| NCBI Gene |  |
|---|
| Relationships |
|---|
| The genetic_marker, MK006265 K3709, is located in gene, LOC108199540. |
| The mRNA, XM_017367392.1, is a part of gene, LOC108199540. |
| The genetic_marker, MK009819 8_20788164, is located in gene, LOC108199540. |
| The genetic_marker, MK009822 8_20788674, is located in gene, LOC108199540. |
| The genetic_marker, MK007912 TP111258, is located in gene, LOC108199540. |
| The genetic_marker, MK009816 8_20788896, is located in gene, LOC108199540. |
| The genetic_marker, MK010979 8_20790755, is located in gene, LOC108199540. |
| The mRNA, XM_017367391.1, is a part of gene, LOC108199540. |
| 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_017367391.1 | XM_017367391.1 | mRNA | DCARv2_Chr8:20785145..20792876 |
| XM_017367392.1 | XM_017367392.1 | mRNA | DCARv2_Chr8:20785685..20792877 |
TCCGTTTCTTCCCCTGACTCTCTAAATTAGGTTAAACCGTTGAAAGCCTC
TTTGTTCCGTTTAAACCCCCACCAGCAAACCAAACAGAATTACAAATCTG
TTTCTAGGGTTTTTGTTCTGCTGGTTTATTCACTCAGCTGTCGATGAGGA
ATCTAAAGCTATCAACTGAGCTCACCTCGATTCTCGAGCTCCAATCAGAA
AACGAAACCATTCAATTCGCCGCGTTCGACATCGAGAAGAATCGCTTGTT
TTTCGCTTCTTCAACTAATTTTATCTACACCGCTCAGCTTCCTTCTATTC
ATGTATATATTCTTATCTCCGTACTCAAATTTATCGATTTTATCGATGTT
AAAAATACACCGTCTCTGTTATGTTGTGACTGAGAAATTTCAATTTATTA
CCTCACTTGCAATGTATAAGTAGGTTGTAGATATACATGAATTGTTATAT
TGTAATTCATTAATTTATCGATATTAAACGCATTATCTCAAGGTTGTGTA
TGTGCAACTTTATATGCAATTTATAATTAGGATGTTGATAGACAGGATAT
ATTGTATATGTAGTGATATTGTTTGATATATAGGATGATAAGTATGAATT
GGAAATGTTTGATCTTGTATTAGTTCAGTTGTAGAATATATATGAGCTAA
CGAATTTTGGACTGTGTGTTACTGTTTAGTTGGATAATAATGAGGTGACG
GTTGATGTTTTAAATTTTTACCTTTAAGTTATTTTTTTACGAGTCTGTGT
TTGTTGGGGCTGTAAAATTGTGATTAAGGCATTGAGTATCGAGTTGGAAA
TCTGATTTATAAAGTAGAGGTAAGAAATTGAGAACTGTTGTTTCTAGATA
TAGGGTGTAGTATAGATAGTCCTTTCGTTGTATGCTAATGACCGAAGCAA
GGTGTTAATTTTTGGAATTTGAGTTTTTTTTTCCCTTTGTATTATACATG
GTATGTGGTAATCATTCTATATGTGATTGTAGCATAAAAAGAAATGCCTT
GTGTTTTTGTGTTAGTACTTAGTATTGAGGGCGTAGTTCATTTGAGAAAG
TTTTGTTTATAAACTTTGAAATGCTTATGATTTGGCAGGATGGAGGTCGG
AGCAAGACATCTTTACCTGTAGTGGTTCAGCCAATTGATTTAGACCATGA
AGACTTTATTACTTCCATGGATTTTCTCATGGAAAAAGAAGCACTTGTGG
CAGGCACTTCTAATGGACATCTATTGCTATATAATGTTGATGACAATGCA
ACAGAAATTGTTGGTCATGTAGAGGGTGGTGTCAAGTGCATCTCACCTAG
