| NCBI Gene |  |
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| Relationships |
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| The genetic_marker, MK005461 K2905, is located in gene, LOC108198614. |
| The genetic_marker, MK008927 85036.32205, is located in gene, LOC108198614. |
| The genetic_marker, MK009899 8_31386563, is located in gene, LOC108198614. |
| The mRNA, XM_017366367.1, is a part of gene, LOC108198614. |
| The genetic_marker, MK019023 8_31386132, is located in gene, LOC108198614. |
| The mRNA, XM_017366368.1, is a part of gene, LOC108198614. |
| The mRNA, XM_017366369.1, is a part of gene, LOC108198614. |
| 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. |
| Transcript Name | Identifier | Type | Location |
|---|---|---|---|
| XM_017366367.1 | XM_017366367.1 | mRNA | DCARv2_Chr8:31380525..31385839 |
| XM_017366368.1 | XM_017366368.1 | mRNA | DCARv2_Chr8:31380525..31385839 |
| XM_017366369.1 | XM_017366369.1 | mRNA | DCARv2_Chr8:31380539..31387037 |
AAATGATTATTACAGTACACAGTACCAAGCTGAGTTAAGTAGGGTTTAAG
CCAAGAATCCAAGTCAACATTTTTAACCCTATCAGCCGGCCACTCATTGT
TTCTCCGGGCACCTGAAATGACATTCCGGACATCATTTTCACTACTCTCC
AAGCTCACTCGTCACCGCCGGCAACTCGCTTATAAAAATCCAATCTTTTT
ACACTCCACCACAATCTTAACCTCCCCGTCATCACCATTTCTGCGTCGCC
ACTCTTTTTCTTCTAATCATCCGCCCGATTTTAAACCCGAACAGGTTTCA
ACCCGACCCGAATTTTCTGATCATGGGTTTGATTATGGACTTTTTAATAC
TGTACCTGATGCTGTTGATGAGCAATCCGATTTCAAACCCGACCCGGACT
CGGTTACGATCCGACCCGATTTTTCTGATCAAGGGTTTGATTCTGAAATT
GGTAGTACTATGGCTGGTGTTGTTACTGAGCAAGATTCGATTTTTCCAAT
TCGTGCTTTGATTTCAGTTCTTGATGGTTATCATGATTTTTCGGGTTTTT
CGTGGTGGGTAATTATATCTTCCTCTGTATTTGCTTTTCGAATTGCTATG
TTTCCTGTAATTATATATCAGTTAAGTATGCTTAAACAGATATCTATGCT
TTTGCCTAAGTTGCCCCCTCCGTTTCCAAGGCCTTTTTCGGGTAAAAGTT
ATGTAGAGCAGTTTAAGTATTTTACGAAGGAGAGGAAAGCTGTTGGTTGT
CCGTCGTTGGTGTGGCACATAGTGCCGGCTGTGATACAAATGCCTTGTTT
TATTTTGGGTGTTACTACGATTCGGAGGATGGCTTTGAATCATCACCCGG
GGTTTGAGAATGGGGGTGTTTTGTGGTTTCAAGATCTGACGCAAATGCCA
