| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017402963.1, is a part of gene, LOC108227684. |
| The genetic_marker, MK003323 K0767, is located in gene, LOC108227684. |
| The genetic_marker, MK010270 6_26826916, is located in gene, LOC108227684. |
| 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_017402963.1 | XM_017402963.1 | mRNA | DCARv2_Chr6:26824809..26831986 |
AGGGGCTGATGAGGTAAATAATAGAACCCGTAATATCACATGAGCAACTC
GACACACCAACACGGCACCGTTCTCTCTCCGTCTGTCTCTTCTCTTCCCA
CAACTCTCATAGGGCTTCGCTCCTCCCCCTTCTACTCTCTCTCTAAAAAA
CATACAAATCACCTATTCATTTTCCACTCGATCTGCGACTCACTCTCTCC
CACCTAGTTTCACGATCCATTCTTATCCGATCCCCAATTCTCTCTCTCTC
TCTCTCTCTCTCCCTCCTCTCTCTGTCTCTCTCGTCCCCTCTCTCTCTCT
CTCTCTCTCTCTCTGTTTCCACTGTTCTTTCCTACACTTAAACAGATCCA
AACAAGTAAATAGAGAGAGAGAGTAGTAGCGTGGGGGCATTTTCGATGGG
AATGCCCGAACGATGAGCAAAGCCAGCATCCAACAACAACAACAACAAGA
CGAAGAGTGTTTCCACGATTCTCTCGATCGCATTCTCTCCTCAACTAACT
CCTCTTGCTCTCCCTCTTCTTCCGAAGAAGAAGAAGACGAACACGACGTT
GCGCATTCCCCTAATTTCAACCCTAATTATGCTCAAAAATCGAAATTCCC
CATGGGCGTTTTGCACAACTACGACGTTTGGATCTCCCAGCCTTCTTCTG
TCCAGGAACGCCGCTCTCGTCTTCTCCGTAACTTAGGTCTCGCCCGTGAT
TCTAAGTTTAGTAGATCGCTCGCTTTGGATCACGGTGAGATTCAATTAAA
CAATGATGATATTCATAATGATAATCAAAATGATGTTCGTGTAGCTGCTA
GTTGTAATGCCGAAATGTTGCGATCTAAATCCGATGGTGACACGGGGAAA
TGTAGTAGTAATGGTAATGGTTTTTGTAATGATTCTGTTTGTTGTTTGCC
CGAAATTCTTTGTATTGATTCCTCTGTGGTGGTAGGTAATGATTTAGGGT
GTTGTCATGGGACGGTTGTAAATAAACATCATAATCGGTCTTGTAGTGGA
TCAGTAGCATTGCCGGGTGGTAATGGTAGTACTGTTTCGCCTAATAAGCC
GCCTCTTGGGAAACATAGTCGAGTGGATTCTACAAGAAAGAGTTTGAGTG
GTAACTGTATCTCGTTTGTTGTTAGGGAGAGTGGGGGCGGGGAAAGGGCA
AGGGTAATGGAAGGGGAGGGGGATTTGGATTGTGATTTGATTGGTAGTGT
TAGCGATCCTGCTTGCACGATAAAGAATCTTGATACGGGGAAGGAGTTTG
TGGTGAATGAGGTCAGAGGTGATGGATCGTGGGAAAAAGTTAAGGAGGTT
GCTACGGGAAGGCAGTTGACTATGGAGGAATTTGAGATGTGTGTTGGGCA
TTCGCCCATTGTTCAGGAATTGATGAGGAGACAGAATGTAGAGGATGGTA
ATGATAAGAACAATTCGGATTATAATGGGAATGGTGATGGGGCAAAACTG
AAAAAGAAAGGTAGTTGGTTGAAAAGTATAAAGAACGTTGCTAGCTCTGT