TCCAGATGGAGATTTGCTTGCGGTGGTTACTGGTTTTGGCCAGATACTAG
TGATGACTCATGATTGGGATCTGTTGTATGAGACGTCAATCGAGGATCCT
GCTGAAGAAATTGATGTAAGTAAGAAACTCTTCCCTTTAACCTCGATTTT
GGTATCTCCTTTTAATTATAATTTTCTTTGTTTGATGCATGTGATGCTAA
CCTACACCACATGTTCATTTTAGAAACAAAAGCACTAACGATTGTGGTGA
ATGAACTACACATTTCCTTATAATTATTAGCGACTGTAATAGCATGTACT
TAATCTACCTTTTCTCTGCATTAATATAAAATCTATATCATATCATGTAA
CTAATGTACAAATAAAAATAACTGAAGTTTACTAGGACATGCATGGAGCC
CTTTATTAACGTAACTTATATAATTTTCTATGTTTTATTTTATATTGATC
ATAATCTGGTTGATTACTTTGTTGAAGGTGGGCCAGTTGGGAACCTCCAT
TTCGTGGAGAGGGGATGGAAAATACTTTTCTACAATAAGCAAGGCACATC
ATTCAGTTCCCATGAATAAGAAAATAAAAATTTGGGAACGAGATACGGGG
GCACTTCATGCTTATTCAGAAGCAAAGTCTTTTATGGGATATATTTTAGA
ATGGATGCCCAGTGGAGCTAAAATTGCAGCTGTTTATGATAACAAGGACA
AACATAATTGCCCTTCAATAGTTTTCTTTGAGAGGAATGGTTTAGAAAGG
AGTTCATTTAGCATAAATGAACGGGTTGATGCAACCATAGAAAATATCAA
GTGGAATTGTAATTCTGAACTTCTTGCAGCTGTTGTCAGGTCTGAAAATC
ATGACGCCCTGAAGATTTGGTTTTTTAATAACAACCACTGGTACCTGAAA
CAAGAAATTAGGTATTTGAGAAGGGATGGACTGAAGTTCTCGTGGGACCC
AACAAATCCATTCCAGTTGATTTGCTGGACTCTTGGTGGCATTGTCACAA
CATATAACTTTGTGTGGGTTACGGCTGTCATGGACAATTCAACTGCCTTG
GTCATTGATGACTCCAAGATACTAGTTACTCCCCTTTCCATATCGTTGAT
TCCACCTCCTATGTTTTTGTTTGAATTAAGATTTCCGCGTGCTATAAGAG
AAATGGCTTTTTGGTCCAACAGTTCTAAGACTCTTTTGGCTGTATCTTTG
TCGGATAATGCTTTGTGTGTTGTTGAGCTTCCTGTAGTGGAATCTTGGGA
AGACCTAGAGGGTAAAGAATTCATTGTTGAGCCTGTCTCTGGGAAACCAC
TAGGATCCTCTGTGCATCTCTTATGGTTGGATTCACATGTTCTGCTCAAT
GTTCCACATTTTGGCTATAACCAGAGCAGTGACCTGGTAAAATCTTCTTC
ACGCAAGGATTGTTTGCCTTGCATACAGGAAATCGAGATCACGTGTTTGG
AAAATCATATCCCTGGCACAGTGACATGCTCAGGTTGGAATGCTAGGATT
TTTGGTCAGATCTCACTCGAAGGGATGGTTATTGGCCTTGCACGAAATCC
TGTTCTTGATGGTTCAGCGTTTGTTCAGTTTATTGATGGAAAAATCTTTC
AGTATAGAAAGCAGGCAGGAGCTGTAGTACCGTCTATTGGAAACCATACT
GATATCAGTATGAGTTTCTCATCATCTTGTCCATGGATGAGCGTGGTTCC
TGTTGGAGATTCTGATCCATCAAATCCTTTTTTGCTATTCGGGCTTGATA
ATTTTGGTAGATTGCATGTCGGTGGCAGGATACTGTGCAACAACTGCAGC
AGTTTCTCATTTTACTCCAATTCCCCTGATCAGATGATTACACATTTGAT
TCTTACAACTAAACAGGATCTGCTCTTCGTAATTGAAATTAGTGATATTT
TGTTTGGCCAGCTAGATGCCAAATATGACAACTTTTTACCTGTCATAAAG
AAAAGACGCGGAGAAGAAGAAAGTAAGAATATAACTTTATGGGAGAAAGG
TGCCAAAGTTATAGGTGTCCTGCATGGAGATGAATCTGCTGTTATCTTGC
AAACAATCAGAGGAAACTTGGAGTGCATCTATCCCAGAAAATTGGTTGTT
GCATCGATTATCAATGCGTTGGGCCAAAAGCGTTTTAAAGATGCACTACA
