| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017371656.1, is a part of gene, LOC108202978. |
| The genetic_marker, MK008607 85036.33328, is located in gene, LOC108202978. |
| The genetic_marker, MK009386 1_36032038, is located in gene, LOC108202978. |
| The genetic_marker, MK010726 1_36032062, is located in gene, LOC108202978. |
| 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_017371656.1 | XM_017371656.1 | mRNA | DCARv2_Chr1:36027522..36033659 |
TTTACCACCCACCCCAACCAGATCCTGAATCCACAATATTTGAATAAATT
ATTTCCTGAAATTCATTAAAATTACTACACACACAGAGACACAGATCTAT
ATGTATATAAATAAAGATAATGCATATTTCATCAGCCACTCCACCACCAT
ACCTCACTCTGCTCATGAGCCATTGAAACAACCTCAAATCTCTCTCCACA
CCCAATCTTGGGTCTCTTGATTCCCCATTTTCTCGACCCATTTCGCAGAT
GGATCGTGCCCGAAAGCTCGCTGGGCGTGCCATTCTGAGGCGCTTAATCT
CAGACTCAAAGCAACAGAGGCCTAATGAGCTCTTACCCCCTGTTATCTAC
ACACCTTCAAGGTATGTTTCTTCATTGTCTCCTTACAATTTCAATACCAA
TCTGGGGAAATCTGTGGGGAGCTTTAATGGGTCTCTGTCAAGATCCTTAA
ATGTTGAATCTTTAAGGCCTAGTGATACTTTCCCACGTAGACATAACTCG
GCTACCCCAGATGAACAATCTAAAATGGCTCAGTTTTGTGGGTTTGAGAG
TCTTGATAGTCTTATTGATGCTACTGTGCCTAAAAGTATTAGACTTGATG
AGATGAAGTTTAATAAGTTTGATGGGGGCTTGACTGAGTCTCAAATGATT
GAGCATATGAAGATGTTGGCTTCAAAGAATAAGGTGTTTAAGAGTTTTAT
TGGGATGGGGTATTATAATACTGCGGTTCCTCCTGTTATTTTGAGGAATA
TAATGGAGAATCCAGGGTGGTATACTCAGTATACTCCGTATCAGGCTGAG
ATTTCGCAGGGACGGCTGGAGTCCTTGTTGAATTATCAGACTGTCATTAC
GGATTTGACGGGGCTGCCTATGTCGAATGCTTCGTTGCTTGATGAGGGGA
CCGCGGCTGCTGAGGCAATGGCTATGTGTAATAATATCTTGAAGGGGAAG
AAGAAGACGTTTATTATTGCGAGTAATTGTCATCCACAGACAATTGATGT
GTGTAAGACGAGAGCAGATGGTTTTGATCTTAAGGTTGTGGTGAAGGATC
TTAAGGACTTTGATTACTCTTCGGGGGATGTTTGTGGGGTTTTGGTTCAG
TATCCTGGTACGGAAGGTGAGGTTTTGGATTATGGGGAGTTTGTGAAGAA
TGCACACGCGAAAGGTGTGAAGGTTGTTATGGCTAGTGATTTGTTGGCCC
TGACGTTGTTGAAGCCTCCGGGTGAATTTGGCGCCGACATCGTTGTTGGT
TCTGCTCAAAGATTTGGAGTACCAATGGGTTATGGAGGTCCTCATGCAGC
CTTCCTGGCAACATCCCAGGACTACAAGAGAATGATGCCCGGAAGAATTA
TTGGTGTCAGTGTTGATTCTTCCGGCAAGCCTGCTTTACGTATGGCAATG
CAGACTAGGGAACAACACATTCGAAGAGACAAGGCTACAAGCAACATATG
CACTGCTCAGGTATGAACCACTCTTTAACATGATTATATGAAGCAGCAAG
TTATTATATGACTTCAGGTACCTGTTTTGTAATATTTATATGAAATATTA
TGTCTCTTTATGTAGGCATTGCTTGCCAATATGGCTGCTATGTATGCTGT
TTACCACGGACCTGAAGGTCTTAAAGTCATTGCCCAGCGAGTCCATGGTC
TTGCTGGGATACTAGCTGCTGGCCTAAAGAAATTGGGGACCGTGGAAGTC
CAGGAGCTTCCCTTTTTCGACACTGTGAAGATTAAGTGTGCTGATTCAAA