GACAGGCCGTAAGGAGAGACGGAGTAGTGATGATAGAGATACTGCTTCAG
AGAGAGGTGGGCGGAGGTCAAGTTCTGCAACAGATGATAGCCAGGAAGTT
TCATTTCATGGTCCAGAGAGAATACGGGTCAGACAATATGGCAAGTCATG
TAAAGAGGTGACAGGGCTTTACAAGAGTCAGGAAATTCTGGCTCATACCG
GATCTATTTGGACAATTAAGTTTAGTTTAAATGGTAAATATCTTGCCAGT
GCTGGTGAGGACTGTGTTATTCATATATGGAAGGTTGGGGAATCCGAAAG
AAAAGGCGATCTTTTGTTAGATAAGAGCGAAGATGGGAATCTGAGCCTTC
TACTTTTAACTAATGACTCGCCTGAGCCAAATTCAGGATCACCAAATTTT
GGGAGCCAGCTTGAAAAGAAACGAAGAGGACGGTCATCTATAAGCAGAAA
GTCTGTCAGCCTTGATCATGTTTTTGTTCCAGAGACGGTATTTGCACTTT
CAGAAAAACCTTTCTGTTCATTTGAAGGACATTTAGATGATGTACTTGAT
CTTTCATGGTCCAAGTCTCAGGTAGTAATGAATTCCTTTAGAAAATATAT
TTGTGTGTGCATTTTGCTGGCTTTATGCTCAACCTGTGACAGCCAATATC
TATTACATTGCTTCCATCTCTTCATGTTAATTAGAGGCTTCAAATTTTTA
AAGCTATGTCTGTTCAGTATATGTTTAATCATGCACTATGTTAGGAAACT
TACATTTTCAGTCGAGACAAATTTATTAGATTTTTTTAGCAGGTTTGTGG
TTGTAGAGAGAGATATGTCTTGATAAATTGTAGCAAGACAAGTGGCGCTA
AATGTCTCTGAACTAGTAGTAGTATGTATCTTTAAAATACTATATGCATT
GAACTCCTTCCTGACAGGAACAGTGATCTCTTGTATGGTCACCAGTGAAT
CTGTATGCATTCATTGATACGGTGGCTTGGATTCCAAAAGTAGGAAGTTG
CAACGCGTGGAATATATTCTAGTGTTACTAATTAAGAAAAATCATTAAAT
ACTTTTATGCATCACATGCATATTTTTTGCTGGTCTTGTTTGTATCTTGT
CAAGTGTCGGCTTAAATATTATTATAATGTGTTTACGTGCACAGTGATTA
TTGATATATATTATTAGTTGAACATAGATAACATAATATGTGGATATATA
CTGTTAGCTGATAGTGATAATGTGATATGTGGGAATGGTGTTGATGCTTC
AGAGCAGTTTTCTCGAATAGTATGCTAACCTTTAGCAATGCTTAGTAATG
CAGTTTCAAATATCCTTGAAGAAATAAATGCATTTTTATTATAAAGCACA
AATAATTTGTAAATATGAAAATAAGTAAGTAATCTGTTTCTGTCCTCTTG
GTTTCTTTTTCCTGGGAAAGTATATTAGATTCCCGTGGAACCTAATTGAT
TGGAAAAATTTTCTCTTCAAATTGATCATTTTACAAGTTTTTTTGCTTTT
AGATTTTAAGAATTAATTAGAAATGATGTGCTTGATTGGTATTAGTAGCT
AGTGATTTGATACACTTGTACTACGACTCAGCCCAGGGTTCATCTTCTAG
GTACTGTCGGTATTCGTAATAAATTATATATTTACTGGTGCAGCATAAAA
TTTAGTACCTAATTGATGCTAAGATGATAGTGGAGATCAAGGAGACTCGG
TAGCTAGGAAGCATCGATTCTTGGGCAACCGACAAATCCCTGTATCCCCA
CAAACCCCTGTTTCGGGCCCTCGGATTCTTTGGGATAGTTAAAATAATTA
AATGCATAATATCTCAACTAAAGTTTTCATTCTTTACAATTTTTACAACG
ATAAATAATTATATGACTTAAATTCTTGTATTTTAGATGCTTGTATCACA