CATGGTAAGGCGGCATAGGATAGATTTTAATATCATTCTTGACCATTGTG
GTTGGCAAAACTTTCTTCACTCAGCTGCAGAGTTTATCAGACAGGTTGAT
AATCTGGCCTATGTAACGGAGTTCGTCTGTTCCATAAAGAATGAAAATGT
GATGGAGACATTGTACAAAGAGTTCACATCTTTACACAAAGAGGAGTTTA
GTTTAGTTGATAATAATAAGGTATCTTCCGTACTGCTGGCTGTGAGAAAG
GCACTTGAGGACCAGATAGTGGAATGCCCCGCAAGAGAACTTTGCATTTT
GACCACCTTAGCTCGAAATGAACCCCCAGCTCTTGAAGAAGCTTTGAAGA
GAATAAAAGTGATTCGGGATATGGAACTTTCAGGTTCCAATGACCCTCGG
AAAATTTCTTACCCTTCTGCTGAGGAATCTTTGAAGCATCTCTTGTGGTT
ATCTGATCCTGATGCTGTATATGAAGCTGCATTGGGTCTTTATGATCTGA
ACCTTGCTGCAATAGTTGCATTAAACTCACAGAGAGACCCAAAAGAATTT
CTTCCTTTCCTTCAGGAATTAGAACAGCTGCCAACTTTATTAATGAAATA
TAATATTGACCTTAAACTAAAAAGGTATGAAAATGCACTTAGACACATCA
TTTCTGCAGGAGATGCTTATTCCGAAGATTGTATGAACCTCTTGAAGAAT
AATCCACAGCTTTTTCCGCTAGGACTGCAGCTGACAACTGATACTGTTAG
GAGAAGGCTCGTCACTGAGGCCTGGGCAGATCATCTTAGTGACATAAAAT
GCTATGAAGATGCTGCTACGACCTACTTAAGCTGTTCAAATTTAGAGAAA
GCTTTAAAGGCTTTCCGTGCCTCTGGTAATTGGGCCGGGGTGCTGACAGT
TGCTGGTCTCATTAAGCTGGGAAAAGAGGAGGTCATTCAACTAGCTCATG
AGCTGTGTGAAGAACTTCAGGCACTTGGTAAACCCGGGGAAGCTGCTAAG
ATTGCCGTAGAGTATTGTGGAGATGTAAATAGTGGGATCAGTCTCTTAAT
CAGTGCAAGGGACTGGGAGGAGGCTCTGAGGATTGCTTATTTGTACAGAA
GAGATGATTTAGTTTCAGAAATCAAGGATGCATCTCTTGAGTGCGCAAGC
GTGTTGATTGGAGAGTTTGAAGAAAATTTGGAAAAAGTGGGAAAATACTT
GGCTCGCTACTTGGCAGTGAGGCAGCGGAGATTATTACTCGCTGCAAAAC
TCAAGGCAGATGAGCAGTCAGTAAATGATCTTGATGATGATACTGCTTCA
GAAGCTAGCAGCAATCTCAGTGGAATGAGCGCGTACACCTTGGGGTAAGC
TAGTTATCTTTACATCATCTTTACATCCTTTGTGTCATGATCTCAGTTTA
CATCTTACCCAGATGTGTAGTCGGCCATTTCTCTCTTTCTAAAGAACCTT
GCCGTATATAACATTCTCTTAGCCATTCAGCTGTTGACTAATGATAACCC
TACAAGTATGTCCAAAATAGACATGATTGAATCTGCCAGTTAAGTCCAGT
ACTTTGCGAACCATAGGTTGTTTCATCTTAATGTACAGAAAGTCTCATGT
AATGTCAGTCGATAGACTAGCTTGTTCTGATATAATTGCTTTTTTAATCG
TTTCAACTTAAAAACCGCTGGAGTTTTGTGGTGTGTGTATGGTAATATCA
CATATATAAATTATAATACATGTGTGTGCAACTTACTCAAATAAATAGCT
CGAATACCGAAGAATATGAACTTTCTACATGTGATCGTCACAAATTGAAT
TATAATGAAATTGCTTTAGGGCGTTTACCAATGTTAATAGTTAATGATTG
CACGACTCGAACAATTTTGAATTTGCCTCTGAAATAAAAAAGAGAGCAAC
TCCCAACTAATAAGACTCCATTTTGATGTAGAAGAATGAGGCTCTTGCTT
GGTGAATAACTACAACTCCAAACTATTGATTGATTGGTTTTGTTGGTGAG
AATCGTTGCAGACTGAAGCACACACTTAAAAGCGCTCCCCATTTTAAAAT
CCTTGATTTCATAGTTTCTTTTGTATTTTGTGTACACAAGCAAATATTTT
AATTTGAATAAAATAGCGCAATTTAACATAATAGGTTGTTAAGTAGATCA
