| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017391712.1, is a part of gene, LOC108218667. |
| The genetic_marker, MK001006 GSSR-007, is located in gene, LOC108218667. |
| The mRNA, XM_017391713.1, is a part of gene, LOC108218667. |
| The mRNA, XM_017391711.1, is a part of gene, LOC108218667. |
| 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_017391712.1 | XM_017391712.1 | mRNA | DCARv2_Chr4:20487690..20495061 |
| XM_017391713.1 | XM_017391713.1 | mRNA | DCARv2_Chr4:20487690..20495061 |
| XM_017391711.1 | XM_017391711.1 | mRNA | DCARv2_Chr4:20487690..20493780 |
CTAGTAAGTTACTGTAAATCAATTATGAATCTGGTGTTTGACATCCAAAA
GCTTGTTATTACACCAAATTAGAAAGAGGGGCAGATTAGAAAATTAGGGT
TTATCTTTCAATACTTGAAAGTTGAAACCCAATTCCCCATCTATTCTATC
CAATATCCATGGCTGCTCACGCCCTCTCGCTGCTCCCCATTTCGACACCT
TCTCGTAATCATTTTTGCTGTAAACAAGAATCAATTAAATCATCACTCTG
TTATCATCTTAGTCTCGCTAGCTCTTTCGTTGGAGCTAAATTGGCTGTTA
ATTATACAAATTCGCGGCAGTACACTCACACACAGCACTCCTCCACGGTG
GCCACCATCTCCGTCAGTCTTCCCACTGGGTACATACTTAACTCTTACTC
ATTTCTATCTCACTTGATTATATGTATGTGGATTTGAAATTAACAAAATA
ACAACTAGAATTGTAATGACTAGAATTGAAAGTATGCACTCTTGGATTTT
ATAATTGTGCGGTTTGAGTATGATATTTAGAAGTGGAATAAGCAGAGGCT
CAAACTCTTCCTAAGTAATCGTACGTTTTCAGTTAAGAACTGAAGTAGAT
AGGCAAAATGTCAAGCGGAGTAAATATACCTTTTCACTTGATAACTTATA
TAACACGGGTCATAAAAGGATTAAGCAGGGGATAAGATTATAATCCTGTA
AACTTCTTTATTTTATGTTTGTTTTGCATAAACATTTGAGATTGGTTTAA
AGATTATAGTCATTTAAAATATGTCATCTCTATGGCAAAAAAAAAAATGT
CATCTCATGTTTGTTTTGTTGGATTGCGGGATATAGGGGCCATTTGGATG
AGCTTAAAATAAGTGCTTCTTAGTTAAAGTAAAAAAGTGAAGTAGAAGTT
AGAAGCAAATTAGGACTTATAAGTGATTAAAGTGTTTGGGAAAGAAGCAG
GAGCTCTGAGAGAAAAGCTAGCATTTGTAACTTTTAAAAAGTGCTTCTGC
TTTTTTACACAAACTGGACAAGAAAAGCAGAAACCAACTTCTTCGGAAAA
GAAGTGCTTCTCCCCTCGTCCCAAACAGGCACATAATTACAATGCCCTCT
TAATGTTTGTTTTATTAGATAGCTGGATATAATTATAATCCCCTAAGACT
AGGTTGGAGGAGGTATTATATAATCCCCTCTAAACGTCAATTTTTTTAAA
AGACTATAATCTCCTAACTCTATACTCCTTTTGTACCATTCATTTCTTTA
CACTTTCCTTTTTGGGATGTGCTTCTCAATTCTTTACATCTCAAAACTTT
TAAAATATTGTAAACTTTTATAATATAAAAACCAATCTCACCCACCACTT
TCATCCATCTTCCTTAATCTATCAATTAAATAGTAATGGATCTCACCACT
