| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017386304.1, is a part of gene, LOC108214352. |
| The genetic_marker, MK011754 3_34195076, is located in gene, LOC108214352. |
| The genetic_marker, MK011753 3_34195086, is located in gene, LOC108214352. |
| The genetic_marker, MK006332 K3776, is located in gene, LOC108214352. |
| The mRNA, XM_017386305.1, is a part of gene, LOC108214352. |
| The transcript, XR_001805606.1, is a part of gene, LOC108214352. |
| 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_017386305.1 | XM_017386305.1 | mRNA | DCARv2_Chr3:34191962..34195463 |
| XM_017386304.1 | XM_017386304.1 | mRNA | DCARv2_Chr3:34192224..34195462 |
AAATACATATTGGTCGATAAACATCAAGTAGTGAAGGATGCTTGAAAAAC
GATGTACAGTACGCAGAAATTATACATACAGCCATTATGCTGCTAGCTAT
AGAGACTACTAGTCCATTTCACAAGCCAAGGGGGCTGAGGTGGTGGTTTT
GCATTTATATAGAGTAGATCGCCAAATTTAACATGACACACATTGTTATT
CACGACATACATCTGTCTTCTCCGCCCAAATAAATCACTCCCCCTTTCTA
TTTATTCATTCATTTTCTTATTTCTTTCTTCACTTCATTCTCCACCTTCT
CACTTCCCATGGCTCCAACCATTGAATCCCATCAAGAAAGCCACTCACTT
GAGGCTGCTCAAGCTGTTTCTGTGCTTGATATCAATGCCCAGATTGAAGT
GCCCTCAAGATCAAGAGTTACTGTGGTGGGGAGTGGCAATTGGGGAAGTG
TGGCTGCTAAGCTTATTGCTTCCAACACTTTAAAGCTCGAGTCTTTTCAT
GGTTTGTTGATTTCTTGATTTTTTTTGCTTTGTAAAGTTTGCATCTTTAT
GGTGTGATTGTTTGGTTTTATGCTTGTTATGTAGTAATGCATGATGTTTG
TGCTGTAATTGTTTGATCATGTGATTGTGAGAGTACCCTCTTGAGTCTTT
TCATGGTTTGTTATTTTCTTGATTCTTTTTGCTGTATAAAGTTTGCATCT
TTATGGTGTAACTGTTTGATTTTATGCTTGTTGTGTGGTAATGCATGATG
CTGGTGCTGTAATTGTTTGATCATGTGATTGTGAGAGTACCCTTTTGATA
TTTTGTGCTGGTTTTTTAGATGAAGTGAGAATGTGGGTTTTTGAGGAGGT
CTTGCCTTGTGGGCAGAAACTCTCTGAAGTCATCAACCAAACCAATGTAA
TCTAAGTTCCCTGACTACTTTTTTTGCTACATGTGTGATGTATCCACATA
TTAAATTTATGGAACTTTTTGTTTCATAGGAAAATGTCAAGTATCTTCCT
GGAATTAAGCTTGGTAATAATGTCATTGCAGTCCCAGACCTTGAAAATGC
AGGTACAAAATTAGTTACATGATTGAAATATTTCTTTAGCGTTTAGAGTT
TCTATGTGTTTAAGAAGTATGTGCGATAGCTGTCAGTAAACTAGTTTTGG
GGTAATTCTGCAGTAAGAGATGCAAACATGTTAGTATTTGTGACCCCACA
TCAGTTTATGGAGGGTATATGCAAAAGGCTTGTCGGAAAGATTTGTCAAA
ATGCCCAAGCAATTTCCCTCATCAAAGGGATGGAGGTTAAGAAGGAAGGT
CCATGTATGATCTCTACCCTTATCCAGGAACAGCTCGGGATTAATTGTTG
TGTTCTGATGGGGGCCAACATTGCTAATGAAGTAATCAACACAGTATTTT
CAGTCACGGGTGCACTTTTTGATTATATAGATGCAGCTGTTTAACATGTA
GATTGACTAATCATAAAACCCTTGCTATGCAGATTGCTGTTGAGAAGTTT
AGCGAAGCAACAGTTGGGTACAGAGACAATAAAGAGATTGCGGAGAAATG
GGTTCAACTATTCAACACTAATTACTTCATGGTCTCAGCTGTGAGTACAG
TACACATGCTTTCTTCTGTCAAACACACTCTTTCAAAATTTATTCAATCT
CGATTATAAATTAATTGAATGCCACATATGGAGTTGATGATCTCTCATAG
