| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017386610.1, is a part of gene, LOC108214548. |
| The genetic_marker, MK003200 K0644, is located in gene, LOC108214548. |
| 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_017386610.1 | XM_017386610.1 | mRNA | DCARv2_Chr3:33415327..33421595 |
TCCTAATACAAAAGTGGCGCTACTTAAAAGCATTGCATAGCCTGATAGCC
ACGGTTCCCCATAACATTAACCACCCAGTATATATATGAGCCCCCCTCTA
CCCTTTTGCTTGCTCTCCTCCCCCTCTCTAATTAATTACTCTCATTTTCC
AAGCAATTACTCTTCATTTACCCCATCTCACCCTCTACATATATTAGTAG
TAGTCCTGAGTGAAAGATAGTCAGAGGAGAAGCCATCAAGAAACTCAAGC
TGCCAAGTTAGCATGGCCAAGACTGTGCTTAAAAAGAAGACCACGGGTTC
AATCCGGTCCATTTTCATGCATGCTGATGGTGCTGATAAATTGCTCATGA
CTCTTGGCTTCATTGGTACTGTTGGTGATGGTTTCTCCATGCCTGTCATG
TTGTATACCACTAGCATGCTCATGAATGATATTGGGGGCACTTCCTCTGG
AGTTGATGCTCAGTTCACACACAGCATCAACAAGGTTAACATAAACATAT
TATATTCAATTCCACTTTAAGTTGATATGGGTTTTTTTGGTAGTGTATGC
AATTATATTGTTGTAGATTTTGTGCAACTGATTCAACTTTATGTGTCACT
CAAAACAGAATGCTTTGTCTTTGTGCTACTTGGCCTTGGGTCAACTTGTT
GTTTGTTTTTTTGGTAAGTTGTTCACTGGACTTGTTTAAAGGTTTTTATG
TCAGAATTTAATATTTACTGGGGGTGATTTTATATAGTTTAATTTCATGT
GTTTAGAGGGATATTGCTGGACAAGAACAGCAGAGAGGCAAGCTTCAAGA
TTGAGAGCAAGGTATTTGAAAGCAGTGCTTAGGCAAGATGTCGGTTACTT
TGATTTGCACGTCACAAGTATTTCTGAAGTTATTACCAGCGTGTCTGGCG
ATAGCCTAGTAATTCAAGATGTTATCAGTGAAAAGGTTTGCGCCGCGACT
CAATTCATATAATAGTGTCTGCATTAGTAGTATCATTTTGTCAAGACTCA
AGAGGAGAGGTTCTTTTAGTGAGATTTAAACCATCAATTTAGGCTACAAT
ATTGTTACTACTGTGCATCTAATCATTATGATATCTATTAATTGCGCCAA
TTGTGTTTGACCACTCAGTACTAGAGGTCCAGAACATTCTGAAGTCATTA
CTCACAATCTGATCCCTGAAAATACATGAATTTTAATGCAATTCATGGTA
ACATTCATTACTTTACGTGCATGCACTTAAATTATATGTATGATTTAATG
ACTACAGATACCTGTGTTTGTGATGAATGTGGCATCATTTATCGGGGCGT
ATGTGGCCGCTTTCTTGATGTTGTGGAGACTTGCCATAGTCGGGTTGCCA
TTTTTGGTGATTTTGATTATACCTGGATTGATTTATGGGCGCACGTTAAT
GGGAATTGCAAGGAAGATGAGAGAAGAATATAACAAAGCAGGGACTATAG
TAGAGCAAGCAATATCATCAATCAGAACAGTTTATTCATTTGTTGGGGAG
AGTAAAACGATTACAGAATACTCTGCTGCACTTGAAGGGACAGTAGATTT
GGGACTTAAACAAGGTTTAGCAAAAGGCTTGGCGATTGGAAGTAATGGCC
TTGTGTTTGCTATTTGGGCCTTCATGTCTTTTTATGGTAGCAGATTGGTG
ATGTACCATGGCGCCCATGGCGGGACAGTTTTTGCTGTTGGTGCTGCCAC
TGCTATAGGTGGATTGTAAGTATATTATCCATGTACAAATTATTTACAGT
ATTTGCATCAATAGTAGTGACAGAGAGTCCTTTCTTGTGTTGGTTGTGGC
CTAGTGCATATTTTTTCATGGGAACAGAGGGTCCAGGTCCGGGTCCAAGC
CTTAGTGAAGGCATGTATGAGCACGAGGGTAAGGGCCAGTCAAACTGTTA
