| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017360249.1, is a part of gene, LOC108193543. |
| The genetic_marker, MK003049 K0493, is located in gene, LOC108193543. |
| The mRNA, XM_017360250.1, is a part of gene, LOC108193543. |
| 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_017360250.1 | XM_017360250.1 | mRNA | DCARv2_Chr7:3363034..3368321 |
| XM_017360249.1 | XM_017360249.1 | mRNA | DCARv2_Chr7:3363351..3368321 |
TCATTTCAAATTCCCACTTTACACACACATCGTTATAAAAAAGTGCGTAT
ATACACACACATATACTTACACCATTTACGAGAGGAGTAGTTATATTGAA
ATTCGTGTCCGGCGTGGGAGGAGTTGTTGTCATTTGAACACATTGGGCCC
CGGTTCTAATAATTTTCCGATCGGTTTTGCCGGAAAATATCTGCCGTGTT
GGTGAGTTTTTTTTTTATAATTGTGATTTGTGTTGCGAGTTTTGTGATTT
TGTGGAGTGATTTGTAAGTTTTTTGGTGTGGTTTAGGTCGTGGAGATGGC
GTGGAAGGATATGGCGTTTATGCCGAAGTTCAGAGAGGCGTTTCAGGTCG
GTTTCTGATCTTTTTGCTCTCGATTTCGTTTATGCTTATAGTGTGTGTAT
TTACTTGAAGTTCTGGCGATTTCTGTGTATGATTTAGAAGTGTAGGTAGT
AGATTACTCTCTCTCTCTCTCTCTCTCTCACCCTCTCTCTGTGTGTGTGT
GATTTGACTTGTATATTATAATTAGTTTCCATCTGAAGTTTAGGTTATAT
ATGTATCAGTTACGACATCTACTAAAAATTGGTTTTCATCACCAGTTTGT
GCGATGTTAGTGTATAATTTCAATTTCATTTATTAAAATCAGTTTATTTC
TTAAGTTTTTGCCAATGGTTTTTGTGTGTATCTGTGTGTGCGCACTTAAT
TTTGATTTCATTTTAGTTTTTCATTTGGAGTTTGGGCGAGTGTGCGCGTC
TATTTGTATGTGATTTTAGTTTCCTTTTAAAGTTTTAGGAATGTTTGTGT
TTAATGAACCTCTAGGTGAACTAGTGAACAAAGAATTAGCAATTGTATAA
TCTGTTAGTATATTCTGTACTTGCGATAACTAATAGTACATATACTGCGA
TTTCAAGCATGATAGGGGTAAAAGTTAAAACATTGCTCTATATAACTTCT
TATTTGAAGAGATTTGGGACTTTTGAATTTGTGTTCGTTCTTGCAATTCT
CTACTCCCTCTGTCCCATTTAATTGTATACGTTTCTTTTCAACTGCTCGA
CACGCATTTCAATGCTCTTATAAAACATAGTTCCGTAACTTATTTTTGAG
ATTTTCTTTTTCTGAATAAAAATATAACATCCAAACTTTAATTCAGAAAA
AAAAAATTTAAAAATAAATTACACAACTACACTTTACAGGAGCATTAAAG
TCCGTGCCGCGTCCCCGTCCCCCAATGTATACTACTCAGGGGGACGGAGG
GAGTATTATTTTAGGTGTTACCAGAAATGATCACAATGACTTGACTATGT
CAATGTAGCATTTCTTTATGTTTTAAGTGCTATATATAGTATTATATGTG
ATGGCATTGACTTGATTATGTTAATGTGACATATCGATCATTCAGTAACC
TTTGTTCATGCAACATCCCAAATTTTTTTCCTTTATAATATTAGTTATGT
TCTTGTAATGAGTTATAAATGTTTGAACTTAAGTTGTTTTTGGAATCCTA
