| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017374004.1, is a part of gene, LOC108204517. |
| The genetic_marker, MK009360 1_19278411, is located in gene, LOC108204517. |
| The genetic_marker, MK010659 1_19278516, is located in gene, LOC108204517. |
| The genetic_marker, MK010661 1_19278614, is located in gene, LOC108204517. |
| 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_017374004.1 | XM_017374004.1 | mRNA | DCARv2_Chr1:19277685..19283917 |
AAATCTAAACATAAATCTTTTCCTTTACAAAACGAGGGTTAATTAGTTCA
CTTATCTTAATATCCGAAAAATTGATTGCTCTATTTTTAAGGGTTAAGTA
AATAAATCTCAGATTCACAGTCACTTTCAACACACACTTGTTGTCTTCGA
TCACACAACAAACCCAAATCAACTACTGTATACTCCCAAGATTTCCACCG
AAAAAACCCACTTTCTATCTGTATCTATTTTGCTGAGATGGGTCTCAAGA
TTAAGCTTTTTCTAGGGTTTATGGTGCTTAATTTTTGTGAATCAGTGATG
GGCAAGTTTGTAGTTGAGAAGAATAGCTTTAGAGTGACATCTCCAGATAG
TTTAAAGGGGACCCATGATAGTGCAATTGGGAACTTTGGGATTCCTCAGT
ATGGAGGTAGCATGGCTGGTACTGTTGTGTATCCTAAAGATAATAAGAAA
GGGTGCAAGAGTTTTGATGATTTTGGGATTTCTTTCAAATCCAAGCCTGG
GTCTTTGCCTACTTTTGTGTTGGTTGATCGTGGAGGTAGTTTTCGATTAC
CCTTTCTGTATTCTTGATTTAAAGTTTGTTAATTTTGATGGGTTGGATTA
TGTGTGAGGTTGGTTTGTTTTGAAGAAATTGAAGTTGGTAGCTTTTTTGT
ATTGTCTTGTTTGCTTGGTTTGGTTCGAGTTTCAAGGTTTTTATAGATGG
TTTGTATTTTGAGGTGTTTATCGCTTTTAGGAGGTACCCTTTTGAGTTTT
GATTGACAGTTAGTTTGTCCATCTTAGAAGGTATCCTTTTGAATATTTGT
CAATTGGTCCATTTCTGGATTTACCCTTTTAGGTTTTTGTGTAAGTTTAG
CTCATTTCCGATTGTGAGGTGATTGAGAGCACTCTTGCTAACATTTCTAT
GTTTGCTACTTTTAGCTCTTACTATCGATTTCTTATGGGTGAATTGTTTG
TATTTTTTCCTAAGGTTTATTGCCTACAATAATTTTGCTGTTTGTGTGTA
GGTATAAAGTATATGTTTTTTTTCTGTAACTTTTCGTTTTTGCATCTGCT
GTTATATGTAGTATCTATATTTGTGGAACACATATCTACAATTGAAAAAT
AAGAAACTAGAACAAAACTAGCCTGTCAGGTTCAGTATTCTGTAGTTAAA
ACCTATACCTCAATATAGGAGTCTTGACTAATTGGATGATTTATTGCTTT
AGTTATCAGAAAATGCAGTTTTAGATGTGAGTACTGCACCCTTTATATCC
TATCCTTGAGAAGCAGAGCAAACATGTAGAATACAGTGGCTAATACAATA
TATTCCGAGACAGGTTCAGAACACAAAGTGTCAATAAAAGAATTTATAGG
TCATTGATATAAACAGGAGAACAAAATCATCAGCTACATGTTACATTTGG
CGGTGTACACTACAAAACAAAACTTGTATGACAAGGACATATCTTCAGAT
TCCTGTGCCATATTCATTTTGTAATCTTCATCTTGAGTTTATACTAACCA
GATGTTGCTGAATTGTTTCATAGCTTCATTATATTTGGTTAAAACCATCA
GTTTCTACTATTCATATTTATGTGATCAGAAATGTTTTTCTCAACTATTT
GATTGCGAATCTTAGTAATCTTGTCTCAAAAGCATTCTATAAGTACCTTA
AACAGATACCTTCCAAATTTTTGAGATATTATAGCTTTCTTAAAGTGTAG
AGGAATGTACAAGTTTTAGTAATAACTTTAGTGTACTTATATATTGTCTG
