| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017387021.1, is a part of gene, LOC108214817. |
| The genetic_marker, MK004117 K1561, is located in gene, LOC108214817. |
| The genetic_marker, MK008210 3_43646513, is located in gene, LOC108214817. |
| The mRNA, XM_017387022.1, is a part of gene, LOC108214817. |
| The mRNA, XM_017387023.1, is a part of gene, LOC108214817. |
| 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_017387021.1 | XM_017387021.1 | mRNA | DCARv2_Chr3:43639719..43646582 |
| XM_017387022.1 | XM_017387022.1 | mRNA | DCARv2_Chr3:43639719..43646582 |
| XM_017387023.1 | XM_017387023.1 | mRNA | DCARv2_Chr3:43639719..43646582 |
AGTACAGGGGCCAGAGAGTTGGTACACACAACGTATCCAAACAGCCACCC
TACCCTACCCTAGTCTAGACAAGTCTGTCGTACCATAATACTTAACACTT
TCACCAGACACAACACCCTCTGATTTATTTACATGTACTTTATACACACC
ATCAACCAAGTCCTCCCCACGCGCTCCCCCAGCGCGTGACTCTCATTCCT
CTCTTATTTTCACCTCAAATTCACACCCACCAAAAACCCACAAGCTCTTT
CAGATTTCAGACAACCCCATCTCCTTATTACAACATATGCTTAGGTATAT
ACATACATATGTTGTGATATTGCTATTTATAGTAACCCTAACTTGAACTC
GTTCCCTTTCACATTACTCCCAGGTTCTATCTTAACTCCTTTTCGTATGT
TCATGTTTATGTTTGCAGAGGGACATGTACATGTGTTTATAGTATGTTGT
TGTGTTGTTTTATGGTTTGTTAAGTGATTGTATGCCTGCCCAGATCTGTC
AATTTTTGTTTTATGAATTGTGTTGGTATGCATTATCTGTGTTGACACTT
GGTGTTTCTTGTGCTTTTTCTATAGAATTTGTGTATGTTTATGTGTGAAT
TGTTTGATGAATTGGGTTGCCTTGTGATCGTAGAATTGATTCTTGATGTG
TTTTAATTGATACTAAAGTTGTATTAGTACAATGTGTGGTGCTAGGACAT
GTTGTAAATATGTGTGATGCTGGGAGTAATTGATGTTAGTTTTGTATATG
GAATATAATTGCTGTAAGATTAGGAATTTATTCTTGAGAATTGTTTCCGT
ATATGGGAAACGTGATTTTTATGTTTCGCAAAGTAGATATCGTTGTTTCG
TGGTACGAGTTGTATGACAAATTTTAATATTTTGTGTTTTTGAGTATGTG
AAGAGTTCCGGATTTAAAGCAGCCTTTTCGTAAAAATTGAGAAGTTAGTA
TCTTTATTGAGCATTTCATCTCTTTCCGGGTAATGGTAACTCCATGCTGA
ACTTGTTCTTTTTTTTGGAGAAATAAGAGGATAATTGTTGTGATAATTCG
ATTTTATTTTGGTCAAATTTCTAAGCATGTTTTGATGTAGTTTGGCATTG
CCTTGGAACAAATTGGGAGCTCTGTTATGCCCTGTAGTTGCTGAATGTAT
ATATGTATGTCCGGTTTGCACTAAATATGACGATTGATGAATTAGTTTTG
CATTGTGATCATAGGAATGAGCCTCAGTGCATTTTTAGTCATTTCTGTGG