TATTCGACTCAATTCTGAAGTTATTAATATTGTTGGATTTTATCATTCAT
AACATCAAATATATAAATATAATATTAATATATATGGTGTATTGCCTCGC
ACCCAAATTCCCATATTTTTTGATCCCGCACCTGCACCCACACCCATGCT
TCTTAGCTCAGTAAACCATGTGATTCTCTAGTTTAAGGCTTTAAGCTTGA
TCTACTAAGCCCCAAGGAATATAAATCAACTTAAGTTTGATTGATTTTTA
TATGCATACTTTAGAAGTAGATGCATTAGCAAGGGTGTTACCTCGGTTGT
CAAGGTTAGTTGATGGGGTCCTTACTGAGCTACTGGTTGACTATTTGTGT
GCACTATTTGAAAGTTAAGAATAATAAATAATTAAATATTTACGTAAAAC
AATACAATGTAAAACACTTGATTTTGAGGTAACATAACTAATTGGTCCCA
AAATCAACATATCAAATCAAATTCTCAAGGCTGCACATTAATTGTACAGA
GATAAATTATTTATATTAATGCACTGTTATATTTATACTAATACTTGTAT
AATTAAGTGATAGATATATACAATTATGACAAAATCAGCCAACAGGGAGC
GTAAATCGAGGTTAAATATACATATATTATTTAATAGAATAATGTATAAA
TTAAATATATCAACTGGCCAGTCGACCGACTTGCCTTTAAAATAAAGCGG
GCAATTTGTCTACTTGTCGACTAGTTGATGATCAGCTGTCGAGGACTTAA
CAATAGTGATTATTTGCAAAGGCAGATGGGAGTAATTTAGGTGAAATAGT
TGGTTCAGAAGGATTACGTTATTATCTAAAACATGTACCGGGCTACTAGC
TATTTGGGTGCTGACTCTATGCTTGGTTTGATCGTAACGAAATGACTGTT
ATGTTTTATATATTCGTAATTCAGCTGGCTGTGTCTTTGTTTTCAAAAAG
AGGTTTAAGGGTGTTTTATGCATCTAATTGTCCCACGGGATTTTGTAGAA
ACAATGACCTAAATTTTCTAAGAAAGTTATGTTAGATACTGTAAGATATA
CCCTTGACAAAGCTGATAGAATGCGTGTGTTTTTAGACTTTAATCGAGTC
TGCTGTACTTAAATTCTGTAATTACCATATTCCCATAAATACGATTCTTT
TTCAGACTGTTATCTTAAAAGGTCATGATCACTGTTTTCAGCATTTGCTT
TCCTCTTCAATGGATAAAACTGTGCGGCTCTGGCACCTGACCAGCAAATC
TTGTCTAAAGACTTTCTCACACAGTGATTATGGTAAGTTTCCATTTCAGC
ATTTCTTATAAAAGCTTAATTTTTATACTCATGGTATAAGCTGTGTGCTT
ATACCCCTTTAGTTTGTTACCTTTTTATGCTGTTCGTCTTACTCCCTTCT
TCCTTTAGTAACTGGCTAAAACCTTATTGTTCTGATTCTTCTGCATTTTT
CTCAACACAGTTACTTGCATCCAGTTTAATCCTGTTGATGATAATTTCTT
CATCAGTGGATCACTAGATGCTAAGGTTCGCATATGGAATATTTCTGATC
GGCAAGTTGTTGATTGGAGTGATCTGCATGAGATGGTCACTGCTGCATGC
TATACGCCAGATGGTCAGGTTGGTTTTAATTGAATGTACTGCTATCTTCT
CATTATTTGAAGTGCCACAGCGAGTAGCTGCCATTCTGTTATATGCCTAT
ATTCAATTGTACCTCAAGATATTTTGTTGATTATGAAGGCTGCACTAGTT
GGTTCATACAAGGGAAGCTGTCGCTTGTACAACACATCTGGTATGGGTCG
TAGCTCTCTTTAGTCCTTGAATCGATTTTGTTCTCCCCTCTAATTAAGAA
AGAAATGCGTGTATGTTTCAGACAATAAATTGCAGCAAAAGACTCAAATC
