| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017403690.1, is a part of gene, LOC108228176. |
| The genetic_marker, MK004201 K1645, is located in gene, LOC108228176. |
| The mRNA, XM_017403691.1, is a part of gene, LOC108228176. |
| 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_017403690.1 | XM_017403690.1 | mRNA | DCARv2_Chr6:5509080..5515549 |
| XM_017403691.1 | XM_017403691.1 | mRNA | DCARv2_Chr6:5511203..5515549 |
TTCGGCCCCCCGCAAACATGACTTGAGCCCAGCCCAGCGAATTCCATCTT
ACCACTCTAATTGCCTTGCCTTTGAGCCAGTCCCTTCTGTATAAAAGTAA
AACCCTCACCAACACACACAGAAACCCTCCAATTTCGCCGGTATCATTTT
GGCGCGAAAGCAAAACCAGAGAATGTCAGCAGGAGGAGAAGACGAGAGAG
AAGAGTACCAAGTAGAAGAAGAGTTCAGCGTGTGGAAGAAGAACACCCCA
TTTCTCTACGATTTGATTCTCTCTCACTCTCTGGAATGGCCTTCTCTCAC
TGTCCACTGGCTCCCTTCCACCCCTTCCACTTACGCCGACGACACCTACG
CCATCCACAAGATGATTCTCGGCACCCACACTTCCGAAGATTTCCCCAAT
TTCCTCCTCGTTGCTGATGCCCATTTGCCGCTCCATCCTGCTTCCGTCCC
CAACACGAATATCGAAGACCCCATTCTTCCCAAGGTCCACCCTTTTCCGC
TACTAATTTAGTTACAGCTTTACAACTATACTGCTTTCCTTTGATTAATT
GATTGCGTATATGGGTTTTACGGGTTGTGCTATTGTTTTGAAGAAACTTT
GCAAGATGATTTCAAGTGTATTCCATTTGCATATTAGATGATAAGAGGAA
AGATAGGTGTTTACTCAAAATTGTGGAGCTTTACGACATTACTGCTAACC
TTGATTAATTGATTGTGTATATCGGTTTTATGGATTTTGCTATTGTTTGG
AGATATTTGACAAAATGTTTTCAAGTGTATTACATTTGCATATTAGATAA
TAAGAGGAAAGATAGGTGTTTACTCAAAATAGTGGAGGCACGGAGCCTTA
GGTAGGCTACATGGATATGTTCATTTGCAAGTGTGTTAGTAGAGGATCTT
AATACATCTATTGTCTTTGTTATTTGTTCTTTACCTAAACCACCCCCTTT
TTCGGATTGAAAAGCTGACCTGGGCTTCTTCCCTTATAGCTATTGCTTTA
GGATTAGGCATAAATATAAGTCAGTTTTTTGGGTTTAGTATCTACTGATT
TATCTCATTTACCCTTCTCCTCTCCTTCACCTCTATGTTTCAGTAATTAG
TGAAAGATTTTTAAAGGTAGAAGTCATCCTATTACTTCTTTATTATCCTC
TCTGGTATGAAAATCTTCATATTTATTATTTTTACTATTTTTCTGTCGTT
AAAAATTTCATTTCTATTCACTTGCCTTTAGTAGCAATTTCTAAAGAGCA
GACAATTGGATCTTTTGAAGTTATTTTACAAATTGGTGATTCTCTTCTAA
TGTATTTCTATTTGGGTTCTCACTGTACTGTATGATAATGGCATCAGTAT
GGTTGTACTATATAGCAGATTAAAAATGGAAACCATAAGGATGTTTATAT
GTAGACACCAATATGGTGATTCTTTAGGCAAACATATAAATTAGTCGGAA
TAGGATGTACTTAACTGTTGCAAGCAGTGTCAACTAACAAAAGGGAAAGA
AATATATACAAAAGAGCTTTAAATTTAAAGAAAAATCTTCAAAGCAGATC
TGTGCCATGGACAAGGAGCAAGACTTAATGCTAATTGCAAGTTTTTCTTA
AATATTAATTTCTTAAATTGTAAAGAATCTAATCTCATATTTCGTTTGCA
TAATATTATTTTAAAATATATAATTAAATCATACTTTATTTAATTAGGAA
ACTCTATTTGATCATAAAAAAAATTAATATTTTTTAACTATAAAATAGGA
TTATTATATATGTGTTGTTCGTTAATATTAAAAGTTATATTATGCAAGTA
CAAAAATGCCTCTCGGACTTAAGATTAGCGGCTCTTTTTAACGGAATCGA