AGCAATTGCTGAAGCTGCTTACAAGAGTGAGATGAATCTTCGGATCGTTG
ATAAGAATACAGTAAGTGTCGGTTTTAAAATTTGAAGTTTATATGTTTTT
GCTCATTATTTTTTGATGAAAAGATAACACGTATTTATTTTTCAGCTTAC
AGCTTCTTTTGATGAAACCACAACCTTAGAGGATGTTGACAAGCTATTCA
AAGTTTTCGCAGGCGGGAAATCTGTATGTGATGCTGATTCTTCAATAGTT
GTATGCTTGGTGGTTTTTTATTTGTTCATTACACTCATGCCATAAAGAAT
GTTCTTGTTACCTGTCAGGTTCCATTCACCGCTGCATCTCTTGCATCAGA
GGTTCAGGATGTTATCCCATCCGGGCTCGTAAGGGAGACACCGTATCTAA
CGCACCCAATCTTTAACTCGTAGGATTCTATCTTTTCTGCTCTCTTCTTT
TAATTATCTAATTTATCTCATAGCTGTAAGAACAATTCTGATAAACTCTT
TCTGTAGATTCCATACTGAGCATGAGCTTCTCCGATACATTCACAAGTTG
CAGTCGAAGGATCTCTCATTATGCCACAGCATGATTCCCCTAGGATCCTG
TACAATGAAATTGAATGCAACAACAGAAATGATGCCTGTAACATGGCCTA
GCTTTACAGATATGCACCCTTTTGCACCTACTGAACAGGCTGAGGGTTAT
CAGGTAGTTATGATGGTTCATCTATAAAACTTCTCATTTCTCTTATTTTC
TTATTGATTTCTAATTACTTACAATTTAGACTTGGTGATAATTTATGCTC
ATAAAATGTCACTCTTTCCTCGTACAGGAGATGTTCAACAATTTGGGTGA
CCTCTTATGTTCCATTACTGGCTTTGATTCTTTCTCTCTACAACCGAATG
CTGGTGCTGCTGGCGAGTATGCCGGGCTGATGGTCATTCGTGCATATCAT
ATGGTATACAAATCTTTAATGCAAAATGTTTTAATGTTAGGTCCAAGAAT
CTGTTTCCTTGCTCTATCGATAGTGGGAAAGCCATGATCCTGTTTTAGTG
GCGTAAATTGGAAAATTAGTAAGAGAGTGATTACTGTCTACATAGTACAA
TAAACATGAAATACTTTGATGATTTTTTATGGATTAATAACATGTGTGTG
TGTGTGTGTGTGTGTAACAAATAGGAGAAAATTTAACTATGGATCTTGAT
AATTTCTCACCAACAAGGTTGAAATTCAGTTACTAGTATAAATAAACAAT
CCATGATTCATCTTTCACTTAAATTTTAGCTGAATTTCCTAATTTTCTTT
ATATTAATATTGATATTTTAAGACCTTCCTTGAGTGGACATAGAGGGTTC
CAGGCTGGCTATAAGATGACATAGCTTTTTTGAGCTTCATTAATGTATGT
TATATGGGATAGCAATGCGTAGCTCTGTAATTAACATTCTTGTTCTTAGG
CACCTTGCATAGCCGCCTTTATGTCAAGTGTTGTCCTACAGTACTTGTCT
TGTGTGAAAGTCGTATGCTTTTATATTATATTCCTTTGACATGTAAGCTG
ATTATCTTCCAATCTATTCACATTTTAGTCATCTTGTTAAAATGTAGGCA
AGAGGAGACCACCATCGTAATGTATGTATTATACCAGTCTCTGCACATGG
AACAAATCCTGCTAGTGCTGCTATGTGTGGAATGAAAATTGTGACTATTG
GAACTGATGCCAAAGGAAATATCAACATCGAAGAGTTGAAAAAAGCTGCT
GAAGCAAACAAAAAAAATCTTTCTGCTTTTATGGTAATAATTATTCGCTT
GACAAATTGGTAAATGTTTTATGAATATTACATTACTGAGTGCGAGATGA
TTTTATGTTAAATTTCAGGTTACATATCCTTCTACTCATGGAGTCTATGA
GGAAGGTATTGATGAAATATGTAAGATTATTCATGACAATGGTGGTCAAG
TGTACATGGATGGAGCCAACATGAATGCTCAGGTTTTCATCTCCTTCTTT
TTGGAAAATTGATTGTCTGCCATCCTTTTCATGATACGACTCCTTGATAT
TAGTTCAACCATGTCAAGTAGCTTAATTGTTAGTTATTTATCAGAACGTT
GTCTTCACAGGAATTATTAGTTATATCCTAGATATGGTTATGAAAGCTAA
TTTGTTCAAAGAAAATTAGTAACCTAAAGTTGGTCACTGTTCAGTGAGAA