TATGGGGTTTGGGGTGCTGTGTTTCCTTTGTTGGTTGCAGGGTTGCATGT
GACAAATGTGGCACTTACGTTTGGTAAAATGTCAATTAATGAGTGGCCTG
ATAGAATGAGGTTAATGCTTAGGGGGTACAAGTTTATTTTGGATGGTTTG
GTGTTGCCTATGTTTATTGTTGGTTTTTTTATTCCGCAGGGGGGTTCGGT
TTATTGGGTTGCAAATAGTGTTTCAACTTTGATCCAGCATTTGTTTATTG
GGAATGCAAGTGTTCGTAGTTATTTTGGTCTGCCAGTGAAGGATGGTCCT
GGAAAGGGGTTGGCTAAGAATGAGAATACCCAAGTAGATGAGGCGCTAGG
TGTAACTTTAGTGGATACATCAGTGAAGCATCCCAAGAAAGTTTCTGCGA
AAGATTTAAGTCCGAAAGAATTGGTTAACCTCTCAATTCAAATGTTAGCA
AAGGGGGATAAACAGAAAGCTGTTCCATTATTAAGACTGGCACTGAAGAA
GGACCCCGAACACATAAGGTCGTTGATTGTCTTGGGACAGACACTATTGC
AAGATGGAATGCTGGCCGAGGCTGTTGAGAACTTGGACCATGCAGTTTCA
AATATACTTCTTGCAGGTCCTCCAAGCAAGGTTGAAGAAATTGATCAACT
GATTCTCGCTTCCATGTGGTGTGGTGTTGCCTACATAAGGAATGGGAGGA
GTGCAGAAGGCATTCCACATTTGGAAAGAATCGGCCACATGAATGAGCCG
GCTGATGCGAAGAGCAAAGCTCATTATTACGATGGGTTACTAATGCTTGC
AAGTGCTTTAGTTAATGAAGGTCGTAAACCTGAGGCTGAAAAGTATTTGA
ACAAGGCTGTCGCGTACAGCTCCGCTTATAATGTGTACCTGGAACACTTG
CACAAGGAAGATGATCATATAGTAAGTGACATGGTCAATAACAAAAGGAA
GGGACAATGAGTTACTCCATGCACAGTATGAATGATATACGAAGACCAAA
AGTTTGCCGTTAGATATCCAGGTGACATATACATATTTTTTAATTTTGTT
TTGGAATCAAGTTCCTGAAAACAATAAAGAGGAAGAAACTATCGCTCATA
CAGAAATACGTCAACGTTTCTCGTGTGGATATATGTCAAACTGGCATCAT
CAGTGTTTTGTTTTTTTGTTCTTTTTTAATTTTTTGCTAATTAAGTATTA
GCAAAAGAAAAAGTGTTTTCATTAAAGAAGCAAGAGAATATAATAATACT
AGGTAGTACTATTGTTTAAGGGTTTATGAGGAAGGAATTGGGCCAAAGGC
CTTCATTGTAACTTAAGAATGCAAGTCCAATGCTAATTTTGAAACAGCTA
TAACTTTTACTACATTTTGGCACTAAAGAGTGTTTTTTGGTGCTAAAATA
GAACTTTTACTCCTATGCTAAGCTTAAGTAGCTATAGATTTTGTTACATT
TTAGTTAAAACTCATATAAAAAAGCATTCCCTCTTTAGTTTTTTCTTCTA
TATAAGTTGATGTGGTAAGGATAGTTGTAGCTAACTTTGGTAATAATTAT
TCATTTGTCTTATTTTCAATTTAGGCATAGCTATGCATGGGATTGATTAT
TTTGCACATATAGTTCCGTAAGACAAATTTTAGCTCGAGAGAGCCCTATA
ACACTGCCCCACAGATTGACATTACAACATAGAAGGGATGGAGGGTGTTT
AGCAAGCTTTACCTTCACTGGGAGTTGTAGCAGTTGCCGTTCTTACTTTA
CGTAGCATCTTAAATGAGTGTAGATAAGTCCCTAATATATATACATAGGA
AATTGAGGAATGAATGTATAATATATATGAATACTGATGTAGCATTGATG