GTATTAAATTGAGTTATTATTGCATTCATTTGTTTGCAGATTGCTTTTTT
GCTCTGAAAGTGTGGAATGTCCAAAATGCTGGTGCTTCTGCTGTTCTTGT
AGTGGATGACACGGAGGAACCATTAATAACCATGGACACACCTGAAGAGG
ATGTTAAGGCTGCAAAATATATTCAGAACATCACAATACCATCTGCACTA
CTCGACAAATCATTTGGTGAAAAATTGAAGAAAGTGATTAGCAATGGGGA
TATGGTCAACGTTAATCTTGACTGGAGAGAATCTGTTCCTCACCCAGATG
ACCGTGTGGAGTATGAGCTTTGGACGAACAGTAATGATGAATGTGGCATT
AAATGTGATATGCTGATGGACTTTGTTAAAGATTTCAAGGGCGCTGCCCA
GCTGCTTGAAAGAGGCGGCTATACTCAGTTCACTCCTCATTACATAACAT
GGTATTGTCCTATGGCATTCACAATAAGCAAACAGTGCAAATCCCAGTGC
ATAAATCACGGGAGATATTGTGCTCCTGATCCTGAACAGGATTTCAGTTC
AGGTTATGACGGAAAAGATGTGGTTATTGAAAATTTAAGACAATTATGTG
TGTTCAAAGTGGCAAATGAAAGCCAAACACCTTGGGTCTGGTGGGACTAC
GTTACTGATTTTCAAATTAGATGTCCCATGAAGGAGAAAAAGTACAACAA
GGAATGTGCTGACAGTGTTATCAAATCCTTGGGTAATGTATTTTATGCTT
TATGCTAAGGATATCAGGATCTGTGGTTGGTGTATTTAATATTTTTCCTG
CACAGGGCTTGATTCCAAAAAGATTGAGAAGTGTATGGGGGATCCAAATG
CTGATTCTGACAACCCTGTACTGAAAGAAGAGCAAGATGCTCAAGTAAGT
TTTTAACTTCTCTATTGTATTTAAAAAAAATATTGTGGTAATAATAATGT
GAACCAGTGTAAGCCTAATTTAAGAAATGTAACTAATAGACAATTATATG
CCATGTAGGTCGGGAAAGGGACAAGGGGTGATGTAACCATATTGCCAACC
CTTGTTGTCAATAATCGACAGTACAGAGGTGAGCTGTTTAATTTTGTATT
TCCTTTGTCATTTCAGGAATTATACTGCTGATATGATATGTGTTCTTGCA
GGGAAGTTGGCGAAAGGGGCTGTTCTAAAGGCTTTATGTTCTGGTTTTGA
GGAAACAACTGAGCCAGCTGTGTGTTTGAGTGGTGGTGGGTTCTATCTTC
TGGTTTATGTTTCGAAACTAGATTTTAGCATGAAAATTTCTTACATAAAT
GAACTTTTATGGTTTTGAGTTGGTATCTCTTTACTCAGATGTTGAGACAA
ATGAGTGCATGGAAAAAAATGGTGGCTGCTGGGAAGATAAGGCTAGCAAC
ATCACTGCCTGCAAGGTACCTATTTAGAGTTGTGGAAGTGCTGTTGATGT
TTTTATTATTCTTACATATTCATGGACCCAGGATACATTTCGTGGAAGAG
TATGCGAGTGCCCTGTAGTTGACGGCGTGCAGTTTAAGGGTGACGGTTAT
AGCTCTTGTGTAGGTAAAGTATTTTAATTAATTTAATTTTTCTTTAAGAA
AATAATAAACTCCAAGGAAGCAGTTATGTTATTTTTTAGGTCACCATGAT
GCAAAAAAATGTTAGTCACTCTATCGGATGTAAGCAGTGTGTCTATGACA
CGATGTTGATTATTAAGATGACTTTGTGAGAAACTTTTTTTTACTGTTAA
AACCCAGATATATAAAATAGTAGGTTTTGAAATCTAATTTTGCTCAGTAA
GGTTGTCATGCAACTTCTAGATTTTCATTAATCTAACCCAATTACCTTTT
CATCGATGCACTGCAATACTATCATATTTCATTTAGTTAAGTTTGGTTTG
TGTTTCCGGTAATTCTAGATATATGCAAACATATATGATATATCTGAACT
CTGAAGTCTGAACAAGAAAGGAAAATTGACTTGTTTAGTAACATGGTACT
GTGCTCAGTCCGTTATAGCTTAAAGGAAATGAAGTAAATCTTATTTTCGG
ACAAGATATTTGAAGTTGTATTATATTATTCATAGTGTAGATCTTACCCA
AAAGCAATGTCATATATTGGGATCTCTCTATACTAATCATGTTTTTGGTA
CTTGCTTTTCTTAATTTAGGCTCCTTATTGCATATATACTCGATTGAAAA
TAAGAAAATGGTGGTATTAGTATATCAGATTTTCAGTTTTGTACAATAGC