AGAACTACTCATTAACACGTCAAAAGTACCATACAATCTGGCATTAAGGA
TCACCATATATGAGATGGAATGTCATAGGAGAGTTTAAGAAAGTCTATCA
AGATGTTCAGGAGGTTGATTAATGGTTACTGAACAGGTGTTATGCAATGG
TAAGGTACATGGCTTTATTAAAAATTGGAGGAAAGAGGGATTTTGCAGAT
ATTAGGTAGTGACAGGGTGAATTGTCTTGATATATGGCTTACAAGTCCCC
CCTACAAGTTTTGATTTAAAATAATAGAAGTTTTGACAACTTATGTAATT
TTTCTTATTTTCTGAGCGGCTGGTCTTCACTCATACTTTGTTGGCTATGT
ATACACTAGTTCTGCAATAATATCTTTTTCCTTATTCACTTGTTGCCAAT
TCTATACAGGAGTTCACTTGTGCTTCTTTTCTGTTTACGTAAATCATATT
TTTTTTAAATTTGGATCTCCTTTGATAAACTGCTTTCATGGCAGAACAAG
GAAAGGGTCTGCAGCTTCTGTTGCTTCGAGTACCACTAGCAAGGCTAGAG
GGATAAGGCGTCAGCGGAACAGAGGAAAAATCCGCGCTGGCAGGTATTTT
GTTATTTCTATGTATTGCTCACTACTTATATTCATTTCAGGGGTATTCAA
AGTTTTAGACCTCTAATCAATCACATACCCACTAGTGTTAATTCGAGAAT
TGTCTTTCAGTCCTGATGAAGAGATGGCTTTGGTGGAGCATTTGAAGGGA
ATGTCTCTGGCGGTTGGTTCAAGGAAAGAGCTTAAATCTTTGTTGGTTTC
TCTTGTAATGCTTAACAAGGAAGACATTGCGAGAAAATTGCAACGAGTAG
GAGAAAACTTTCAACTGTGTCAAATGGCAGCAGTAAGTCTAGCTGCAGAT
GCGACGTCGAGTGAGATTATAGATGAACATGCTTTCTCTCAGGAGCTTTA
CATGAAGAAAGTAAGGAAAGAATTACTGCATTCAGAGGCCTTCTCCTGGC
AAGTCAAAATGTTTCTTTCTCTTTGATAGGTAAACCATTTTATTGCTCTT
CTATTTGTTGCACTATAGTCTTCAGGGAGATGTTCCCGAGCAATTAATTG
TTGGCAACAAACTATCCATTCTTTTTTATCGAAGAAAGGAAAAAACCCCA
GAGTGGGTGTCTAAAGCACGGATGGGCTCATGGGCTCACTGCAAGCACAC
AAGAAATCTAAGGTTAATGTCTTTCTGCTATAAAAAACCGTGGATAGTTT
GCTGCAACAATCGATTGGCAGGGACCCGGACCCTAGTCTTTATTATATTT
TTCTTTTTATGAGACAGATACTTATGCCTTGTTTAAACAGTGTAACTAAA
AAGAAACATCATATCCTCAAAAATGGCTATCGATGCATATGTTTTATCCT
AATATTAGAAGGTTCAGAACGAGTTCCTTTATTTGTTTGTAAAATCTTGG
TTTGATCATTGATGCAGTTGGTCAAATATAATTCTGCCAGCCATACCATA
GAATGTAGTTTCAGATGAGATGGAAATATATTGAAGCTTCAAATTTAGTC
TGAAATCAAAGCCTTTCGATTTTTTGACATGCAAATCTGATATTGCAGTT
GAATAATGGTCCCATGGAGCAGTTTTTCTGTCTCAAGCCTATGCATGTAC
ACTCTCTAACCCATGCCTGGGAGGCTGGGACCATCAAAATATACAATTGC
CGCAAGACCACTTTTTCAAGGCTTATTTTATGTGAATGAAGGGTATTAGA
ATTAGTTCCCTAAATATAATGTTCTTCGGGCAAGATGGCACAATGAATTC
ATCTATCTTAAAGGTTAATAAGGTGGTTCAAGTTCCCGCTGCCTCGGCCA
CTTGCCTTGTTAGTGGAAGAGTGAGTATTCTCCAAGCCGTGTTTCTGCTT
TCTTATATTTGGCTCGGTGGTCCATACGTCCATGTATGAAGATCACTTGT
CTGTTCCCGATGTTCCCATGAAAGAAAAGGGAAGGAAGAAAGAATGATGA
TATTAATCAGTTTTGTAGATTCATCTCCTAGTAAAGCATGTATGTTATGT
ATGGGTTGTGAGTAATATGCTACCAAATTTCCATATTTTATATCATATTA
TTAGTTTTATGTTCAATATGATTTTAGAGTAA