AACCATAAATCTTAATCTTAAGTATATCCGTCATGCTTTTGTATGTTTTC
GGACTACAAAAGGAGCTTCTGCATTTTAACAATTTATGCAAATTACAAAT
AGTGAAGAATAAGAACACATGGTTACTGTAAAATTAAATAATTAATTAAC
AATTAATGTGTAAAACAATGAGATACTTTTCCTTTTCACTTGGCATGTAC
CTGTCAGCATGTAATATCACTGCATACCATGACTGTATTGTTAGCAACAA
TATAATACTATGAACAGATAAAATGATCGGTAACACTGGATACCTTAATT
TTGCTATATGAAGCACATGGCTGATATTATAAATTGTCCAGATTATTAGA
TTATTTGGTTTCTGCACTAAGAGTACTTGTTACTCTCTGAAGTTGCTGTA
TGTCATGTGGAATTAAATCCTCAATTGGATTTGAGTATATGACCTTAGTG
GTAAATATTTATAAATTTCACTGATCTTGATTTGCATTTATTTTTTCACC
TTCAACAGGGCAGGACAAGGGAGGTTGAGCTTGGAATGCATACCATCAGG
TCACATGGAGCCACAGTTGCAAGGAGTCATAAGCATGACTGGGTTATCTT
GCTATTACTCGTCGTCATAGAGATCATCCTGAATATCATACATCCTTTCT
ATCGCTTCGTTGGGAAGGATATGATGGAGGACCTGAAATATCCAATGAAG
GACAACACTGTGCCTATATGGGCTGTTCCGGTGAGTTAATTTGTACAGTG
GTATAGGTTAATATATATTTTTATTGGAAGCTGTCTAGTGAACAAAAGTT
TGATTCACTGATGCTATCGTGTTTCACCTTTTCAATTTGTCTGGATAAGC
ATCGCTGATCACCATTTTTTGGTTATAACACAGATATATGCAGTTTTGTT
GCCTATTGTTATTTTCAACCTCTTTTATCTCTGGAGGAGAAGTGTTTATG
ACCTGCATCACAGTGTTTTAGGTGACTACCTCCTAATTTGTATAGGAATC
ACTGATTGAGGCTCTTATCTTCATGTTGTAACTATTTCCTATAGATGAAT
GCTTGTACTGAATAATGACTTGAGCTACATACTTAATGTGCAGGCCTCTT
ATTTGCTGTACTGATAACTGGTGTCCTTACGGATTCAATAAAGGATGCAG
TTGGTCGTCCTCGGCCTGATTTCTTCTGGAGATGCTTTCCTGATGGCAAA
GATGTATGAAAGTCAAATTTCTTCATAATCTATTAACTATTTAAATTATT
ATCCTGTTCACCTAGAAGACAAATGACATTGCTAACTCAGTTTTTCTCTA
TAATTCGAAACTTGAAATGAGATCACTGACTCTTATATTTTGGGAAATTG
GTAGCATTATTATGTGATTTATGTGAAGGTGACAATTATAAGACATCATT
TTACTCTCTTTTAGCCTTTAGGGGTGTAGTACATTTCTGTTAAGTCAAGG
TAAAATGCAACTAGAATAGAATCACATGCATAAATCTGGAAATTTAAGCT
TTAGCTATAGTTGTTGAATTACAAAATTAGCAGAATCACAGGCTGTTATA
GCATTTCTCTATTTTTTTTCCGTTTCTGAATTTATGACTTCAACTTAAGT
AGAATTACTGCAATTGTTGATTAATGTATTAGAAGTTGACAACTTTGTGA
TCCTTGGACTTGTAGTGCTGCAAAATTCTCAATCCAGTGGTTGTGCTTTT
GATTATTTGCCCCTTTTTCATATGTAAATAATATATGAAGAATATATTAC
TATTTTAATTGCAATTGTATACACAACCAAGTTATGTATACATATATACA
CAACCAAGTTATATATACATGATTGCTCACTTTCAAATCTTGTGCTACTA
TTGTTTCAGTTCTATGACCAATGGGGCAATGTTATATGTCATGGTAAAAC