CCGTACTATAACAATGTATGGGGCTATGCCGCTTAAAGAGGTTGTGGATA
TATGTGAATTGTGGTGTTAATAGTGAGTAATCTAGTTCCTTATATCGAAT
ATAATAATGTAAGGTTTAGAATCATTATTTATTCTCATTATAGTAGATGA
ACTGATAAGTTTGTATAGCAGTAAGAGGAATGTGATGGTTGTGAGAAATG
ACACCATTGATTCATGGTACGACTTTTGATATTTAAGACCTCTGTTATGC
CTTGTACTTGCTGAATTTAGTTGTGCAATAGTAACAATACAATAGAGCCC
ATGTCGCAGCATGTTTTACATATAAATGCAAGCACACACCATTTTGTATG
ATTAGGTTTTCAGATTACTACAACGAAAGACTAATATTTCGTGTACTAGC
AGTTGTTACAAACTTTCCTTAAGCAGTGTTACTGATATATTCAGTTGCTT
TCAACTTCAAATGCATTACTGGTTTAGTATTTGCTTATTGAGTATTGACT
TAGAAACGCAATGCTAGTCGGTACTGGTGTAGCCAATTTACTAGGTCTGT
ATGCAGGACCAGGCTGCTGCTAATAAATTTATTCATGTCGTTTGGAATCA
TTACATTGATTTCCATCAAATATGGCAATGAGTGTTTAGAAATGTAATAT
GGACATACATGGGTTCCTAGAGATGGATTGTTTCCGACTTTGATTACTCT
CCATGGGGTTTTGTCACATGTTTAAGTTACACAAGTACAACTGATTTTTT
TTTTTTTTCAGATCTTTTTTGCTTTTGTTTTGTACTTTGGTTTCTTCAAG
GCTAATAGATGTATTATATTTGGTGTTGTGATGCTGTCCATGCAGAATAA
ATGGAATAATTAAAATGATATTTAGTGGGTACTGACGAAATCATGAGAAA
GTGTGGACTGATAATTTACCACAATCATCTGGTTGATCTGGATGAACTCG
TGCTAATATATTATGGTCTTCCAGAAAAATCTTAATTCTGGCTATATAAA
CCCTGCATTATAATGCAACTTAGTATTAGCCAGGTTGTTATCCTTGATGT
TACTAAGCGTTTTACAGTATTTAGTAGTGCTTAGATGGCAACTTATTTCG
CCCTCCTTGAAAGTAGACAAGTTTAAAGACAAACTTGTGTAGTAACTTTT
TATCATTGTGCCATATAAAATAGAGGTTGTCGCTCTTAGATTTTTCTATT
ATTTTGTATTAATTTGCAATATTATTTAGTTTTGAAAGGTAACTTGTGAG
TTTTATTTACTCAAATGTCGATTATTGCCAAAAGACCGAGTTTGAGGCTT
TTACATGTGGATCCATAAACTTTAGGGCCTATTTCTAGAATTATCCATCA
TAACCTTTAGCCCAATTTGAAGAGAATTTGATGCAATCCAATATGACGCA
ATTCTAATTATTGAAAAAAATTCTATGAATGCCCAAGTCCACTATTTCTC
ACTAGTATAAATTCAACCAAACAAAGTCCAAGTTCTAGAGGAAGTTCAGA
ATACCTAGCGCAGCTTATTTTTCCCCTTACCGATATTTTCTGTGCTTTCT
ACAAAGGCGATGATTCCTCCGGGTACTCTTCCTTTTCTTTTGCCCAAATT
CATCTGGGAGAATTGATCTCTTTGACTCGTTCATGGTGGAAAAAGTTTCC
AATTGTATGGCTTTTTTATCATATTTTGTTGGTAATATATGTTTATTAAT
TTTTCCTGGTTGAAAAACAGATCTCTTTGTATTTTGAGTTGATTTGTCTT
CTAATACACAGATCTGATCATGTAGAATGCTGTTATTCCTCTTTCGCTTT
GATAAGATAATATTAGTTTTTCTTTTTCTAATGGAAATATAGCTTGTTCT