TTACCCACTTTACTTACTCTTTCACACTACTTTTTACAGTACAGGTGAAC
TGAACAAAATCCATGTTATTTATAAGGATCATGAGATAAAAAATAAAAAT
GTTCAACCTATCTATTTAATCTATTAACCTATATGACTCGTGAAGAAGTT
CAACCAGTCTTTTTAATTTCTTAACTGAAAAGATATGACTATACATGAAG
AGTTTGAGCTTGCCTATTCATTTTCTATGTGCAGTACTCAAAAGTGTCAT
ACATTCAATTAATCTGACTTGCTTATATTCTTATATTTCAGTTTTGGATT
AATATTGCATCATTTTTAATTGCAGGACACCTGATAGAATCTCGAGGCAG
AAGTCTCCCAAGTAATTTCTCAATTGAATAATATTTGTTCGTATTGCAGA
ATCATGTTTAGGAGTGATTCTAAACTAAAATGCTTGTTTCTAGGGATAAT
TAAGTAAAATGTTCTGTTTTACTATTTGTGGTGATAGTGATGATTAATGT
TTTTCTTGTGTGTGTGTGTGTGTGTGTTTAAGATGGTCAGCTAGGGCAAT
AAAGTCGTATGCAATGGCTGAATTGGAAGCTAGAAAGCTTAAGTATCCTA
ATACTGGGACGGAAGCTCTTCTCATGGGAATTTTGGTCGAAGGTTTGATA
ATGTTGCTTTTCTGTTCGGTTGATTATTTCATTGTTAAGTTTTTCTTAAT
CTAGTTGACGATGATTGGAAGTGTGGTTGCTTGTATCTGACAACTAACAC
TGTTAGAAGCCTGATATTACCTTAAAAATGGTTATATTTTATGCAGAATA
AATAACATATAATTATTGTATATAGGGGCTTGTGATAAAATCGCATGTCA
TAGTATGCAAATCACATTCAAATGTATTATTTTTTTTATATTAGGAACCA
GTTTAGCTGCAAAGTTCTTGAGAGAAAATGGTATCACTCTTTTTAAAGTT
CGGGATGAGACTGTCAAATTGCTTGGAAAATCAGACATGTACTTTTTCAG
TCCTGAGCATCCTCCATTCACAGAACCAGCTCAGCGGGCACTTGATTGGG
CTATAGCTGAGAAACTGAAGTCAGGTGACTTTCTGTCTTCTAAACTATAA
GATCTCATCGGGTAATATTGCAATCGTGGTTTTAATGATGGCGGCAGCAA
CTATAGCTGTGCGCTTGTACTAAGATTAAATGAAATACAGTTTGTTGCTT
AATGCTGTTGATTTTTCCATCTGAAATACTGCTACATATAAAGCAATGAC
ACGTCACTGAATTTTAACATTGTTCAAAGTTCAAACATAATCAGTAATAA
GTACTCATTTTAGGACACAAGTACATGACAATTAATTGAAGGGTCTTTCT
AGTGTGTGCCCATGGGCACACACTAACAACTACTTTTTGTATAGGTGGAA
GATTTTGGTTGGTGGAGATTTTTGTGCATGCAGGGGGCCATCATTATTAA
TGATATGGGAGCCAATCAAAATGCACCATCTAGCTAAAAAGTGGTTGTTA
GTGTGTGCCCATGGGCACAGACTAGAAAACCCGACAGAAATGTGGAAAGA
ATTTTTAATATATTAACAATTTCCTACTGAAGATTCATCAGAAATGTGAA
AGTAAAAATTTATCTGTTTACAAATAGAATTGCTGAAAACCAAACTCCTT
AGTTCAGGGACAAGGACTAAGCAATCAAGGTCTCGATTCTCGGCACAATC
ACAAACTTAAGTTTTTCAATATACTAGCAATGTTAGCTAAGCACGCAACA
CATGAATTACCCTATATATTGTATCCGCCCTGGATTATACCCTTACGAAT
TTCAATTGTAATTCTGAAGATGGCGGCAACAACTACTCCTGGTCCCTCGT
ACCAAAATATTCAAATGATATAAAGTTCCTGATGCTGATTTTCCATCTTG
AGTAGGTTAAGAATTAATGTGTACAATATATATGTGTGTGACTAACAATT
TGTGTATATCTATACTATACTATTAAAGCCGAAACATTAAAAGTTTGGTC