ACATGAGATTAGGGAAGGACACAAGAGCTTCCCAAGTGGCCATACTTCAT
GTAAGCATGCTTTTTACTCTACAATACAAAAACTGTATAATGGTTCATAT
AAAAATTGTAGTATAATTTTGTCAAGAATAAAGACATATGGCAGAAACAC
ATTGCTTACGTTTTCCAGTTTAGTGTATTAGGCACTCCCTTATGTTTAAA
AGTTTCTCTAGTTTAAATTTTAATTAGCAAGTACTACATTAATCTGCCAA
AATGCCTTATATATGTCCTAATATATGCGGCCACTAAAGCACACAGTATC
GTCATGCTTGTATTTTTGTATACTTGTTTAATTACTAGTAGACTGATTCT
ACTGTGGGTTTCTATTAAAACATAAATATGACAAATTAGCATGATGCTAT
TGCAGGGTCCTTTGCAGGTTTGGGGTTTCTATCTCTGTACTTGGCCGGAA
AGATAAGAGTATTTGATCGCAGGGGACATGTGGCAAAACTTTGCATTGTC
TTTCTTCCTCTCCTTGCTGCTGCCCTTGTTGGTGTATCCCGAGTGGATGA
TTATTGGCACCATTGGCAGGATGTGTTTGCAGGGGGTCTACTGGGTATGT
TCACCATTTTTGCTTGCCATACTATTAAACTATTATACTTGCATTTTATT
GTTAGGTAGTGGCTATTACTCAAACTTTTTGTTATTAAACTCCAGGGCTC
TTCGTGGCAACAATGTGCTATCTTCAATTCTTCCCACCACCATATCACAC
TGATGGTAGGCCCTTTAATTCCTTACTTTGTTGTTCATAAGCTTACTTTC
TGGCAATTGATTTTCTACAACATTTTTACCCCTCCCTCCAAGGGATTTTG
AGCATTTGTTTTGAGGTGTTGCTTTTGGCATGCAAAGTTTTAAATCAACT
AGTTAGTCATTTATCGCTATCGGTCGGTAGCTGAGTTTTACTAAATTAAC
AGTTCAAGTGCTAAAGTTAAATATTATGTCTAAATGTTATATAGCTGATA
CTTGCACACAATTAGCAGGATTATTTATGTTAGTTAGTGCTACTGCTACA
ACAATCAGATTTCTACACCGCAGCGTAAAGGAGTAATTTCTTAGGGTGAT
CTCCTAAATTTTGTTCAAAGTGCTTATGCTTTAGAGTATTTTAATTTTGT
TTTAGGCTGGGGTCCATACGCACATTTTGATGCTATAGAGGAGTCACGTT
CAAATCCAAATTCAGCTCCTGCAAATGGATTCATTGTGCATGAAACACAG
TTTCAGCCAGATTTTGTGACAGTGCCTTTAGGCCACAACTCAAGCTTGCA
GCTGAATGACATGGAAGCTGGCAGAATGTAGAGCTGGAACGCTGATTTGT
TCCTAGTCTAGTCATATTTAGCTCTGTCTATAGGCTCTTTCCTTGTGTAC
AAATCACCTGGTAGTTTTGGAAACGCGGTATATACCGGATGAGATATTAG
TTAATCACATTAGAATGGGTTTCAGCCTTCATAATATTGGTGCTTTCACA
TTGGAGTGTACTAAAACTTGGATTATCATTTTGTATGTTATATTTTGTCC
AATTGAATTTCCGAGGTCCACATTTTTCTTTAAAGGAGATGAAGGTTAGA
GTATAAGAGGGTATATATGATGAGAATAAAAGGTAACATCAGGAGAAAGC
ATAAGCAAGTAAAGAACTGTGGGATACTTATTATTTTATTTTTTTTACTT
TATTGCCACTTGTTGGAGGGAAATAAAATCGAAATATATTGAACATGCAG
AATCATTCTTACTGACAATTTTCTACGTGCTCCACACGGGATTAATGGGT
GCTACGAGGATGTCGGCAACAATATTGTTAGTCGATCAATCAGTTCAGCC
TGCCCAGTGCAGTAGTAGCTAACCGGTGCAGGGTCTT