GTTTTCTAACTACTCTCTTCGTGTACATCTGCTCAATATTTGCAAATTCT
TGATGTGATTACGTTTACAAATTATTTGTCTAATATTGACTGTATTTCTA
GTTTCACTTCTTTTAATTTAGTTATAGGAGATCAGTTCATAAATTTCGGT
AGCCCGTAGGTATATAAAATGCAGCATCTGGTTTATGAAATTTGGCAAAC
TTTCAGATCAGATTGTTAACATGGTTTGTTGTGCATATCTGGTAAAGCCC
TATTTTTATATAGCATCCTACTTGATCAAGCAAAGCAGGCAACAAAAGTT
GGCAATAGTATTTCTATGATTAATTACCTTTTTCTTTTCTTTTTTGTCAG
ATATGATTAATTACCTTTGATTTTGTGTATCTGCTCCCAAATTATTTAAC
ATAGATATTAGTTCAACTCGGGCACCCTTTTAAGGAACAACATGTTTAGT
AAACATACATCGATACCCTACCTTTTATATGCTAGTGCATCCTTGATTTC
TGATTTGTTTCTCGATTTTGATTTCAGCTTGAGCAGTTATAGTTATCAAC
CTATTATTTCTCATTTGGTTGACCCTTTTCATTATCCTGTTCTGCTGCCT
ATGATTTGTAAATAATATAGATAGAATTAGAGAAGATTTTGGGGGACAAA
TGTGATGAGATGAACTATAGGATAATGGATGAAAAAGAGCTAGTTGCATG
CTATTTGCCAGATCTTAGATTCTTAGTTTTACAATTAAAGTTTACAAAGG
AGCCATCTGTAGTTGCTTATAAAACTGCTATGTAAGCAAGAACATAATGT
TTTTGAATGAATGAGCCAATGCCTACTAGTTTCTCACCCTTTTTACATGT
TCCAAATCTTATCTTAGCTTCAGGTGTTCGAAGCATTTCTTCCAGTGTGC
AAAGCACTCCAGAGAAAAATGGACTCTCAGATGATGCTTCAAGAAGTCCA
GACCCTCTTCAAGAGTCATTGAATTTGGGTCAAGAAAAGGATCTTCTTCC
TAATCTCTTAGAAAAGGAAAAGCAAAACTCTGCTTTGTCAGTGTGCAAAA
TGCCTGACCAAGTTCCTAAGGCAAGTAAAAAACATTGGAAGAACCAGGAG
GTTAAAAAACCATCATTTGCTCCAAATGGTCAGGCTTCTAGGAAGCAATC
CAGAAAGGCTAAAAATCCCTCTCGATTTCCTGAGGCTACAGAGAAGTGTC
CTGCTTTAATTCCAACTTCATTGATCTGTCAAAATCCTGCATGCCGAGCT
ACTTTATCTGATGATGCATTCTGCAAGAGGTGCTCATGTTCTATCTGTCA
TTCATTTGATGACAATAAAGATCCAAGTCTTTGGCTGGAATGCATGTCTG
AATCTGGTGAAGGAGACTCGTGTGGCTTATCTTGCCACGTTGAATGTGCC
CTCCAAAGTCGAAAGGCGGGGGTTGCTGATATCGGGCAAGTGGTGAAGCT
AGATGGGAGCTACTGTTGTGCATCTTGCGGAAAAATTTCGGGAATACTAG
GGTAAGCTGCTTCTTTTAGTTGTGTACAAATGTGCTTGTACAGTTGTACT
GTATATTGGTGTTCTATACTAGAGTTGCAATATATTCTTCTTTGCCTCCT
GATGATTTTTTATCTTTTATTATAAATTATTGCAAACACTAGCAGTCTTG
AAAAGGTAAATCGTCTTTCATAGGCAACTTCTCATGTGCAACTTCTTTGC
AGGAGAAAATTTTGGTCACGATATGGTATTTTGATATTTCAGTTGTATTA
GTTACATTAATGCTGCGCAAAACTGTGTCTACATGCGAGTGAGATACTAA
TCAGCTTTTACTGTGGCAGTTGTTGGAGGAAGCAACTTCTTATCGCTAAG
GACGCACGACGTGTCGACGTCCTCTATTTCAGGATAAGTATGAGCTACAG
