACAACAGTTCTGTTTTGAAACCAAAGAAAAAGA
CCACAGATACTGAGATTCAGACATATCCTGAACACTCCGCCAACACTTCC
TCGATTGTTGGATTCGGTCCAGACCGTTTCGATCCAGTTAAGGAATCTCT
AGTTCAAGAACTGCCTGAGTGCGAGAATATTAAACTTGAATCTTTGCGTA
AAAATCGAGATCCTGTATCAAAGAAGGATTTGGAGAAGTCTATTGACTCT
ATTCCTGAGGAGGTCAAGGTTAATATTGTGGCTCACAAAGCTGCTGAAAA
CATGAATGCTCCTAATATCCCATTTTATGATATGTCCGCCTCTACACCTG
ATAAGGCTTATCCACTTGAAAAAATTATTGAAAAAGAGGAGTGGGACTGC
CTTGGCGATTTACTCAATATTCCTCGAGGAGCAAAATTGAGCCCTGAAGC
GTACCCAAGTTTTGTACGCAACAGAGTACACAAGCTGGAAAAGATACAGG
ATGAGCACGAGAAAAGGACAGTGGCTAGTGTTCTTCAGTACATTACGCAT
CTCATCAAGTACAAAGACAAGCATTTATCGGGCTGTTACAACAAGTTTGT
GAAGGATCACAAATTTCCAAGTATAATAGAAGAAAAGTTCCAAGCCATGT
TCAGTGAATCAAGTTCTGAAGCTCTTCCACCTGCGAAAAGGGAATTACTC
GTCAACTATGTGTTGGTGCTATCACTTTTTGTCGATGGTTATAAGTCTAA
TGCCAAAGACATAACGAAAGATCTGAAGATTAAAACCGAAACAAGGCCGA
GGGAAGGAGGATTCAGAGCCACCCTTTTTGTCTTTGGACTGATGCTGTTG
GATAATATAGGCTTTGTTGCTAACATGGCAAGCCTAGTGCTGTATTTCAT
GAATGTGATGCACTTTAGTATATCTGGCTCTGCAAACACCCTTACCAACT
ATCTGGGCACTGCTTTCTTGCTCACATTAGTTGGAGGGCTAATCTCCGAC
TCGTACATGAGCCGCCTCAACACTTGCCTACTGTTTGGAGGGATCGAGTT
GCTGGGATATTTGTTGCTGATTATTCAGTCTCATTATCCTGAGCTGCAAC
CTGAAGTCTGTGGGAAGTACAGCTGCGTGGATGGTACTAAAGCTCTGCTA
TTTTACGCTTCCATATGTTTTGCTGCGCTGGGAGGCGGTGGACTTAGAGG
GTCAGCACCTGCTCTGGGTGCTGACCAGTTTGATCCAAAGCAAACCAAAG
AAATAGCCAGCTTCTTCAACTGGTTTCTGTTCAGTATAACTGTTGGAGCT
TCTATTGGGGTCACAGTTGTTGTGTGGGTAAGCACGAATAAGGGTTGGGA
CAATGGCTTCATCATAAGCATGGTTTGTTCATTCATAGGTTTCTGTTCAG
TTGCAGTAGGGAAGCCTTATTATCGTGCCCGTGTTCCTGGAGAAAGTGTC
TTACTAAGAGTCTTAGAGGTTCTGGTAGTGACAATCAAGAATTTAAAGGT
GGAGTTACCACAAAATTCACGGGACTTGTATGAAATAGATGACATGGGAA
GAGAACGCATCAGGCACAGCTACCAGTTCAGGGTACTAGATAAAGCAGCT
ATACTTCCCGAAGGAACTACTCCAAAGAAATGGAAAGTGTGCACAGTGAC
TCAAGTCGAAGAAGTTAAAATCCTAACAAGAATGATGCCAATTCTGCTCA
GCACTACTCTCATGAACACATGCCTTGCTCAGTTACAAACATTCTCTATC
CAACAAGGTTCCCTGATGAACACAAAACTCGGAAACTTTAATGTCCCAGC
TGCCTCAATTCCCATCATACCGCTATTCTTCATGTCCCTTCTCATACCAC
TGTACGAAATTTTACTGGTCCCCTTACTGAGGAAACTAACAGGTCATCCA
AATGGAATCACTCACCTGCAGAGAGTCGGGGTTGGTCTAGTTCTCTCCGC
GATTTGCATGACACTAGCAGGAATCATAGAACTCAAGAGAAAGAATGCAT
TTGTAGACCACAATACCCGCATTAGCCTCTTCTGGCTATCATTTCATTTT