AACAAAAACATTACTAGCATACTAGAGTAATCAATTTAGCACAATATACA
GACAGTGGCGAACCAGATTTTCAAGTGATCCCTGGACTAGTACTAAAACT
CTAACTGTGGCTAAAAATATGTTTTAGCTAGTTTTTAAAATTCTACCAGT
GATTAAATTTTATATTTTTTATTTGGAGGCCAGTCTGGGTTGGAGCAGGG
ATCAACCCCAGCCTAGTTCTGACACTGTATACAAATAAATAAAGGTTTCA
TGTATTCTAACTAGCGAATGATGAATACAGGTTCAAGATGTGGAAGGAGT
TGAACTATGTGGGACACTGAAAAATGTTGTGGCCATTGCAGCAGGTTCTT
GGTTTACTGCCAATTCTTATTACCTTCTCCATCTATACTTGTCTTTCGCA
ATAGGCAGATGAATTACTTGATTTCTGATGTCAGGTTTTGTGGATGGCCT
TGAGATGGGAAATAATACAAAGGTTCAAAAAATTATATTTCATAATATAT
CGAGCTTTCGAGTCACCTTTTAAACATCATGTTCTAATTATACACTGTTA
ATCTTTAGGCTGCAATAATGAGAATCGGATTAAGAGAAATGAAGGCATTT
TCTAAGCTGCTATTTTCCTCTGTTAAAGATAGCACCTTCTTCGAGAGCTG
TGGTGTAGCTGATCTTATAACAACTTGCCGTAAGGAGGCCATATATGTGT
AGACCTGCATGCATTATTTGAGTTCATTCAAATTTAGCAATACTTGCAAC
ACGATAATCAAAATTTAATTAATTGTTACAGTGGGGGGAAGAAACAGAAA
ATGTGCAGATGCTTTTGCTAGGAATGGTGGCAAAAGGTTTCTCAGATTTC
CATTTGTTAGAAACCTCTGGAAATTTAAGCATTAGCAATCTTTGATCCAG
TCTGCCTCTAAATTATCTGCAGGTCTTTTGATGAGCTTGAAGCTGAGATG
CTGCAAGGCCAGAAGCTCCAGGTAGATACCAAAATTTTAGTTACAAGAAC
AAGAATGGTTCACAATTTCACATGTATCACTTCGAGTATTGTATGCTTTT
GAAATTCAACAAAAGACAGCATTGCTATCTGGATGTCTGATGTTGCTAAT
TATTGTTCCTCTTAACTTTTGAAGGGTGTTTCCACGGCAAAAGAGGTCTA
TGAGGTTTTAAGCCACAGGGGGTGGTTAGAGTTGTTTCCTCTCTTCACGA
CGGTCCATGAGATCTGCAGTGGACGTCTTCCACCATCAGCAATTGTTGAA
TACAGCGAGCATGCACCAAAGTTATCACTACTGGGAGGCTCTGCTCAGAT
ATACTGAGTTCAGCCAAAATATTGAAGTAACAACTATTATATATCTATTT
TTCTGGCTAATTTAAATGTCTTTCCTACCTCTGCATCCCTTTGAGACATT
GTTATATAAGAGGTGTAACAAATAGCATATTCCAAAAAGAGAACATTTTG
AAATAGATCAACAAAGATTGCTAATACAGACCGAGCTTCAGAGCTTGTCA
TATTTGATGCTCATAGAAACTCTTCACAGATTTTTTAAAGTGTGTCCGTT
TTTTTGTTGTCTATTATTTTCGTATCAGCTGAAACGGTGAATGTTTAGAG
AAACCAGATGCCAGAGATGAAGCTAGATTGTATCTTGGCAGCAGCTTGGA
CTTTTGAGCCTAGAATACCTCCTCATACATAATGGTATCTTCTATTTGGT
TGTTTTTGGTTAATAGTTTATCTGTAATACTGGATGTAGACTCGAATCCA
ATACTATGTTCTTGTATAATGTTTGATTATAATTAAAATTTGGTTGATTT
ATGCTTCGGCAAAAGAGCAAATTAATCACCTGAAAGCTAAAGTTCTTTCT
AGTGTATATTTCCAATTAGTTTGCACAGAGAAAACCTAGCTACCATTAGT
GAAGGAAGCATTCGGCAAGCATAGAAAAGAAGGTAAATGTATAAGAATCC
CAATATACAACTACAACTTTCTCATGCAACAGTTATTGAAGAGCATAGAC
AAGCCAAGTGCAAATACACAAACCAATAAATAATAAAATTTATACCCACA
ATACCAGGCCAAAGCATGAATGCTACATTTTTTGTATACAAAAGAAACTA
TCCTGTACGTAATCTCTCCAGTTGGTCGACACTTTTCCGACCTCTATCTA
GTTGATGATCCATGTTTTTACGGGATTTATCAAAGCAATCGACACTTCTC
CGAGACCTCTCCATTTGATCAAAAGACATCCTTATCTTTTCCAGCTTGTC
AACATTATTACCAGATGGGATTTTTAGTTTTTCATGCCTGTCTGTGCTGT
GTCTTGGCTTCTCCCTCCTGTCAGTACTCTTCCTAGAAGTCTCGTAGACA
TCGGTACTTTTTCTGGATTGTTCAAAGTGGTCTGTGCTTCTCCTAGAACT