TAATCTGTTAGAGAATTGATTATTCTGTACTCTTTAATCGTAGCTGGTTG
AAAATGAATGAGTTCAGTATAGGTATTGTTATTATGAAATGTCCAAAATG
ATGAGTTTAAGTTGTAATAGTCATTCCTTTGCTGTTCAAAAACCCATATA
TTATTTGTGTTCTTCCACATAACTACTTGGGGCACTTTCTTATAGCAGAT
TCTAAGGATCCAGGAATAATCATTTATCCATCTGCTGAAGTCTTGAAGCA
CATTTCAATTCATTCTTTAATTTTTTTTATGTACATATTAATATAATTAA
TAGTCTAATTTTAATGTTCCACCTTTTTATCCACTGAACAGATCAAATAG
GCAATTCATGTAATTCCTTGGGTTAAATTGTAAGCTAAACAATGGTTTTT
AACTTTTGTGAACTTTGTACATCCTATGTTTATTTGCAGCAAGTGGGCCT
GGTCGCTGTAAGGTCAATAATGGAGGTTGTTGGCATGAAACTAAGGGAGG
ACATACCTTCTCTGCTTGTTCGGTTGGTGACAAATCTTTTGACTATGTTT
CAAAGTCCTCAATTTAAAATTGAATTTAATGTCATATTATGGTTCTAATG
GAGAACAGGATAAAGGGGATGGCAAATGCGTGTGTCCTCCAGGTTTTAAA
GGCGACGGTGTGAAAAGTTGTGTAGGTAAGAGAACCAAAAACTTGGTTTT
ACTTGCTGCAGAAGAATATTATGTGATTGATCATTGGTTTTATTAATTGA
TGCCCATTGTTAGAAAACTACCTTGTGTGACATAAGTACTGGTCATTGGA
CCTGTTTAATCATTGTACTCGTACTGGATTTCTTAAGACCATGAACCCAT
TTAATTTCCATTAGGGTGAAGATTATTAGACTATTGTAAAGAGGACAACT
TTAAGCAAATGAGCAGTATTCTTTTGTAAATTTCATATTATCTCGTGGTA
TTCGATAATCTGATGGCTGTGAGTTATGCATCAGTTTTTCACTTTCTTGT
AGCGCATATTATTTTTAGAGTTGATTGGGATTTTGAACTTTTGTAACGCA
GTATTTTCCGGGTACTTTGTCAAAAAGAGATTCTTTTTTGGTAGCTTTAT
TGTTGTCAATAAGTGCCTTGATACAACATAAGCTCATGTTTACTGTTGCT
CTAAATGTAATTCGAATTTTCTAAGTCATGATTTGCTCACCATCCAGATG
TTGATGAATGCAAAGATAAGAAAGCGTGTCAGTGCCCTGAATGCAGCTGC
AAGAATACCTGGGGTAGCTATGAATGCACATGTTCCGGGGACAATCTTTA
CATCAGGGAGCATGATACTTGCATAAGTAAGTTAGTAGGGGCAAATGTTA
CGTCATCTCTTTAAAGACCCTTTAGTTACAATGTTAATCATTTTCTTTGT
GTTTATGTGAGGCAAAAGGCTGCTTTCTGATTTTATTCCATTGATTTGCA
GGTACAACTGCAGCCGAAGGAAAGTCTGCATGGACCGCTGTTTGGGTCAT
TCTGATAGGTTTGGCTATGGCTGCTGGTGGTGCATATATGGTGTACAAAT
ATAGATTAAGGGTATGTATGGTGTTTCTGCTGATAATATTGCTAAGTTAC
TTTGTACTACAAATAGTTAATAAGTAAGCTCATTACCAACTTTGGAACTC
AAAAAATAACTACAAATATTATCTTTATTCATACTCAAATCACTCATTGA
AATATGTGTTTCCAGTCATACATGGACTCGGAGATCAGAGCCATAATGGC
GCAATACATGCCCCTAGACAGTCAAAATGAAATTCCAAATCATGTCAGCG
ATGACCGAGCTTGAAGGAAATCGACCAAGAGGAAGTCTGATCATTTTATT
TATCAGAACTTTGTTTGAAGCAAGGAGTACACAAGCTATTTATGTTCAGA
TAAGAATATTAAGACCTCTTGCGCCTTTTTAGTATATTTTGGACAATAAA
AAAGATAGATGCAAAGAAATTGTCCCAAAATCTGTGTAGAATTAGTAATT
ACTATGCCAAGTAAAGGTAGATTGAAAAATTATTGGATAAATTCTGGTGT
AATATTCTTGTACTCTTTTGGTTGTATTCTTACCACAATTGTTCTCTCCA
CTTTTTATGGATGATAGGGTAGGCTGACTTTCTTCTGAGCTAGCTAATTT
GTATTGGTATATGGCACTTCACAATAATGAACTCCTGGAACAGTTTCTCT
ATTTATTATATTTTTCTTTCCCGATTTTTGAA