GGTCGGTCGGTACTTGGGCCAAAATACGGGCCTATCTATATAACCAATTA
TTCTGGGCCTATTTATATAAATAATTATTCTTTTTAATTTGGGTCAAAGT
ACGGGCCTATCTATATAACCAATTAATAATAATCCTTTTAAAACTGAAAC
ATTAAAAGTTTGGTAGGTCAGTACTTGGGTCAAAATACGGGCCTATCTAT
ATAACCAATTATTCTGGGTCTATCTATATAACCAATTATTCTTTTTAATT
TGGGCCATAGTACGGGCCTATCTATATAACCAGATAATCCTTTTAATTGA
AATATATTACTTTTTTATATTTTTGACTAAAAAACTCAATCTTCTAAAAT
AACATTGAGAAACATGGTAATTACTTTTTTAACTAAAATATATTATCTTT
TTATAAATTTTCCAACTAAAAAATTAATCTTTTACAATTAATACGGACAT
GGGCGACATATTTATACGTAAAGATGTGTGCCAAAAGTCTAAAAGTCAAA
TAATAAAAAATAGAGGGAGTATTATTATATTGGTCGGGCGGTCGGTACTT
GGGCCGAAGTACGGGCCTATCTATATATATAACCAATTATTCTTTTTAAC
TAAAATAAATTATCTTTTATATATTTTTTAGATAAAAAAAAATCAATCTT
CTAAAATAATATCGAGCAACATAGTAATTGTCTTTTTAATCAAAACGCTT
TATCTTTTTTAGATTTTCTAACTAAAAAAACCGAGTTTTTACAATTAACA
CGGGCGCCATATATATAAAAATATAATATCATTAAATATAATTATTAATA
AATAACATGTGATATTATTCAACCAAAATACATTAATAACATTATTTTTA
AATACTCTAATGATCTCATATTAAAAGAAATATTACAAATCTGTCATATA
CTATATATTATTACACTATTAAAGCCAAAAATAAAAATTCACTTGGTTGG
TCAGTTAGTTGAGTTTGGTGAATCGTTTGGTATTCGACCCACGGAGCTCT
TAAATTTATAACATGTTATAGTATATTTTTTATTATCAATTAAACCAAAA
CATCAAATTTAGGTTAGTATGATGGGGAGGTATTTGGTTCATGCGTATGT
TTTATACCATATTATTAATTATTATTAACTAAATATCAAAGGTTGATTGG
TTAGTTTATATCTGAGTTTATAGGCCACCTTAAATTATAACATGTAAAAG
AAAATATTTTAACATTCTCATTAAAATATATATGTTCGACCTAATTTTCA
ATTAGCCATTTAACGGACTTAACTATGAAGAATTTATCCAATTGTTAAGT
AAAAAATCTATTAAACCATGTTATTCTATCATAATTTTATTTTTACAATA
AAATTAGGTAACTTTAAAATATATATAATAAAATAACAAATATGTTAACC
GCCCGTGCATTGCACGGGTTATAAGCTAGTATGATATATAACTAGAATAA
AGAGAATTGTAAAATAAAGCAAAACAAAACAAAGTAAAACAACACAAAAG
TATGAAACAGATCTACACAAGAATTATATACAGTGGTAATGGTTAGATAT
AAAACGGACCTGTATTGAAGCAGCACACATGAAGAGTTCAATCATAGTTT
TGCAAGCTATTAATTGTTGCAATGTATATAATTCTTGTGTAAATCTGTTT
TACCATAAATTGCTAGAAATTAGTGTGTAGAATATATATGATGTGATTTC
TATATGTCCAATTTATGTGGCCATCAGATATATTAATTAAAAAACTGCAG
GTAACTGTCAAATAGTTGCAACTTTAACAGTACCCATCCTAATAGTAACA
ACCAAGTTTACATTTATTATATTAATAATAATAATATTGTTATTCTAATA
TAATATTGCTGGATACGAAGTTAATTACATGCTACTAAAGTTTGTCATTT
CTGAAATATAAATGAAAAATGAATAGTCATTTTATGACTTGACAATTTGA
TGAAAGCAAGGGAGAATGAACTTAAAATTTATAAACAAGTTCCTCAAGGA