GATCGCAAATATAGACTGCAATAAACTTACCAACCGCCACGTTTCAAAGT
ATGGATAGTCCTATGAGTCAAAATTGAGGATCAGAAACATTTAATTCTTC
CGACTAATATAAACGCGTGAACCAAACGGACACCTAAATACATAGAATTC
GGCCCCTCGCAAACATGAGTTGAGCCCAGCCCAGCGAATTCCATCTAACC
ACTATGATGCCTTGCCTTTGAGCTAGTCCCTTTTATATAAAATTAAAACC
CTGGCCAACACACACACAGAGAGAAACCCTCCATCTTCGCCGGTATCATT
TTTGCGCGAAAAGCTTGAGAATGTCAGGAGGAGAAGAGGATAGAGAAGAG
TACCAATCAGAAGAAGAGTTCAGCGTGTGGAAGAAGAACGCCCCATTTCT
CTACGATTTGATTCTCTCCCACTCTCTGGAATCACCTTCTCTCACTGTCC
ATTGGCTCCCTTGTGCCCCTTGCACTTACGCAGACGACACCTACGCCATC
CACAAGATGATTCTCGGCACCCACACTTCTGAAGATTTCCCCAATTTTCT
CCTCGTTGCTGATGCCCATTTGCCTCTTCATCCTGCTTCCGTCCCCAACA
CCAATCTCGAAGACCCCATTCTTCCCAAGGTCCACCCTTTTTCGCTACTA
ATTGAATCACACCTTTACAACTATACTGCTTTCCTTTGATTAATTGATTG
TGTGTATCTGTTTTATGGGTTTTGCTATTGTTTGGAACATATTTTACAAA
ATGTTTTCAACTGTATTAAATTTGCATATTAGGTCATAAGAGGAAAGATA
GGTGTTTACTCAAAATACCGGAGCCTTAGGCTACATGGATATGTTAATTT
GTAAATGTGTTAGTAGAGGAGCTTAATTCATCTATTGTCTTTGTTATTTG
TTCTTTACCTTAACCACCCCCTTTTTTGGATTGAAGAGTGGAGCACTAGG
AGTCTTTCTTTTGAGGGAGATGTTTAGCTTTCCTTTACAATGTAAATGCT
TTTGGTATATTAGGGCCCCGGGCCCCTAGTGCTCTCACCACCGCTTGCTC
GTGGTCTTTTTAATGATGGACTAGATTTTTGTTGAATCTATTAACTTGTA
TATTTTTAGGTGGAGATAAAGCAGAAAATACATGTTGATGGAGAGGTGAA
CAGAGCACGTTGCATGCTGCAAAAACCATTCGTTGTTGCGGCAAAGACTA
GTAATGCTGATGTGTACGTATTTGACTGCACTAAACAACCGATGGATCAT
CAAGGAGGGTCTTGTGATCCAGATTTGAGGTTGAGGGGTCATGATAAAGA
AGGGTATGGATTGTCATGGAGCCCATTTAAAGAGGGGTACCTCTTGAGTG
GTTCAAATGACTGCAAAGTTTGTATGTGGGATATTTCAGCAATGCCGCAA
GAGAAAGTGCTAGATGCATGCAATGTTTATAAGGTACGTGTGGTACTTGT
TGTCTCTCTTGGACTTTTGATGATGTGAAGTCTTTTTTCAATGTAAAATT
TAACCCTCACCTAGTTATTTACATCAAATTATCACTTAGGAGCATGGAAG
TTTGGTTAATGATGTTTCATGGCACTCGGAGAATGAAAATTTGTTTGGCT
CTGTTGGAGATGACTGTCGGCTAATGATTTGGGATCTACGAGCTACCAAG
CCCCAACAGTCTGTAGCTGTTCATGAAAAGGAGGTTTGACACATTTCAAT
AGTTTTTCATCTGTGTAACAGTCTCGCTGTTTAGAATTCATGTTGAGCAA
GAACTGAATTTGCGCTCAGCAACACACCTGTTGTGCTTGACTGAAGTCAG
GATATGAACTTAACTGGAAAACCTGGCAGCTCTGTAAGAATATAATCTAT
CATATCCACAATCTGCTGGTGAATATTTACTTGGATATAATTGGTGTTTA
ATTTGTAATATAGTTATTACAAACTTACTGTAACTGGTCATGTATATAGA
CAATGATTTCTTTCAAATTTAAGTGCTAGTAGTCACGTTCTTATACATTT
TCCGAAGTTATGAAAATAATGTTTGAGTTGCAGTTTTTGTCATTAATAGT
GTGTCATTCTTCTTTTTTTTTTTAGCCAGTGCCATGACAGATGACCTTTG
TTATTATGATTGGATATTGTTAGTGATCTATAAAACTTTCCATTACCATC
TACAAGAAGCATGTCTATATTTTTAATGGTATTTCTTTTCGGTTTCAGGT
TAACTATTTATCATTCAATCCTCACAATGATTATGTATTGGCTACAGCGT
