| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017374716.1, is a part of gene, LOC108204985. |
| The genetic_marker, MK006193 K3637, is located in gene, LOC108204985. |
| The genetic_marker, MK005005 K2449, is located in gene, LOC108204985. |
| The mRNA, XM_017374717.1, is a part of gene, LOC108204985. |
| 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_017374717.1 | XM_017374717.1 | mRNA | DCARv2_Chr1:46506021..46513780 |
| XM_017374716.1 | XM_017374716.1 | mRNA | DCARv2_Chr1:46506021..46513780 |
CCCCTCCAAAATCTCGCGAAACTGAACTCACCAAGAATGCTAGTTTCACA
ATTACACCTCTTGTGATCTCACATGTTTACTCAACCAATTTATATAACCT
TTTCCCTAATAATTAAATGTCTACTAGTTTTCTCCCTTCCATTCACTTCC
CAAACCTCTTTCAATAAATCCCCACCGTTCTCCCCTCCTCTAAATTTCTT
CACATTCATTATATACCCACATTTTCATCTCACACACAAACACACACACC
GGAGCTCACAATGAGCTTCCAAGTTGCATCAAGTTCCGGCGTCCATGATG
CCGGAAAAAATAATAATCTGAAGGAGGAGGAAGAAAAAACCAAGAAACCG
CCAACTCCAAGCGTCTCGTTATTTAAATTATTCGCGTTTGCGGATTCTTT
TGATTATTTTCTAATGTTTTTTGGATCGGTGGGAGCTTGTATTCATGGTG
CTTCTGTTCCTGTTTTCTTTATTTTCTTTGGAAAGTTGATTGATGTTATA
GGACTTGCTGCTTTGTTTCCTGCTGCAGCTTCTCACAAAGTTGCCAAGGT
AATTTTATTTTTATAATTTAATTTAACTTAATTTAATTTAATTTACTTTT
CTTCTTATTAATGATTTATGTTATTGTTTTTTGCAGTATTCGTTGGATTT
TGTATATCTAAGTGCAGTTATATTGTTTTCATCATGGATGGGTACGAGTC
TGATTTCTAAACTAAATTGTGTTAATGTAATTAATATTGAATAGTGTTAA
TTAATATTGCATATTTGCATGTATATTGAATCGATAAAATAAAGAGGTGG
CGTTCTGGATGTATACTGGAGAAAGACAAGCAGCAAAGATGAGGATGGCC
TATCTGAGGTCTATGTTGAATCAAGACATCAGTCTTTTTGATACTGAAGC
TTCCACCGGAGAAGTCATTTCTGCGATCACCAGCGATATTATCGTAGTCC
AGGATGCCATTTCTGAGAAGGTAATTTCAGTATAAAAAAAATTACGATTT
TTTTGAGTTACATTTTCTGTGAACAGATAAATATCGTAGCAAATGTTTTT
TTGACGGGACTTGAACTCTCGACATTTTATTAGCGATGGATGATAAGATG
CGGGTATTTGTCAGCCTGTCGGGTTAACATCACTAAATTTTAGGAAAAAT
TAATTAGACACTAGTAGAGATTATAGTGCCGGTAAGTTTCAAATTTAGGA
CCTTGATTTTGATATCTGTAAACTAGACACGGTAACAAAATTCAACATCA
TTGATGGCTTTACCACCAACTTTATTAATAACACCTCCAACTGTCCGTCC
CATTTGACAGCCTTACACTACAAACTTGCAATATGATTTTTTTTTTTACT
TTTTTTCCATGATATATTTGAGATCTCGAATTTAATCATCAAATTCGCGT
GTTGGGCATTTGTGTAAGGGAGTATAATTTTGGTCGATTCATCGGACTTG
GTATAATTTCTCAGAATTTTAGTATGAAGCGGGGATAGTAGTGTAAAGAA
ATGGAAGAAACGGATATTCCTGTTGAGAGGCTGTTGTTATCATCCCTGTA
ACGAACAGGAGTGAGAAGTGGGGCGAAGAGAGAGTTCAACTTGTCTTACG
AGAGCAGTATTAATGGGTGGGTTCGGAGTTGAGTGAAAGTTGTGTTTGGT
TTGGTGGTTGTGAGTTTCATTCTTTGGCTAATATGCTTCTCACATCTGCA
TGAATTGACACCCCTATTAATGTCTCTTGTATTTTATGCACTCTATTATT
GATCGAAAGTGATTCTTATTTTTCATAATTTTTTCATTGTTTTTAAAATG
ATTAATATCCAAATAACAAATTAAAATCATTGTAATGCACATTGCACAAT
AACAAGCCTGCAGACTCTGAATCATATGACCCTACCTAGTATGATCCTGC
ATCAGTTGAATGAACTTTGGTATTCATCATTTTTGGTTCATTGTTTGGTA
ATGATCTCTTGATTTTATTGGTTTGATCTTGGTGAAATTTGAATGGCAGG
TGGGAAACTTTATGCACTACATAAGCAGGTTCATAACAGGGTTTATAATA
GGGTTTATAAGGGTATGGCAGATAAGTCTTGTCACACTCTCCATCGTTCC
CCTCATAGCTATTGCTGGTGGTGTTTACGCTTTCGTTGCTTTTGGTCTCA
TTGCCCGTGTCCGCAAATCCTATGTCAAAGCTGGGGAAATTGCTCAAGAG
GTCTCTCCTCTGACCTCTCTATCTTCACACGCATTCTTATGATCACTTAA
ACAGACGGATATATTTCTATTATCACTGCCACACGCACGCACACATTTTT
ATGATCACTGCCATAAACGCAAAGATAACAATTTGCCTGGTAATGATGTA
AGTTCTGTCGAGGATGTGATTGTCAATTTCAAAAAGTAGATCCTGCTTCT
TTTTTTAGTTGCCTCATTAATAGTACTGGGATGAAATAGTATCTTGTTCT
GCTTTTTGCTCACATATTAAAAGCTAATTATTATAATAGATTCTATTATA
AAGCAATTCATTTACTACCATTTACTGCATATATCATGTGGAATGTCATG
CATTGTCTTCTGCAGGTAAATATCCAATGTAATTGATTCAGATAAAATTT
AACAGTGTTCTAGAAGTATCAGTATGGATTTTTCGATTGTGATGTATGGA
TGCATTATATTCAAATCGGAAATGTTATGTTTCTGTTTCAGGTGATCGGA
AATGTGAGAACAGTACAAGCATTTGCAGGGGAGGACAAGGCAGTGAAATC
ATATACATCAGCATTACAGGACACCTACAAGTATGGGAGGAGAGCAGGTC
TAGCCAAGGGTCTAGGACTTGGCACCTTGCACTGTGTACTTTTCCTTTCG
TGGTCGATGCTGGTTTGGTTTACAAGCATAATTGTTCACAAGCATATTGC
TAATGGTGGAGATTCCTTCACAACCATGTGCAATGTTGTTATTGCAAGCT
TGTAAGTCTCTCTGGTAGTGTGATTTATTATGTGTTGCCATTATATTGAA
CATGCTGTTCTTACTAATTCTCCTTTAATCCAATTATTGTCTGCCTTCGT
ATTAGAAGAAACTTTCTTTACCTTGGTCCCTTGACTTTGGGTTGCTGTAA
TAACATTCTGCATTGTCAAAACATTTAATTACATGATATACATGATATAA
TTACATGAAAAATAAAAAGTGGAACATTCCCAATAGCACAAATTTTTGAC
ATATGTATGTATGACGGCACTTTTCTGATGCCCTCTTTGTTAGAGCTTCA
TATATCATTATTTGCACCGGTCCTTTTTCATATAATTGCAACATGCTGAT
GACGACATCTCAGATAGTAGCCATAAGCTGTTGGCAAAAATGAATATTTT
CAGTGTGCAGTAGTGTGATTATCTGTTTTGCACAACTGTTGTGTAAGCAG
ATTCATGACTTATCATATTCAAGGTCTGAGATTATGGAAAATAATATGCC
TAGACCATTTCAGGTCACTTGGACAGTCAGCCCCTGATATTACTGCATTT
CTCCGAGCAAAGAGTGCTGCCTATCCTATCTTTAAAATGATAGAGAGAAA
TACTGTAAACAAAAACAGCGGAAAAAAGGGTGGAAAGTTGCAGAAAGTTG
AGGGGCACATCCAATTCAAGGACGTGTACTTTAGTTACCCATCCCGCCCT
GATGTGGTAATCACCAATAAGCTCTGCCTTGATATTTCTCCTGGAAAAGT
GATAGCACTTGTGGGAGGAAGTGGATCTGGAAAAAGCACAGTTATATCGT
TAATTGAACGCTTCTACGAGCCCCTCTCTGGACAGATTTTACTAGATGGA
ATTGATATCAGAGAACTTGACATAAAGTGGCTTAGGCATCAAATTGGATT
AGTTAATCAAGAGCCTGCCCTTTTTGCTACAACCATCAGAGAGAACATTC
TCTATGGGAAAGATGATGCGACCATTGAAGAGATCACACGTGCTGCAAAA
CTTTCAGAGGCACTGGCTTTTATCAACAATCTTCCTGAAAGATTTGACAC
TCAGGTACAGATCCAAATTTACAGCTACTATAGTTCACTTGTTGGTTCAA
CACGAATGTTGATCCCTGTAACACACACAAGGAGGGATATTGTATGGTCT
ACCTAAAACGTACGGCATACTATATCTTCTGCTTTATACAGTACAACTGT
GTTTTCAAAACATCTAATTAGCATTATAATAAAAGCGCAACATGGATGAC
CTTGTAATGATATTATACAATTTTATAGGTGGGGGAAAGAGGGGTGCAAC
TATCAGGTGGGCAGAAGCAGAGAATTGCAATATCTCGTGCCATAGTTAAA
AACCCTGCTATACTTCTTTTGGATGAGGCTACAAGTGCACTCGATGCAGA
GTCTGAAAAGAGTGTGCAAGAGGCCCTTGACCGTGTGATGGTTGGACGCA
CAACTATCGTTGTGGCTCATCGGCTTTCTACCATAAGAAACGCAGATGTA
ATAGCTGTTGTTCAAAATGGAAAGATAGTGGAAACCGGAAGCCATGAAGA
ACTTATTTTAAAACAAGATGGTGCTTATTCATCGCTTGTTGAACTCCAGG
AAGCAGCTTCCAAGCAACAACTCCCCTCAAACGGTCCATTGGGACAACCA
CTCAGGTTCTGCAAAAGCATACCGGCTCTTTTGTTTAATCAACTAATGGC
CTCTATTACATGCTTTTCTTTATAAGAGATCATTATTATATTCTCCTTCC
AAACTATTGAACAAACTCTTCTACTCTCTAATGACAATCTCCTATGTACA
AACACTTATTATATTTTCTAATTCGTTTATGTACATATGCTAACATTTTG
TTACCTCTGCAAATAAAATTTCAGCAGTAAATTTTCACGTGAATTATCTG
GAAGAACAAGAAGTTTTGGCGGAAGTTTTCGTTCAGATAAAGAGTCTGTT
GGCAAAGTTGGTTTTGAAGTAGAAACTGTCAAGTCGTCTCCAGTTTCCTC
TGGAAGATTGTACTCCATGGTTACTCCAGATTGGATGTATGGGGTTTCCG
GAACCATATGTGCACTTTGTGCTGGAGCTTTGATGCCTCTCTTTGCCCTT
GGTATCACTCAAGCTCTTGTATCTTATTATATGGACTGGGACACAACACG
CCATGAAGTTAAAAAGATCTCCCTGCTCTTCTGTGTGGGCGCTGTTGTTA
CTGTCATCATTCATGCTATTGCTCACCTGAGTTTTGGGATAATGGGAGAG
CGCCTTACTCTTCGTGTTCGTGAGGGAATGTTTTCTGGTAAAAATTTGCG
ACAATACCTTCTTATTCTCCTTCGTTTATCAACTTTAATGCTGACTGGAT
CACGCAAATGAAACAATATATTTCTTTGTCGTACATCAATCTAAAAGTTG
GCAATACAATAGTAGACAAATTAGAAGTTTGTATATTTATTTCTTAGCAT
ATGCTATACATGCTTTTATTATAAAAAAAATAAGAAAACACAACAACCTT
GTGGTAAGATGGTATTTCCCTTGCTCTTTTTACCCGAGGTCGAGAGTTTG
AACAAGATTGAGTGTGTGAGTATGTTTAATTATCAAAAAGAAAAAAGGAA
AGATTTATTTGTATATCTCTTCCCTTTGATAAACTATGACCTTGAATTTT
CATCCTTATCTAAATAATCTCCTACATCTTCTTGCAGCTATTTTAAGGAA
TGAGATCGGATGGTTTGATAATACAGAAAACACAAGTTCTATGCTCGCAT
CTAGATTAGAGAGTGATGCAACTTTACTGCGAACTGTTGTTGTTGACCGC
GCTACCATTTTAATACAGAATGTAGGTCTGATCATCACTTCATTCATCAT
CGCTTTTATTTTGAATTGGAGGCTCACACTTGTTGTCATTGCCACATATC
CGTTGATCATAAGTGGCCACATTAGTGAGGTTTGTCTCACTTGCCGCCTT
ACAGTTACAGTTGTTTTAGTTTATGACCTCTTATCTTATCTGTAGTTCCA
TATTGGATTGACCTCCGTACATTTGATCTCTTTCTTTTTGTTCCTTTTAC
TCATACTGACTCTGAATTCCTTTCTAGAAACTCTTCATGAAAGGGTATGG
TGGGAACTTGAGCAAAGCTTATCTTAAAGCCAACATGCTTGCTGGTGAGG
CAGTGAGTAACATTCGCACTGTTGCTGCATTTTGTTCAGAGGAAAAGGTA
CTCGATCTTTATGGGCGTGAGCTTGTGGAGCCTTCCAAGCGTTCGTTTAC
TCGTGGTCAAATTGCTGGTATATTTTATGGAGTCTCGCAATTCTTCATAT
TTTCAGCTTATGGCCTAGCCCTGTGGTAAGTACCCCAAGTCCTGTAGCCT
TTTGTGCCATATATTATATTATCCATATTTTTATAAGAAGCTTATATAGA
TGCTATAAGGTGGAGCTTTGATACAAATATATATTATGCATAGGTATGGT
TCTGTTTTGATGGGAAAAGGACTAGCTAGCTTTAAGTCTGTTATGAAGGC
ATTTATGGTTTTGATAGTTACTGCATTAGCCATGGGTGAAACATTGGCAA
TGGCACCGGACCTTCTAAAAGGTAATCAAATGGTAGCATCAGTTTTTGAG
TTGCTGGACCGTAAGACAGAGGTGGTGAGTGATGTCGGAGAAGATGTCAC
TAAAATGGATGGTACAGTTGAGCTCAGGGGTATTCAGTTCAGCTATCCCT
CAAGGCCAGACGTTCTAATTTTCAAAGACTTTAACCTAAGAGTTCATGCA
GGCAAGACAATGGCTCTAGTAGGGCAAAGTGGATCAGGAAAAAGCTCTGT
ACTTGCTTTAATACTTCGATTTTATGACCCGTTGGCTGGGAAGATTATGA
TTGATAGTAAGTTTTTCAAGAGTATCTATTAACTTGAGACACTGAACTAG
GAATAACTTAATACTGTAATGTTCTTTTTGGTTTACAATTTTATATAAGC
AAGCAGTCTGATTTAACAAGCACGTGATCAACTCCCACAGGCAAAGATAT
CAGGAAACTAAAGCTCAAGTCTCTCCGGAAGCACATTGGTCTTGTCCAAC
AAGAACCAGCTCTGTTTGCAACATCAATCTACGAAAATATACTTTATGGT
AAAGAGGGAGCCTCTGAGGCTGAAGTAATAGAAGCTTCAAAACTTGCTAA
CGCGCATAGTTTCATCAGTGCTCTTCCTGAAGGCTACTCAACTAAAGTTG
GAGAACGCGGTGTGCAATTGTCTGGTGGTCAGAAACAAAGAGTGGCTATT
GCTCGTGCTGTTCTAAAAAACCCTGCAATTTTGTTACTAGATGAGGCCAC
AAGTGCTCTTGACGTGGAGTCTGAGCGTATAGTACAATCCGCTTTAGACA
GACTTATGCAGAACCGAACAACAATTGTGGTGGCACATCGACTATCCACC
ATAAAAAATGCAGACCAAATATCAGTTTTGCAGGATGGGAAGATGGTAGA
GCAAGGAACTCACGCCACTCTTGTCGAAAACAGAGATGGTCCATACTACA
GATTAATCAGCCTACAGCAGCAGCAACAAATGTAACCACACAAACAAAGC
AAACATCAGGTTGAGGGCTTAATCTCAAGTACATCTCTTTTCTCCTAGTA
CCCCCATTTTTTTCCCTCAACCAACCCATAAAGTGTTACCAGTGCAAAAA
TGATTATCTAAAATATTCAAATAATTGAAAATATGAAGTAAATCCATACA
TATTGAATTTCCTGTTCATTTTACTGTACTAATAAACTCAGGTATAGGAA
AACTCATGATTTTTACTTTGTCTTGGTTTCTTTTGTGTGGTATATTTTCC
TTGCATGCA