| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017360832.1, is a part of gene, LOC108193967. |
| The genetic_marker, MK002230 ESSR-125, is located in gene, LOC108193967. |
| The genetic_marker, MK010119 7_17426452, is located in gene, LOC108193967. |
| The genetic_marker, MK002714 K0158, is located in gene, LOC108193967. |
| The transcript, XR_001801332.1, is a part of gene, LOC108193967. |
| 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_017360832.1 | XM_017360832.1 | mRNA | DCARv2_Chr7:17423028..17428368 |
CGCGGGAGTAAAAAGTAAAGCCAAAGCTTGAGCTGAGAGATTATCGGAGC
ATGGCGGCCATACAAATACTCATGGCATGTCCAAAATTACAACAATTGCC
ACTACCACTCTCTCAATCTCACGGGGGTGTATTCGATTGGGATTTTAATG
CATTGTTTTTAGTTTATAGATTTTAATGGATTGTATGGGATTTTGATTTT
GTGCGGATTCTTGACGAAATGTCGCAGAGTTGATAGGATTTAGGTACAAT
GCTTCAAAATCCCATTGAATTTGGTGGGATTTCAAAAAACTTAAAATACA
CTGAAGAATGCCACAAAATCCATCATTTTATGAAATGAAAAAAAATCCAT
CAGCATTTGAATACCATCAGATTTTAATGGATTTTAAACAATCCCAATTG
AATACCATCGGATTTTAAAGCATAATTTAAAATCCCAATTGAATACCATC
AGATTTTGTAGCATAATTTAAAATCCCAATTGAATACCTCAAGATTTTAA
TGGATTTCAAACAATCCCAATCGAATACCCTCGGATTTCATGAATGCAAA
AAAATGCTTTAAAATCCCAATCCAATACACCCCTCTCAATCTCATAGGCC
TTTGCGTTCATTTTTGTTATTACAATCACCAGCTTCTTCTTCTTCTTCTT
CATCTTCATCCAAGAAGAAGCGGTTAGAGATTAGGTGCCAGGCTGCTGAT
GTTGATGCTGATTCCTCTTCGCAGCAGATTTATCAAGGCTTCTATGGCCC
TTGGTCTGTTGATTCCTCCGACGTTCGCGAGGTACGCTCGCACTTTACAC
CTTCTGTTTCGCTCATTTTTATTATTCATTAACTCTGTTTACGATTGGGA
ATACGTCAATTCAATATAGATTGTGCTTTTGTCTCGATTGGCTGCAAACA
AATTATGTAAATCAAAAAGTATATCAGTATGTTGGCTCGTAATACCTGAT
GAGGGGATGGGGCTTATTAGGGTTTGTTTTACTTCTCTCGCAAGATAAAG
TGGAATAAAACAACGATGTAGTCATCGGAAAATAAACTTATGAATAGATT
ACCGACTGATATTTATATCAAGCCAATAATAAAACTATGATTGGGGTCTG
AAGAAACACCTGAACCAGCCTCACACGAAAAGAATACACAACTGCTAAGC
CTGCTATCATGTAACTAAAAACATCATGTAACTGTTAAGCCTGCTATCAT
GTTACGAAAAGAATAAAACGTCAACGGGTTCAATTGTATATGATTTTTTT
GTATTATTGTAACGACTCCACTACCTTTGCTTGGAAGTTGGAGCCGGAGA
GAGAGCCATAGAGTTACAAAGAGGGGTTAAAATCATGACATCCTCAAGCT
TGCACAATTGTTATAACTAGTGTTATGTAACTTTAAATTGAAATTACTCT
TCTAGACTTTAAATATACTCTTGCATAAAAAAACAATATTAGCAAGTTAA