GCTCTTAGATGGGACTTCTAGGTTCAAAGAACTCCATGAAATTGTAGCTA
GCATTAAGGTGAAACTTGATACTGAATTGGGTCCAGCAAAGGGTATTTCA
ACTAAGATGGCAAGATACATTGTTAGCAGACTTTCTGTCGCTAGTGATGT
ACAGGCCCTTTGCTCTACTGCAATTGAGAAAGCAGATGAATGGTTGGCTG
CAGCTTCAAAGGCAGATCCTAGTCGTAGAGGTAGGCTATTAGCCTATATC
TTTCTTATTTCAATCAATTTTGTTTATTACATCCCTTGATTGATCACAAA
AGACTAAAAATAAATAAAAGCCTCCCCCCTCCCCCGCCCTTCTAATTTTT
TAATCCCTTCTATTGTCCATCAGAGGGTTCACTACCGGCAGCTTGCAAAG
TTCTGTTTAAAGAAATAGAATCTACTTCAATTGTAGTTTTGCTTATAGAG
CTGCCTACCTCTTCTTTAGAAGACATCAAGGGCTACAAACTTTGGTATTG
TAAGACTAGAGAAGAGTCACACTCAGAGGAACCTACTTGTAGAATTTTAA
AATCTCAAAAGAGGGTTCGCATTTCAAATTTGCTTCCTTGCACGGAGTAT
TCCTTTCGAGTAGTATCATACACAGAAACTGGTGACATGGGACACTCTGA
GGCAAAGTGCTTCACCAAGAGTGTGGAGGTTATCGGAAAGACTCCCAGCT
CTGTTGGAGTAAATAATATAAAAGAGAGTTTGCAGGGTGTAGCAGATACA
AATGTGGGCACAAAGCACAAGACTGGAGCAGAGGTGGAATCTAATTCAGG
ATTTCAGGTCCGTGATCTTGGGAAGGTATTGCAGATTGCATCATCTCAGG
AGCAGGGCTGCCTCAATGAGCTTTCTGGTGAGAGAATAGAAAATTGCCCT
GGAGTTAAAGAGCCTAACCCTCAACCTGTACATGATCCACTACCACGTGT
CTCGTGTGAGCTTGATCTGAATGTTGCTTCTGTACCTGATTTAAATGAAG
AGTTGACCCCTCTGGTTGAGTCCAAGGATGAAGATAATGTTATTGCTCTG
GGAAGGGTTGAGCCAGTTGGTGATGAGGTCTCGCGTGATAATCAGAGAAA
TGATGTAGAGAAGTCACATGGTAGTGGAGACTCACAAAATTGGAGCCACA
GACCCAATGGGGATGTTTCTGCTGTGGACTCCAAAGGAAAAATGAACAAG
AAGAGGGCTGCTACTGCAAATGAAGAGTTACATGATTGTGATAGCACTCT
GGTTAATGGATCGCCTTGTGGGCTCCACGCCGCATCAGGGTCTTTGGGCG
AGAACTTTGAGTACTGTGTTCGAATAATACGGTGGCTAGAATGTCAAGGT
CATATCAAACCAGAGTTCAGGTTGAAACTGCTGACATGGTATAGTTTAAG
GTCAAGTGAGCAGGAACGTAGAGTTGTGGACACCTTTGTTCAAACTCTTG
TTGATGATCCAAGTAGCTTGGCAGGACAGTTGCTCGATTCCTTTTCAGAT
GTCGTGTCCAGCAAGAAGCGTAGAAATGGTTTCTGCAGTAAGCTGTGGCA
CTAAATTCAGAATGAATGAAGAGAGGTCTACTTAAATCTGATCCTTTTGC
CATCCTCTCTTATAAACGCCTGTTGGTTGGTCTGCCTGTTATTGCAGGCA
ATTCGTCCTCTCTTATAAACTCATGTTGGTCTGTTTGCCTGTTATTTGCA
CAGGCAATTCGTTACCCTTTATTTTCTGTTATAGACTTGGAGTTTCATTA
TTACTCCTGTCATTTTATATCGTACATTTCCTAGGGATGGAATATTATTT
CGGTTTATTTTTAATTAAACGAAGTTGCATCGATGGGAAAAATCGATAAA
ACATTCTTGGTAA