AATTTGCACAACAAAAAGAAAAAAGGGCGTCACAGAAAAATTACTGGATT
TCAGGTAAGTTCTGTTGTTGGACATATTTTTATCTAGGTTTTATGGATAT
GAAACCTATGAACTTTGTAAAAGTGTCTTTAATTTGTATTACTTGTATGT
ATTTTCTGTCAAGAGCCATTCGCAAATGCAGATTATACTTGTACATTAAT
GCTGGTCAAATTTTTGCTCGATAATGTCTCTAATTAATCCAGTTGCTCAG
TTTGCACCAGGAAGCAAATCAGAAGTACTTATAACGTCTGCAGATTCACG
AATCCGAGTAGTAGATGGAGTTGATCTAGTTCACAAGTTCAAAGGTAACC
AACATTCACATTCATGGCCTCTTGAAAGTGAAACATTTTCAAGTAGACTT
TTATAGATTATTAGAACTTTCCTCTCGGTCAAGAGTAAAATGTTCGAACT
CAATGTGATTGCAAATAACGGATATATTAATTTTCATCATTTGTTGTTAT
CTGTATTGATTCCTCGAGTTGGACCATTTTCTTTAGCCTTTAATTGGCCA
GGTCTAACAGTATGTGTTTGTAGTTGGAATTTGCAGTTGGCCCGCTTAAA
TTATGTTTAGCATGTGTATATTGAGGCAGCAGCCAAAAGGTTGACAATAA
GAACTTGACTTTTGATTAGTGATGTGCGCCGGGTTTTATTTTGTGGGCGA
CACTGTTTCTATATTCACAATAGTTTGACATTTGAGGTTGTGGCCTAGTG
GTAAACACACATGACACACCATGGTCCTCCCCCATGACCATTGTTACGGG
ATCAATTCCCTACCCCCCACCCACACCAAAAAAAATAAAATGATGATGAT
AATCGTTATGCTTACAATTCTATATTACAAATCCGAATTGGATTTTTTTT
TATTCATTAGCTATTACATTTTCGGGGTTTTTTCCTCAATATTTTTGGTT
GGTGAATTGTATGATTTTCGTTACAGGGTTCCGCAACACAAACAGCCAAA
TATCTGCCTCCCTTACTGCTAATGGGAAGTATGTGGTGTGTGCAAGTGAG
GATTCTCATGTCTATATCTGGAAACATGAAGCTGATTCTCGACCTAGCAA
AAGCAAAGGTGTGAATGTCACACGATCATATGAACACTTCCACTGCCAAG
ATGTATCTGCAGCCATCCCTTGGCCAGGTATGGGGGACATTTGGGGACTT
CAAGATGGTTGTTCTGGAGAACTCAACGGACTTGATGATCATCCTGAAGA
AGCCTCCTTAGCGAATAACCCTCCTACACCAGTAGAAGATGCTAACGTTA
TTGAGAGCTCACCTTTGGCAACTGGATGTACAAGTAGCCCATTCCATGGA
ACCATCTCTAGTGCAACAAACAGTTATTTCTTTGATAGAATAGCGACATG
GCCAGAAGAAAAACTTCTTTTAGCTGCTAAGAAACGTAGCCCACATGTGA
GTGTGGACTTCTCAAATGGCGTTAACCAGAGACGATCAGCCTGGGGCATG
GTGATCGTAACTGCTGGTCTTCGAGGTGAAATCCGAACTTTTCAGAATTT
TGGAATGCCAGTGTGTATTTAGGGTCCCGAATATGTTGTTGGAGAGGCAA
TAGCTATCGCAGGTCATCACCCCAATTAATCCAAGTTGGCAAATTTGTAC
AGCAATATTTCACAAGATTTGTTATTAATGGTGAGTTCCATTTCTTTTTT
GATTTGTGTTTCTTGCCAGTCGAATTGATGATAGGTAGTCTGACTAGGCA
TTGAGAAAAAAAAGAGTAGATTTGTTAGGAATTACATATATATACACTAT
AGCTTTCTTTCTATCTGTGTAAATGCACCGGTCAGATATAAATTTTTTCA
GTTGTATTAATATCCAGTTTTCGGTTA