CCTTGCCAAAGGATTACCAATACGAGTAAAGGTAATGCATCTAGTACAAA
CTAATAAATTAAAGACCTCGTTTGGAAAAAAAAAAATCAATCAAAAGCTA
AACTGTATAACTATAACAGATTTCCAGAATATTCTGAGTCACACAGACTA
AGACAACTCTCTCTTAATTTTCACAAACTATCATACATTACCCTTGAACT
AGAGTAGCACAACGAGCATCACAAATTAAAGTTCATGGCAGCAATACAAT
AAGTTGAAACAAATTACACAAATATTCAAACATATTACAAAAATATTCAA
GACATTCAAACAAATTACAACTGTTCTGAAAGGAGGGGTCATGAAACTAA
TGAAATCCACCAGTAATTGTCCACAAACCACCTGCTAGCAATTACTAATC
AATAATCATCAAGGGACATGTTACTGCCCTTGGACAGGTTATCGATGGCC
ATGTCACTGCCCTTGGATTGATGTCTGCCCTTGGACGTTGACCCGAACTT
TAATCAGCAAAAAGATCTTTGAATGCAGTTTTGAGTCTTTTGACCTCTGT
ATAGAACTCCAGCAGCTGTTTAATAGAAACAAAAATAAAAAAAATCTTGT
TAGTTTCTGCAATCACTTCAACAGCCGACTAGGTATACTTTCGTACGCAG
ATGCACAACTCAATCAACAACCTCACTCTTCACAGCTCTACTCACTACAT
TACATCAAACACCTGGAGTGCACAACTACTAATACACATCGGATCACTAA
AATTCAAAAATCACAACCTTAACTTGTCCCCACACAGCTACAACAACTCC
TTACAATTCACAACCTCAATTACTTCTCAGATGCAATAATAGATCCAGAT
CACACCAAAACAGCACAATATTAACTGTAAAGCTCTAAAAACAGAGTTTA
ACCTAATACTCCCTCCATCCCAAATTAGATGATCCTTTTGACAAAAAAAT
TTATCCCAAAATAGTTGAGCCTCTCTCTTTTCAATGCACATTTATCACCA
ATCTTCCATCCTTACCCTTTCTTATTTATCATTTCCAATGTAACATCTTA
CTAATACTATATAAAGTCAACACAATAAATAAGGGCATAGATGGAAAAAA
GATGAATCATTTAATACTCCTTAATATGTGTGAAATGAGCAAAAGGCTCA
TCTAAATTGGGATGGAGGGAGTATTTTTTTTGTGGTTTTCTTCATTAACA
GCAACTAATGACACTTATTAGGTCAAAACACGACTGAATAAGCAGTTTAG
AATTGAACAAACTAAGAGCAGATCTGCAAGTACAGATCAAACAAACACCT
CAGATGTAGAAAATACTAAAGGTCTGAATTTTGAACTGAGATTACTGTGA
TTCTAAGCTCGGACAACTCGGAATAGAGTGCACAACACAATGGAAGCAAC
TAATCATAAAAAACCACAAAAGCAATCTACTCGAAATTAAACATAAAACA
ACATATATGAAAATAATAATGCACAATTACAAGCACATTACAGAAATGAA
CATGGCTAGTTGTTGGGAAATACTAACAAATAGAATGTGAACAAAGTATA
TGCCTAAAACATGACAATGACAAATTAGGGATTTGAATTGGGGTAAACCA
TTGAATTGGGGGTATACAAAGACCAGAGCAAACAAACAAAAACACAAACA
CAAAGACGTGCCCAATTTCGGATCCCTATTAATTCACAAATCCTAATTTC
TTTTAAGACTACAAATCTGATACTTGGATCCGCACCCGTGACTGACACCC
ATACCCGACTCCGGGTAACATAGCATGTAATCATATTTCTATATACACAA
CTTAAGTGCCTCGCATTAATTCAGTCTTTTCCTGTTCTGCAGGTTATCTT
ATATAGATCAGGTTTGGTCACTGCTGCTGCCTCCTTTGTGTTTGCCGCTT
CCACAGCTTTCCTGCCTGACCATTCCTTCCTCACTGATCTGATAAAATCA