GTGCCCCTGTGGAGGTGATTTCTCTACAACTGATACAAATTTCTTTAAAT
GCCTGGTATACTCTGGAAACAGCTCTAAATCACAATGGTTTCCTCCCTTA
AGCCATAGAGGTTCGTACTTTTCGTTACACATTTCCCATAGTTGCTTCCC
ATGAGAAAAATCAACGACATCATCGGCAGTTCCCTGCACAAACAATTAAG
ACAACCCAGATGATAAGAAGTTATCTAGTTTAGGGTATCATGTAAAAGAT
GAAAAGAACAAACCTTTCAAGCCTAATCTGATCTAATCATGAACCATTAC
AAAGGGGCCACACAGCAGTGTGGCTAGTGGCTACAATTATGTACAAACAA
ATGTTTTTAATAAGAACATTAACAGCTCCCACACCAGTGACCCACATTCT
AATAAGTTGCCTATTGTAGAGATCATTTTCCATAAAACTTAACAGCAAGT
AGCCCTTGACCTATCTTGATAAATTTAGCAAGAACAGATATGACACCTGG
TTGGTATATGCTGCCAGACAAGACAGCCAGCTAAACAATATATTTATTAA
TTTATTTTTTATGTCTTTTATGAGATGGATACATATTAGTTGCAGGAAGA
CTAAATGACTAATGACTTCAGTACCTTGCAAATATCATTTAAGCTCTAAA
CTGAACAAATTAATGTCTAATGCATACTTACATGAATGACAAGTATTGGA
CAGTGGACCAGAGGGATCTTGTCAATGTTCTGCAGCGAAATAAAGATGAA
AAAAAATTACATTTTTCCTTACAAAAGAATGCAATTGAATAAAACATACA
AGAGGAACTGTGTAGAGAAGGTGTATGTTACCTTGTAAATGTCAAACCAG
TATGTGCGCTTTACAGGATACATAACTCTTAAGCCGGAAAGTATAGGACT
GTGCAAAATAACAGCTCTTAACTTAGGTAGACGAGTTGCAAGATCTAAAG
TCGGTCCGCTGCCAACTGACTGTCCATAAAGGATGATATCTTCCTGCTTA
GTCCCAAAGCTCTCCTCAAGACACTTATATGCCGCTTCAATATCTGCATA
TGTATTCTGCTCACTTGGCTGCACCAGAGGAATTATATGAACACATGTTT
CTAAACAATATTTCTTGTAACGTATCTATATAATTCTAATGCCACACCTT
CCCGGAGGACTGCCCATATCCGGAATAGTCATACCTGCAAAGAAGTACTT
GCATATCAGATAGGTGAGCTATATAAAACCAGCCTATATAAAATTTAATA
ATTAAGCCACCTTTCTATACTGGTGTAAACGTTTAATCTCTATTTACCAC
TAAGAGAATTAAGTAATATATGAATGTACAATGAATTAGTTGGGGAAATG
TATCAAGTATATCAAGGAATTACCCTCCCTACTTCTGCATTAAAAGGATT
TCTTAGTGGTTATTAAAAATTTAACACTTTTAACAATATTCTGACTCCTA
TCTATACCCTGCTGTCAAGTAACTTAACTATCATCTATGCCCGAGGGTTA
TTGTTATAAATAAAAACGTGTTTCTTCGAGCTCATTATAAGCATGTTAAC
ATCTTACTTTAATCTGTACAGGCAAAGGAGGAGGACATATAAGAAAATTT
GAACTGATAGACTCACAGATCCCCAACTTTCCGGTTATCACTTTGCCTAA
GCACATGAGGGTGCTCATTTTTTCACATGCACTTGACAGATAAATTCAAA
GGACAATCACACACTGCAAATATATATGTTTACTGTTCTGATATATTCCA
GTCTCAGCCTTTGAAGTAATGGATTAAGCTAGCCATTTGCAATTAATGCA
AGATTTTGGAATGAAATGAACCCTTTACACTGAGGAATTGAGCAGCTATA
ACAGAAGGTATTGAATGTAGAGTTAAGAAACAATACAGACTTCACAATTA
CATGTAATAACATATCCAAATGACAATCAAAAAGACTAGCAGCAGAGTCA
TACAACAACACACAGGCATCGTTCTCGCCTCAATTCTCATAAGAATTTTG
AAATTCATAACAAAATTAATTAAATCCAAATCTTATGCTTTTTCCATTGT
TAATCCTAAATCTGGTTCCAAGAACGGAGATCAAAATTTGGATGAAGCTA
AAAGATCTTCCCAAACTACTCATCAAACATCAATCAGATCCTCCAAGATG
AAGCTCCTTGTAATCTAACTATCAAGAACCCAGATGCAAAAGGCAAAAAT
TTTGGGCAAAAAAAACCAAAAACTCAAGAAAAAGCCACTTAAAATACTTT
TAATGCACCAAAAAAGTTCAAATTCATCCTTTCTAACTCCGCGCTTAAAA
CTCTTAAAAATACGTGTAAAAAATCAAAACGACATCAGATAAATCAGATA
AGGAAGAACA