TCTGATCTTCTAAAAAACCACACATGCATATCCAGTTATCCATAAATATC
CAACAAACATTTTGATTTGGACAAGCATAATCCATGAAGACTTCCTGTTA
GTCATGGCAGAACTGTTTTGCTAATGCGTGTCACTATTTTCTTGAAGGTG
TAACTTTTTAACTTGATGATTAATCTAAACTTTTTTCCTTGACTTAGATC
ACTTGGTGCTGCTTTATCGAATATGAAGTACTTCTCAGAAGCCACTGCAG
CTGGAGAACGGATACTGGAAGTAATAAACAGAATACCGAAAATTGATTCA
GACAACATGGAAGGTGAAATACTAGAGAATGTATCTGGGGAGGTGGAATT
CAAACACATTGAGTTCGCATACCCTTCAAGACCAGAAACTATAATATTCA
AGGACTTGAACCTCAAGATTCCTGCGGGGAAGGCAGTGGCATTGGTAGGT
GGGAGCGGCTCTGGGAAGTCAACAGTAATAGCATTGTTGCAGAGATTTTA
TGATCCAGTAGGGGGAGAAATAATGGTGGATGGAGTAGGCATAGAGAAGT
TGCAGTTGAAATGGCTGAGGTCACAAATGGGGCTGGTAAGTCAAGAGCCA
GCATTATTTGCAACAACAATAAAAGACAACATACTTTTTGGCAAAGAAGA
TGGAAGCATGGAGGAGGTTATTGGGGCGGCCAAAGCTGCAAATGCTCATA
ACTTCATTAGTCAGTTGCCTCAGGGTTATGATACCCAGGTTTGTTTCTGC
TTTGTCTTTTTCCTTCCCCGCTTGTTCATTAAAAAATTGGTCCTGGTTAC
ATTTAATTTACATTAGTCAGACATTTAAGATAAACATTAATAACAATTAT
TTTGATTCGTTTACTTTTCTTATCATATAGTTTTCAGTATAGGAGGGGAG
GTATGATTGGAAATATCACATTGCCACGAGGGGGAGGGGGGGCACAGGTG
AAAGAGAGGGCGTCTGTAACTAGGCTATAACTTATTCCTTCCCTTCATAG
TTCTTAGTTTAGATGTTTATATATTTCGGAAGACACCCTAGAAGCTATCA
ACTAATTTTACCTGAATTCTACGATTATATTAATTATATAACTTCTACAT
TGATGATTGTAGTTCTCAAATATAATATCTTGCCGTCCAAGTGTTACTGG
TTAAGTGACATATATTCAAATTCATAAGAAAGTCTCCTTATACTTACTTT
TTTATGTTTCATGTAGTACATTACAGTTAGTTTCACAAGTTCCAACTGAA
GTTCTTAAATGCTCGGGCATGCTATTTTGAGCTAAAACTTTCAATTATTT
AAGTGTTCTGATTCTTTTCCACATGTAGCTTGTTTTATAAAAACTAGCTA
CTCCCATGGTTTAGTAATTTCATAGAAAATTTTACAGTTGCTTAATTTGC
ACAAGTATTTTTCTGATAACATGACTTGACAGTAACTGGATTTCAATTAT
TAAGTTTAGTTAGTTTTTATATTGAAGTGTCTGAGTGTCCAACCAGCACT
TATCATACTTAAATTTTAAAGTATTAATTAGGTTTTAAAGAGTTTACATC
AGTTGTTTAACTTAACTGTTCAGTTTATCAAGGCGAACTCTTCAACTGTA
GCACTTGTCCAGTAGCTTCACTATATGTCGCCAACTCACATATACCTGAT
AATTAGGTATTCAATTAGCTTTATATGATTAGGATAATGCCTCTATGGCT
TCTGGAGTAGCTAGTCAATGTTAACTAACTCGTGCTCTTCCTGCATGCAC
ACAGGTGGGAGAAAGGGGAGTGCAGATGTCAGGAGGACAAAAGCAACGAA
TAGCAATAGCTCGAGCAATAATAAAAGCACCCCGTATTCTACTTCTAGAC
GAGGCCACCAGCGCTCTGGACTCCGAGTCTGAACGTGTTGTACAAGAAGC
ACTTGACAAGGCCTCTGTTGGTCGCACAACCATCATTATTGCCCATAGAC
TCTCAACTATCCACAATGCTGACCTCATTGCTGTTGTCCAAGATGGTGAA
ATAAGAGAAACTGGATCACACAATGACCTCATTCAAGACCCAAATAGCCT
CTACTCAATTTTAGTCCACCTTCAACATTCACAAAAAAACTGTGTGCCAT
TGTCCACCAGTACTAATTATAAAGTTGCTTCAATATCAAACGTTGACATC
AATAATACGAGCAGTCGAAGAATATCTATGGTTAGCCGATCAAGCTCAGC