TATATTTCAGAAGTTACCAACAAAACGGGAGAACATTTCTTTAATCAAAG
ATGCAATCATTCTATTGTGCAGTGTTACTAGTTAAGCTGTTGTAAGTTTA
GGTATTGTTGATAAATGATTCATATTCCTAAAATATGCACTGAAGTGACT
ACTTTCTCCTCTGCCTATAGGTTGGGCTGACAAGTCCAGGCTGGATCGGT
GCTGATGTTTGTCATTTGAATCTCCACAAGACATTCTGCATTCCCCATGG
TGGAGGTGGTCCTGGCATGGGCCCTATTGGTGTAAAAAAGCACTTGGCAC
CTTATCTTCCATCCCACCCCGTGGTATGCCATAAGTCAATAGTGTCATTA
ACTGTCACGTGCATTTATGTAGTTTAAATTCTATATCCTGTTTATGTAAA
GGAAAAATCTCTTTAGAGATATAAATTGGTTATATGTTTTAAGCTATACG
AGGCTGTGTCGTAAAATTGTCATATAAATTTCCTAGCATATGATGACAAT
TAGACATACAATGAGTTACATACCAAGATTACTCGGTGCATAAATATGCT
ATATCTATATTCTGTGTATTATATATGAGAACATTTCATGTATTAAGAAT
TTCTAAATGATGATTATCTATAACAATACATATACATTGTTCTGATTCAT
AAGATATATATTTCTAAAGTTTACCGTCTTGTTCTGATATCTCTCCGTTC
TTCAATAAAGATCTCTACAGGAGGTATACCAGCTCCAAATGAGGCACAAC
CCCTCGGTACCATTTCTGCGGCTCCATGGGGTTCTGCTCTTATATTGCCA
ATATCGTACACATACATTGCTATGATGGGATCTGGAGGGCTTACAGATGC
TTCAAAGATTGCCATCTTGAATGCAAACTACATGGCAAAACGTTTGGAGG
TCTTTACTTAACTATGTTTTGCATTTACATATTTTAGTTAAGTTAGGATA
TACAACCTATTACCCTGTTTTTTAAACTGCAGAATTGCAAATATTTCTTC
TTGTTTGCTTCTATTGACGTTCTACCTTTGCTCTCAACAGAATCACTTCC
CTGTTCTTTTCCGTGGTGTCAATGGAACAGTTGCCCATGAATTTATAGTT
GATTTGAGGGGATTCAAAGTAATTTTTATTTCCATCTTTAGACTTCGCTA
TCCCCAATTTTTAATGTGTTTTAAAGTGTTCTAACACTTTCAAAAATAAA
ATTATTTCAGAATACTGCTGGTATAGAGCCTGAAGATGTTGCAAAACGTC
TCATGGACTACGGTTTCCACGGGCCAACAATGTCATGGCCTGTTCCAGGA
ACGCTCATGATTGAACCTACTGAAAGTGAAAGCAAGGTATAATTACAGAG
TTAATCTTTTCTAAAAGTTTATGAGGTTATATATATTTATTCCCATATTC
TGATTATATGTGGTGTTTATATAATCCCCTTACAGGCAGAGATGGACAGG
TTTTGTGACGCCCTTATCTCCATCAGAGAAGAAATTGCACAGATAGAGAA
AGGAAAAGTTGATGCCAACAACAATGTTCTTAAGGTAAGTGACACTGCCA
TACCCACACTTGTTCTACTCTTTTTTTTTTAAGTCTTGACAATGTTTTAG
AGACTAATTGAGAAACAAAATGCAGGGAGCTCCTCATCCACCATCACTAC
TCATGGCAGACAAATGGACAAGACCATATTCTCGAGAATATGCAGCTTTC
CCCGCCGCCTGGCTCCGATCCACCAAGTTCTGGCCAACCACTGGTGTGTT
TCTCGCTCTAATTTCATGATTTATTTTCTTCCAAAGTGAAATGTTCCCAT
TTGTAGTTTCCATTCAAATAAGTTCATTTCCATGAATTTTTTTAATACCA
TATAAATTGTTTGTGACATAGTGTAATTAACGATTATAAATTATTCAATG
TCATCTCAGGACGTGTGGACAATGTATATGGTGACCGTAACCTGGTCTGC
ACTCTTCTCCCAACAAATGGGGTCGAAGAGCAAGAGGCAGCAGCTTCTGC
ATAAGTTCATGCATTACACTGCCAAGGGAAAGTTCCTTTCCAAACATGTA
ACATCAGTTTCTCCATATATCTTATTTTCTCCTGTATATAGTTTATAAAC
TTCACATGTGCTGTCTTTTCTCTTCAAACTATATTTGAACAGCAGCAGCA
GCAGCATTAATACATGATCTGTCTTGATTTATTTATA