TACTATTAATAATGTCTGATAATTAGAAAAAAAAATACACAACTATATGT
AGAAACTTAAGAATTTGTTGTAAATATTCTAGTCAAATTACTTTTTTTCC
CCGCTAAATAAGTCAAATTACACGTTTAAGGATTGGTAGATACCATGAGG
CCTAAATGTTCATTTTTCAACTGATTAAATTTCATCTGTTCTGTGATGTG
CTATCATCATTCTCAACCTGGCTGCACTTGATACCGAATATAATTTAATA
AAAATTTAAAATCAGTTACTTCTGTATACCACCATAGATAAAGGTGACAG
CAAAGTGTTGATTCTGTTATACCCAACATGTACAACATGTTTGATACCAC
ATGGATGTAAGGTCTTAATCACTTCATCGTGCTTATCTTTTAGATATTTC
TCCAAGGTGTTGGGAAAAGGTTTGTGATATACTCAGCAAAAGAAGGTTGC
TTTTTGATATCTAGGTCACTGACGAACACTTTCTGAATTTTGTTGTTGAA
GCAAGGTCATATACACAGCAAAGAGGTAGAAAGTTTTATTTTATATTATT
GAGTGCCATACAAATTTTAGCTGTATTTTATTTTAAGTTGTTTCCTTAAA
CCTTGTTGAGAGTGAAATCATGTCCTTTTGTATTCAGGCTACTCATTTTT
TTCTGGATACATTCTGCTCTATAAGTAGTCATATCTAGCATGCAAAAAGG
ACCTTCTTCCTGGCATTAAGTTAAAACATCCAGAAAGACTTGTGCACTTT
ATGACACTCGATATTTCTGTTGTGCCCATTTCTGAAAAATACAATGAATT
TTAGCGATTACACAGATGTGAATAAGGAACAGTGTTTCATTCAGGTTTGG
ATAGACAGCAAGGTTTCTCTCAGGTTTGGATAGTAGCAATATCTCACTCC
TGGAATGTTTTAGCTTTCCCTTATTTATCACTCACAGTGCTTAGATATAC
ATTTCCTTTACTTATATATTAACTCAGTTTTGTGGAACTTATCATGCCCT
TACGCGTGCACCAGGCATGTCCAGCTAACAAATTTTATTTCCAACTTTCC
TAGCACTGTGCTTAAACATATATCTATAATTTTTCCTAGATTGTCCCACT
GTTTCCGCTTCTCATGCTAATTTTTGGGTAAAAGTTATGTAGAGTTTAAG
TACTTTACGGGACAAAGAAAAGCTCTTGTTTGTCCGTTTGTGGCATGGCA
CTTTGCGGCTGTGGTGATTTAAATCCTTTTTTTTTTGTTTTGGATTTTGC
TATCATTCAGATAATGGCTTTAAATCATCAAGCAGGTTTTGACATCGGGG
TTATTTTGCTTATTTAAGATTTCACTCTAATGCCACGTAGGGTTTCTGGT
GCTGTGTTTCTTTCATTAGTTGCTAGTTTGCATGTGACTAACGTGGCACT
TACGTTTGGCAAATTGTCGATTAGTGAGTGGCTTGATAGAAGGTTATTGA
TTAGTTTGCAGAAGTTTTTTTTTTGGATGGTTTGGTGTTACCTATAATTT
TTTCTGGGTTTTTATTCTGCAGGAGGGTCAGTTTGTTTATTGGTAATGCA
ACTGTTCGTAATTATTTTGGTCTTTTGATCTGCTGGCGAAGGATGGTCCC
AGAAAGATGTTGGCTAAGAATGAAAATGCCCAAGTAGATGATGCGATGAA
GGTCATGGGAGAAACCCGACGTTGCGTTTCGTATTCCACAGGGTATGATA
CTGGTCTCTGCGATCAAAAAAGAGGGTTGTAATAAAATATGTAGGAGCTT
ATTTATTAGAAGCTTTAAGTTCATCTCCAAAAGTATAAATTGCATTGGAA
TCAGAATGGTTCCTCCTACTCAAAACTCTTGTGAGTGAGCAAAACAAGCT
ATACCTGATACCTCAATAGCCCTTGATCTGGATTATCGGTTGAAAGAAGC