CTTCAGATGCAACTGTTGGTTTGTTTGACTTGCGAAAATTGTCAATACCT
TTGCATATTCTCAGTAGTCATGCGTATGTTCTCTTTCTCTCTTCATATAT
ATATATATATATATATATATATATATATATATATATATATATATATATAT
ATATATATATATATATATATATNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNATATATATATATATATAAAAGCAAATGCT
CAGGTAAAAACCAGGCTTAGCCCTGAAACATATAAATGTATGAATGTATG
TATGTATGTATGTGTAATTTTACACACATTACTTGAGCTTGATACTTGAT
ATTATTGCCTTGCATTTTGATTTTATAAGTTGATGGACTTGTGCCATTTT
TTAGCTTGACATAATCAACTAGAATTGGTTTTCCTAATCTACTTTGAGGT
TTTTAGATGTGTTAAATGTATCTCCGGCCGCCATCCTCTTTCAATTGAAT
AATAAATAGTACTGGCCCTCAAATTTTAAAGAGGATATAGGCCTGTAGGG
ATGATGTGAAACATATGTGCAATTTTTTTACCGTTCTCTTGACTGAGCTG
AGGGAACATAGAGGCCTCGAATAATGGATAATGTATCCATGTAATTTTGT
AGCAAAACTTGTTAGAAATCATGTAAAAAAGAAATGACACCGTTCTTATA
GTAGCCAAACTAATTCTCTGATAATTTAATATTTTATAATGTAGTAGTCA
TGATATAAGAAATTTTCGAATTTGATTTTCTATACTTCCCAGAAGTAGGA
AGATATGCATAGTACATGAGCGACAATCATCTTTATGTTCCTAAAGCATA
TTAGTAATTTTAATCAAAAAGAAAGGAGAGGTAAATTTTGACCTCTCTTT
GTCAGCACCAATGAATGCGCCCTCACTCCCGCATCATAATCTTTTAATGT
GAGATATATATTGCTGTTGATTGTTTGTTAATATTGAAGTTGCATTGATG
TAGGATGATATGCCTTCTTTTTTACAGGGAGCAAGTATTCCAGGTAGAAT
GGGATCCGAATCACGAAACTGTGTTGGCATCTTCTTCAGCTGATAGGAGG
TTGATGGTCTGGGATCTAAGCAGGTACTCTAAACTTGAGAAATAGATGTT
TGTTTATCTTTCATCATCATCTATAGTCTATGCTATGCCCCTGAACTGAT
TCTATTACATTTTAGCTCCTTTTCTAGTCATTAATCTTTTCTACAATTAC
CAATGAGGAATGAGGCCAGTCCTCTTGATTGCTTTCTGAGCTGTAGCAAT
TGTACATCTCCAGTAATTTCGAATGATAATTAACAGATTTAGAGAGCTAG
TTTCGGATGCCAAGAACGCATTTTAGCTTACAAGACTTTGAACGCCTCGA
TGTGGCTTTTGTTTATGCACAATATAGAAAAGCTGTGAATAACAGAAGCG
CTTCTGTTTCCTTGTTTCCATTTGTTTGTTGTGAATAAAAAAAATGACCA
TAACAAAAAGAATTTATTTTCACTTATTGTCTTTTAAGTTCTAACAGTGT
CCGTTCAACTGACTGGTGCTTGGACACGTTCTTATCATTTATATGGCATT
TGCTGAGGTTTTGTTTATTCTCAACATGAAATGTCTTATCAGCAATAGGA
CAATCTTTTCCATCCTAGAAAGGCATTTGTATCTAAAATGCAATTAAAGA
TTCATGATTACGACTACAGTTTCCCTCCCTAATCAATCTGACCATTATGG
AATTATTTATTTGTACGTGTATGACTACTGTTTTTTTCCCTTTAATCTAC
CCTACCTTTTCGGAATTGTGTCCTTGTACATCCTTGGAGACCCAACTTAG
AACATGAATACATTTTTCTGTATTCTTGCAGGATAGGAGATGAACAGCTG
GAGGGAGAAGCGGAAGATGGTCCTCCTGAGCTTCTCTTCTCTCATGGTGG
CCACAAAGCAAATTTATCAGATTTCTCGTGGAACAAGAACGAACCATGGG
TTATATCAAGTGTAGCCGAGGACAATACTCTTCAAATCTGGCAGATGGCT
GAGAGCATCTATCGTGAGGATGATGACATTTGAAGTGTTCATCACTCATT
AATGTAAAAAGACCTTTGTCTTGAAACAACCTATCCCTATTAGAGCAATC
ATGTATGTACTGCACAGATAGAGTATAGAAGTACTTTGTCTGACTTGATG
GTTCTCTTGTTTGGGCTTCCTAACTAAAACTCATAATAAAGGTCATTGCA
TCTGTTTTCAACTTAAAAA