CAACTCAAGAGGAGGTGAGTATGTTAATCTTGACAACAAACATCCTACTG
AACAAATTTTTCCAGTACCATCATTTAAAAGACTACTAGCAATGAATCTT
CCTGAATGGAGGCAAGCTATATTAGGGAGTTGTGGGGCGATTTTATTTGG
TGCCATTCAGCCTGTTTATGCTTTCGCTATGGGTTCTATGATATCAGTGT
ATTTTTTGCCTGAACATGATGAAATCAAGGAGAAAACAAGAATATATGCT
CTGTGTTTCGTTGGGTTGGCAGTGTTCTCTTTTCTTTTTAACATAATTCA
GCATTATAACTTTGCTGCTATGGGTGAGTACTTGACAAAGAGGATCAGAG
AAAGAATGTTGTCCAAAATACTCACTTTCGAGATTGGTTGGTTTGATCAA
GATGAGAATTCTAGTGGTGCTGTTTGTTCTAGACTTTCCAAAGATGCCAA
TGTGGTATGTATTATATATACATCTTGTGTTTTTGCATAATGATATTAAA
ATGCTTGGCAGTGATGTTTATGGATAACAGAAAATTTTAACATATATTTT
TCCCTTCCAGGTGAGGTCTCTGGTGGGTGATCGCATGGCACTTGTAGTTC
AGACATTGTCAGCAGTTATAATAGCTTGCACTATGGGCCTAGTAATTGCA
TGGAAGCTTGCACTTCTGATGATTGCCGTTCAACCCCTTGTAATTGTTTG
CTTTTACTGCAAACGTATTTTGCTTAAAAATATGTCATCCAAGGCCATAA
AATCACAAGACGAGTGTAGCAAGCTGGCTGCTGAAGCTGTTTCAAATCTC
AGAACTGTCACAGCCTTTTCATCTCAGTCACGAATACTCAAAATGCTCGA
AAAAGCCCAAGAAGCCCCACGGCGTGAAAGTGCTAGACAGTCGTGGTATG
CAGGTATTGGTCTTGGAGTTTCTCAAAGTCTCATGTCATGCACATGGGCC
TTAGACTTTTGGTATGGTGGCAAACTCATTGCTGATGGGGAGATTAGTTC
CAAAGCCCTCTTTGAGACTTTTATGATATTAGTAAGTACTGGTCGAGTTA
TAGCTGATGCTGGAGCTATGACCAATGATCTCGCCAAAGGTTCTGATGCT
GTTGGGTCAGTTTTTGCTGTGTTGGACCGATACACGCTCATTGAACCTGA
AGACCCCGATGGCCATAAGCCTGAAAAAGTAATGGGCCACGTCGAGCTCC
GGGATGTAGACTTTTCATACCCCGCGAGGCCAGATGTGCCAATTTTTGCA
GGTTTCACAATCAAGATTGAAGCAGGGAAATCAACAGCATTAGTGGGGCA
AAGCGGGTCTGGTAAGTCAACCATAATAGGGTTGATCCAAAGATTCTATG
ATCCACTCAATGGTTCAGTAAAAATTGATGGGAAAGATATAAGATCATTT
CACCTTAGATCCCTGAGGAAATACATCGCACTTGTCAGTCAAGAACCTAC
ATTGTTTGCTGGAACCATACGTGAAAACATCACCTATGGAGCATCTGAGG
AGACCGACGAAATAGAAATCATCGAGGCAGCCAAGGCAGCGAATGCTCAT
GATTTCATCACCGGACTAAAAGATGGATATGAAACATGGTGTGGTGACAG
AGGAGTACAGTTATCTGGGGGTCAAAAGCAACGCATTGCCATCGCCAGAG
CAATCCTAAAAAATCCAGCCGTGCTTTTGTTAGATGAAGCTACAAGTGCT
CTTGATAGTCAATCAGAGAAAGTGGTGCAAGATGCACTAGAGCATGTCAT
GGTGGGGAGGACCAGTGTGGTAGTGGCACATAGATTGAGTACAATACAAA
ATTGTGACACAATTGCAGTGCTGGACAAAGGAAAGGTTGTTGAAAATGGA
ACCCACTCAGCCTTGCTAGCAAAGGGATCCACTGGTGCCTACTACGCGTT
GGTTAACCTTCAAAGAAGAGCCGACACTAACAACTGAAAGCTTTGATTTT
TGTAATCAAGCTTCTGGTTTTTTCCATCAAGTAGTTGGTCTGATGGAGAT
GTAGTAAGGCCTGACATAGCATATATTATAGGAAACAACATCCAAGGAGC
AGGGAAAACATGTTTATTCAACATCAATGTTGCGTAAGCTATATCTTTTT
ATGTAAAGAAATTCAGCTGAATGATTGCGTTATGAGCAATAAATAACATG
TTTTGCCTTTACATCTAA