GACTCATCACACATGTGAACACATCTTTATCTGTTTATGATGAATTGCTA
ACCTAGCTGACGTATAGGTTGCTGTCCTGAACTGTTGATATTGAAATTCA
GCTCTCAGTATGGAATTCCAAACTGCAGTAAATTAGTTGTGATCATGTTT
TTTGTTGAGATATATCAGTTATTGATAGTGCTTATTATGATGTCATGTGA
ACTATAGGCGAAGATGGGGAAGTAACAGCTGCTCACTTTCTTCTGGGAGT
GTGGTCAGAAAAGGAATCAGCTGGTCACAAGATCATGGCTGCACTTGGTT
TTGATGATGAGAAAGCTAAGGAAGTTGCCAAATTTGTAAGCTTTAAATTG
AAATTCTTATGTGCTACTTGACTAGTTTTTTCTATGATTATCGACTCCAA
TTTTGATAGTTAATTGAACTTTTGATTATGTAGATGGACAAGGATATAGA
CTTGGGCTTCAAGACGAGAAGTTAGAGCTTTGGAAGTGAGCGTAATTTTT
GCTTATTAATCTTCTTAAGAAATTTCTGGGACATATGCTTGGGGTCCTCT
GCGATACTTATGTCCCATATATTCTTTTAAGGCTTCTTAAAAGTTCATTG
TGTCAATTCCTTGTCCAGTGTGTGCAGTCTCTCTTCACAATTTTACCTTA
CTCCCTTTAGCTATAAGATCTATACCTGGTTTCCGTACCATGCTATCCTG
TCGATCCATTTTGCTACTATTCTGGTAACTAATATGGTGACTAAAATAAT
CTAGGTCAGTGACCTCATATCATTTAGTCTCATCAGCTATAATTTGTGCA
TTGGATATGATAACTATTACAAATACTTAAAAGTTAAAACGAAGAATCTC
ATGCTATGAAATAAAGTAAGAATCTGAGATGGGGGGTGAATGCCTTAAAG
TGACAAGACAATGTCAGTTGGCAACCATTCTGCTACTGTAGTAGTAGAAT
AACAAGATAACTAAGATATCTTATATATTAATGGCCTCATATGTCAAAGG
CATTACAGCTATACTTGGACATTTGATTTTTAAAGATTACATCTTAATGA
TTTGGATGATTTCACGTATGCAAAGAGTACTGTTACTAATGAAGAACCTA
TCATATTAAGGAGTAAAGAAATGACTTGAGATGGGTGGTAAATATGATCA
TATTAAGTAGTAAAGGAATGATTTGATTCTGTAAATATGATTGTAGATAC
TAGATAGGGGCAAATCAGAATGATCTTTATAGGAACACCACCCTGTTGGA
AATTTTTGCCTAAACCGTAGGACACAAGGAATAAGTGTGAGCCATTAGTT
TAACTTAATTAATCCTTTTTTAAGAGCTTATCGCATCTCACTAGGCATGT
AATTGGCCTTCTTTTGTCTGTCATTTGGCCAGATAAAACTTGTTCTATTT
CTTTAATGTGTTCACAGATCTGATAATCCTCTGGGTGTGGAGCTATATAC
AGTGCGATGTCTTGTGTTGCAGTTAATTGTAGTAATTAGGGTTAGAATTG
TAAGCCACCTTGGTTGATTTACATTATGCAGTTATTTGGATTGTTTCGGA
AACACCCACCCAATATATATCCCTTCCATTTCGGCCCTGCTCAGGTGGAC
TGGTGAAGAGAGTGCAGGGACATGTATCCTCGATTGTGTGGTTGGCTGGT
CGCCCAGGGTGTGTTGGTGCATGGTTATATCATCAGGTCATGATGAGAGA
AATGAATCTAAAAGGCAGAACAGTACTTACTGATTGACTGAATATTGAAG
GGCCATGCTTTGCAACTCCCTCACGTTTTTCTCTGTTTTCTCTAGATATT
CTGTTTAGTAATTGATTTTATCTGTAGACACTCTCAGATCTACGTATTCA
CAGAAGGGGGTTGGCCCCGGCCAGGGAGAGTTTAATCAGCCATCAACGAA
CCAAAGACTGATAAAATATTTTTTCTCCCTACCAGGAAAAAGTTATAGGC
AGAAGAGAAATTATCTTCCAA