AATTATGATTTTCTCTATGCACTATGTGCTGCTGGTTTAGGACTATCCTT
GTTTCTGATCCACATCTATGTAACTGAGATTAAGCGCACTCTTCAACTAT
TTTGGGGCCTTGGTGTTTTAGGATCTTTAGCCACCAGTTTCACCCTTGCT
GAACCAGCTGGTCAGAACTTGGTACAATATGTAGCTGACCACCCAACTGC
TGTCTGGCTCGTTGGTCCACTCTTTGCTGCATTTACAGGGCTTGTATTTA
AGGAAGGTAATTTTACTCTCACTCTCTTTGTGTGCTTGTTTTTTTATTTT
ATAATAATGATGGCATATGTTGTTTTTTTTTTCATCAGGAGGGGATGGTT
TTTTTTCTTCCTCAACTAATGCAATAAACTTATATTTTTCCCTGAAGTAT
TAGAATATGCTATATATATATAGTTCAATTATTCATCAACAAAGCTTATA
ATTAAAAAATAGACATAGTTCTAAATATTATTCAACTTCATAGCAGGTTG
AGTGTCTTAAATAATGGGCTATCAAATATGTGCTTTAAAAAAATTATGTG
CTGTGGCTATATCAATCTAGGTTTTGCTGATGTTTTTCTCTCACATCGAG
TACTAATTTGATTCTTCATCAATGAATCAGGGCTTTGCTATGGAAAGTTG
GAAGCTGGAATTCTCACATTTGTAGTTCCTGCAGTTCTTCTTGGGCACTT
GGTAATTCTAATTTTCATACGCAAGCCTTCCGTTTCTTGAGTATATGATG
AACCTGGGAGCATTTAGTGTGAAGTTCTTTTGCATTGCCAAATTAAAGGA
CATAAAGATTGAACACTTTGATAGGAATTTGATCAAAAAACTAGGCCAAT
CTGCTAAAAGGAAGCAATTTGAGACCTCTCATGTAATAAAAACCTGACCA
CAAGCTTAGTAGTTAATACACAATAAACCCTCTTTTGATTTATAAATGAT
TTTTGTTTGATTTGAACAAAAGAAATTGCCAAAGTTTTTTATTAAACTGT
GAGCATTTTTCAGTACTTCGTTATCTATGCGTGCATTGGAAAAGGTTCTT
CCTCCATTTTGGACTTTGAGATGCACAATTACAATGTGTATTTATCTAAA
CAGTTTTGCCTTTTAATCTATATGATGTTTACAGCAATGCTCAATCAACT
TGGAGTTCTAGTAATCACGTGATATAATATGAAGACCATTTATTGTATGT
TCTGAATGAAGTATATATTTACTTCTTGCACATACTACACAGAAAATTGT
ACAGCTATTTCTGGAATCTGAGATGGTAAACTATTGAGCCGTCAATGCTT
CCTTTTCTAACTAAGGTATTATTTTGAAAATACAGACAGGTCTAATGGAT
GATGGACTTAAGATTTCTTTACTTGGTCTGTGGACGGCTCTGTTTGTGAT
TTTTGCCGGGCGGAAGTTCACTCAGCCAATCAAGGTAAAATTTTCATTTA
TTTCAGATATTCTTAACAAATAGATTAATGTCGAATCTTATAGAATCAGT
TTGCTGTTAAAGGATGATATCGGTGATAAGTCGGTCTTCATGTTCAATTC
TCTGCCAGAAGAGGAGAAGAAGCTTGTAGTTGAGAAACTTGAACAGAGAA
ATTATACAGACAATCTTGATAAAAGGGAATAAAAGACAGAAAGAATAGCA
TAATATGGTTGGACAGTTATTCTTGATAAAAGGGTATAAAAGACAGAGAA
AGAATAGCAAAATGTAGTTGCTCAGGTAAGCCTCTACAGGATCCATGTTC
ATGTTACTTGTGAGATTAGTATAAGCTTTTGTAGACTCATGCACTAATTG
TAAATATGTTCACTCTGTACGCACACATGTAAAGATGCTGCTGCATATTC
TGGTTACACGGATAACGGATTATCTGATATGATGACTTCTCCATATTTTG
ATAATGTTTCCCAGGAATGATCAGCATTACAATTTTGTAA