ATTCCTGCATTAACCTACCTTTTTAAGAAAGAACAAAGCTTTTCGGGATC
GGACGTCCAATAGGCCTTAAGAAGAGATGTAAATATAGTGCATACATCAG
TGAAGCATCCGAAGAAAATTTATGCGATAGATTTAAGTCCTAGAGAGTGG
TTAACCTTACAATTCAAATGTTGTCAGAAGTGTCATCAACAGAAAGCTCT
TCCACTACCAAGACTGGCAAGTGCTTCACTGAATGAAGGTTGGAAGACTG
ATGCAACAAGAAAAGCTCGTTATCCTGATGGGTTACCAAAGCTCGCTGGT
GCTTTAGTAAAGAAGGTCGTAAGCCTGAGGCCGAAAAGTATCTGCACAAG
GCCGTTGTGTACAGCTTTGCTTCTAATGCTTACTTGGAACCATTGCAAAT
TGAAAAGCTTCGTTTAATTAGTGATCTGAAATCTGATCAACAAAAGCAAG
GACCAAAGAGTTGCTTCATGCAGAATATAGATGTTGTACGGAGAATAGAA
AGTTTGCTTCTCTACATTTGGGTGACTGATGCATACTTGTTTGGTTTTGA
ATTGGAACACTGTTCCTATGCGTGACATGTGTGATCAGCATTTTTCTTGT
AGGCATTGTGAATTTGAGGGGTGTTTTCCATGTGCCTGTCTCTTTTTGCC
GATAGTTAATCCCAGCAAGACGGCCATAGCTGCATGCTAGATATACCTAC
ATTATAAGGCATGCAGTCGTCAGATATTTAACGAAATCCTTTGTTCATAT
ACATATAATTACAGTCTTAAAAAATATGGTGAAACAAGAAGCTGAAGACA
AAATACAGCAGAAATTTTATGTTTCCATGAGTGAACAGAAAGAGGCAGAA
ACTTATGCTCCTTAAGAACTGAGTGCTGCAAAAATTCCTGCTGTATGTTA
TGTTAAGCTTGTTGTTTCACTATTTCTTTTCAAAACTGTAATTATATCCT
GTTATAGAATACACAATATAAGGTTGAAACTTTTTTCTTATACCTAATTG
AATGCTGCACAATATTTCTTTTGTATTTTGTGTCAAGTCTTTTGCTAGAC
TATATTGTACAGATAGTTTGTAATTAAGGTTGTTGGAGGGAGAAGAGTTT
TGTATACTTCTGCCTTTTTGGTATTGGTAATTTGGGCTGGACCAAAGTAT
ATAGTAGGCTGTAGGCCCAACATGTCTGGCATCAATTCCTCCCATGTGAG
ACTGATTGGCCTAGTTTCCACCCAGGCCTTAATAACAAGGCATGTAAGGT
TATCCTTATATATCTAACTCTTTTATCTAGTGGTGTAGCATCATCAGATA
CTATTTTCTTGAGAGACTGAAGACCATCCCCTCTTTTAGATCGTCTCAGG
GTGTGAAGGTGCAGCATATAGAAGCAATGGATGGAATTCAGCAACTAGGT
CTCCCCTTGCTTGGAGTTGTAGCTGCTGCAGCTGTTACTTTTTACGTGGT
CAGCTTTAATGAGCTTAGAGAGGTCTCTTTCCCCCCCGCTCTCTATGTAT
ATGCATGTGTGTTGGTAATATGCAGATTGTTGTTGATAGGTGAATCTGAT
GTGTTCTTGTAATGTTGATTGTGCAGAAATCTTTTAGAGATCTGGATGAT
GCCGAAGATGATGAAAATGGCGGGTTTAAGCCTTATATGAGGTCCAGAGG
AAGGAGAGCCAAACGAAAGGCCGACAAACAAAACAAACCATAATTAGTTA
CTTAAAGATTGCATTTTTTTATTTTTTTTTGAGTTTCTTCACTTAGCATG
GAATATTAGTGTTTAAGTGATTGTTTTTGTCATTGGTATGGTGAATTTTG
TGATGATTTAAATAGAGAATGGGAAGCTCTGGCTTTATATAGACAAATAT
ATCTTCTTTTCC