GCAGTATTTGGAATAGCAGACATGTTTACATTGGTAGGCCTACTGGAATT
CTTCTACAGCGAAGCTCCTCCTCGCATGAGATCACTCTCTACTTCTTTCT
CATTCCTTTCGTTGTCAATAGGCTACTACTTGAGCTCCGTTTTTGTGGAG
ATCATCAATTCTGTAACTGGTAAACTTAGTTCAAACAACGTCGGGTGGTT
GGAAGATATGGACATGAACAAGAATCATCTCGAAAGATTTTACTGGTTCT
TGGCAGTTATCAGTGTGCTCAACTTTGGGAATTATATCTTCTGGGCTAAC
TGGTACAAGTACAAGAAAGATGTTCCAGTTGACAGACAAAAGCTGATGGA
TCAATCTTTCTCAGACGCGAGTATGCGTTTTACAGCCAAAATAGATGATT
TGATCCCTCCTAGTAACAAAATTTAATCAGTAATCCCTGTA
MASKNKRKKAKNKNQNNLQGESKPHCLPPKQDHIIKTETEKLFERVKAKV
EALKAAISTNAGSIPFHDTSASTPEKAESLEKKIENGGPDDLHDLPNVSE
RAEVTADTDPLLVSDKVQNLANIKVPQPVSNSGSDPKILKRENDDNTGLK
PKKKMKKKASNIKIQTLLKQSDDSSPIVGLGPASIDPVKESSAQELPECE
VPQPVSNSGSNPRIFSSKNEGSTVLKPKKVTMKKKKKKTTNIKIETLLEN
SSNISPIVGCDPSSFNPVKESLDQDLPDCEVPQPVSNSGSIPKILNCENN
TTNIKMQTLLEQSANTSTVVGCGPASIDPVKESLVQDLPECEVPHPMSNS
GSNPKILISENDNSTALKPKKKTTDVNIQTRLEQSANTSPIVGFGPASFD
PVTESLDQELPECKVPQPVSTSGCDPRISKCENDDSTVLKPNQKTTDIKI
QKNIEQSATASPVVAFGRGIFDPVEESLVQELPECEVPQPVSTSGCDPRI
SKCENDDSTVLKPNQKTTDNKIQTNIEQSATTSPVVAFGRGIFDPVEESV
VQELPECEVPQPVSDSGSDPKILSCENDNSSVLKPKKKTTDTEIQTYPEH
SANTSSIVGFGPDRFDPVKESLVQELPECENIKLESLRKNRDPVSKKDLE
KSIDSIPEEVKVNIVAHKAAENMNAPNIPFYDMSASTPDKAYPLEKIIEK
EEWDCLGDLLNIPRGAKLSPEAYPSFVRNRVHKLEKIQDEHEKRTVASVL
QYITHLIKYKDKHLSGCYNKFVKDHKFPSIIEEKFQAMFSESSSEALPPA
KRELLVNYVLVLSLFVDGYKSNAKDITKDLKIKTETRPREGGFRATLFVF
GLMLLDNIGFVANMASLVLYFMNVMHFSISGSANTLTNYLGTAFLLTLVG
GLISDSYMSRLNTCLLFGGIELLGYLLLIIQSHYPELQPEVCGKYSCVDG
TKALLFYASICFAALGGGGLRGSAPALGADQFDPKQTKEIASFFNWFLFS
ITVGASIGVTVVVWVSTNKGWDNGFIISMVCSFIGFCSVAVGKPYYRARV
PGESVLLRVLEVLVVTIKNLKVELPQNSRDLYEIDDMGRERIRHSYQFRV
LDKAAILPEGTTPKKWKVCTVTQVEEVKILTRMMPILLSTTLMNTCLAQL
QTFSIQQGSLMNTKLGNFNVPAASIPIIPLFFMSLLIPLYEILLVPLLRK
LTGHPNGITHLQRVGVGLVLSAICMTLAGIIELKRKNAFVDHNTRISLFW
LSFHFAVFGIADMFTLVGLLEFFYSEAPPRMRSLSTSFSFLSLSIGYYLS
SVFVEIINSVTGKLSSNNVGWLEDMDMNKNHLERFYWFLAVISVLNFGNY
IFWANWYKYKKDVPVDRQKLMDQSFSDASMRFTAKIDDLIPPSNKI
| Relationships |
|---|
| The mRNA, XM_017363111.1, is a part of gene, LOC108196040. |
| The polypeptide, XM_017363111.1, derives from mRNA, XM_017363111.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |