| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017402539.1, is a part of gene, LOC108227414. |
| The genetic_marker, MK009646 6_155594, is located in gene, LOC108227414. |
| The genetic_marker, MK007777 TP82081, is located in gene, LOC108227414. |
| The genetic_marker, MK008324 6_160096, is located in gene, LOC108227414. |
| The mRNA, XM_017402538.1, is a part of gene, LOC108227414. |
| 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_017402538.1 | XM_017402538.1 | mRNA | DCARv2_Chr6:155248..163334 |
| XM_017402539.1 | XM_017402539.1 | mRNA | DCARv2_Chr6:155248..163334 |
TCGTAGACCGCTATTACAGCACGGCGTTTTTGGTCACAGCCTTATACGGA
TCTTTCTCGGGTTTACTCTCTTTCCTTCTGTTTCATCAAAGATTAATTAA
ATCTCGAGCTCTCTCTCTCTCTCTCGATTATACATACAAAATACATACAG
CCGTCTCACTCTTCAGCTCTCCTCCATCCTCAATCTCTCTCCGCCTCAGG
GGTACTCTCTCCCTCCCTCCCTCTCGCTCGCGCTGCTTCTATAATTCATG
TATCTGTATGTTTACTTGTGTATATATGTATCTGTTTGTATGTGTAGCTT
TCGTTGAATTGAATTAGCTGTTTGTATGTGTTCAGCCTAACAAATTAGGT
GAATTCGATGTTTATTTGTTGTTTTTATATGTTTATGTTGATTTTTATTG
AGCTTGTTAGATGTAATTGTCCGTGCTGGGAGCATCTGATCTGCAGATTA
ATTGATCTGTACTCGTTGTGATTTCGATGAATTTCTAGGTCAATTTGAAC
ATACAGGTGTGTGTGTGGATATAGTTTCTGTGTTGTTTGTATTTGGTTGC
TTTAAATTTGATGAATTTATAGGTCAATTCCAACATGTATATGTGTCTGT
GTGTGTGGTGGAAATTTAGTTACTGTTTTGTTTGTATACTGTTTGGAGGA
ATTGAATTGATTTGATGTCTGAGGTGTAATTAGGAGCTTTGTTAGGAGCA
GGTGTCTCTAGGCGAGACGACAAATGAAAATGATAAGCAAAATGTTTGTG
TATATTAATTGTAATAGTAATTAATTTACAAAACTGATAAGGTTATGCGT
GAGTATATTAGTTCTAGGTGTTTAATGACTTTGCTTTGTCGGTGTTTGTG
TGTGGAATTTTGTCCGTGTTATGGTTTGTTTTCTATGTGTGCTAGGAAGC
ACCGACACTCCAGAAAGGCTGCCGAATCCGTGTCCGACACGGCAACTCGG
CACCGACTCATGACTCGCCATGTGGCCTGTCGACACGCGACATGTGGTGG
ACTGTGGACACAGGAGCGACAGGCGACCGACTCGGCCCATCAAAAAAATC
CCAAACCCGTATTATTTTTGTCAGGCCCAAACCCATTTGTTATTTAACCT
AATATCACAGTTGTCATCTCTTTTATAACATCTCTCTCCTCTTTTCATCT
TCATATTCTTCCTACATTGCAATCACTTGCATTGAAGTTACTTGGACAGC
CTTCATCTTCCTCTTGTTGCGAAAGGAATTGGAGCACATATTCGTTTATC
CATTCCGTGATAAGTAATAAAATACCACCAACTGCTGAAGACTTGGTATT
TGTTCACACGAATCTTCGTCTTCGCTCAAGGAAAAGTCGTGCATATATGG
AAGGAGAAAGCATGATGTGGAATGTGGAATGTTAGTGGCGATGCTTTTTC
ACAAGTGGAAGGTGCAGGTGTTTTAGAAATTGTAAATCTCTCCCTTGATG
AACTGGAGATGGAGGCTGTTCTTTTTACACAAGATGATCATTCGAATGAA
AATGCAGAATAGATGTGTCTCATTATGAAAGAAACTCTATTATTATTGTG
AATGAAGTTATTTAATATTTGACATATATAAATATTATATCTTTTTATTA
CTTTTTTTTTTGCCGTGTCCTGTATCCAGGACTCTTTGAGAATTGGCGAA
TCCCCGTGTCCTGTGTCGCCGTATCCGAGTCAGTGCTTCCTAGTATGTGT
GTGTTTGGTTCGTTCGTGTTATTTTTAGCTTTTTAAAGGTGAAATATGAT
AGGGCTAACCTGTTGAACTGAAGCAGCAAGTTCAGTGAGGAGAAATATAG
ATGGAGAATATTCAAGAGGTGTCCAGGCTAGTTTACGTAGGATAATCAAA
AAGGACAAAAGTATATACATATCATATAGTTTGGACCAGTAATGGATTTT
GATAAAGAATACAGTTAAACTTTAAGTTTTGAAGCAAAAATGGACCCATA
CCTGCAAATTATGTATAAGATGGCTGGACGGCTTGTATGTGGATGATCTT
TGTGGAATGTGCTAATAACTTGTATCTCTTGTGTTAGTTCATATTTATGT
TGCACCATGATTGTCTAAATGATATTAACTAGTCTGTTTATATATTTTTT
GACAGGTAAGTGTACGGGACATGTCGACAGTGAATCATTTATTACTTCTA
TGTTAACTGATATTTATTCTTACTTGTCGTCAAGCGTAATTTTGGTAATC
ACTTGTGAAGTGTTGGTGTTTGTCATAATCTGGTCATTTTTTGTATGTAT
CTCTACTGTCATCACACTTTTTATTGACATGATTGTACTGTTCTAATTAC
AGAGTATCTACAACTTGAAGATTGTATATTTTTTGTTTCCAAGGCCATGA
GAAGTTATAGTTATTTCTTGTTGAAATTAGTAATTTAAGAGTTACATGTC
CTTGCATATATGACTTTAAATATGTGATTTTTCCTGATTGCTATCAGGCC
GTTTAGCTGCACCATCCTGCAGTTCATTTGTGCATCTCAACGTGATTTGA
TTTTTTTTTGAACCCTATTAATTTGGTTGCTCTGTCACTTACCAGTAGCA
CTAGTTTGCCTTGCAATTGGGCAGTAGCCTGCTAATTTACTGATCATTTT
TCTGTTGTTTCATGATTGCAGATTGCAGTTTGCAGTGTTCTTACAGTTGT
GTGTCATGTTCCAACAGCTCAGTATGTGAAGTTACTGCACAATGTTGAAT
ATAGCAAGAGAAAGAAACAATTTTATCTTGTAGCTGGAATTAGTACTCTC
ACAGCCTATACATTATAGCAAAAAAAGTAAAAATGTCAAACAATCTTGTT
TCTCAGCAACTTTCTATGTCGAATGCGGACATGAGCCAGATGGAGCCTAC
TTATGTGAAAGTAGATTCTTCAGTGAATATGCAAATGGGTGTGATGGGAT
CTATCCCAGATGTGTATGCATCACATCAGTTTGCGATGTCAGATCAGCAG
ATGCAGTTGGTAGACCCTTTATCCTACATTTCTGGACCACAGAGCTACAC
GATGTCTAATACCCATTTAGGAAACATGGAGTCAATGGTGGACAATGTGG
GTTTGCATAAGTCTAAGCCAGACCAGAAAGATGTACAAATGGATGCCATG
TTTACCAATCCAGGTCCCCAGAAGTTGTTTCAGCCAAACAAGCGAAAGGC
TGCAGTAGAACCGATGTTTAATAGCACTGTCCCAAGACAGTTATCTATGC
CTAACAAGCGTGCAACACATATGGATTCATTATCAACCTCACATGAGCTG
CCTAACCATTCTGGTACAAATAGGAAAGGTGGGACCCTGCAATCTGTTTC
AGCTGTATCTGGGTCTCAAACACCTGCATCAAACAGGAGAACAGTAAAGA
ATGACTTAAACTCGAATAAACCTGCTAGTCAGCGGGTACAGACCCCGAAG
GGTCGTACTGCTCAGATAGGAACACCGCGTCAGACAGAGTCATTTGAAGC
TGTCAGGTCCAAAATGAGGGAATCGTTAGCTTCTGCATTGGCCTTGGTCA
ATCAGAACCAGAGTTCTTCGCCTAAGCAAGAGAAGAGTCCTCTACACAAA
GACGATAACAACCCAGAGGTGATATCGCAGAATGTCAAACTTTCTGAATC
TACTTCGGTCCCTGTTGATGCTGCTGTTGCACATGAAAACATCAAGGATG
ACATACAAACAAAAGATATAAGCTTGGTTAATAATCCCAGTCATCGCCTA
AGCACATTTGCTGAGAACTTGACTCATGAAGGCATTGAAAATCTTCCAGA
CACCTGGAAAAACGACGTATCAGATTCCATGTACAATGCTGTTTTGCCTG
AAGAAGATGTTGCATTTACAGACAGTTTCTTTGCCAAAGATGAGCTTCTT
CAGGGACATGGGCTTTCCTGGGAATGGGAAATCGGTATGGAGGTGGAAGC
AAAGCAGCAATTACAATCTTCCAGACAGGTTAATGTTCCGGGAGATGATG
ATGAGCAAAAGGTCAAGCATTCTGATAATTTGACATTGAAAACTGAAGAA
AAAGTGGCTCAGGCTGCCAATCAAGCGGGTGCTGGAAGGGATGAGAGTTT
TTATACTCTTCGGACTCCTGAAAAATTGGCTTTTGAAATTGAGGCAGAAC
TTTTCAAATTATTTGGGGGTGTGAATAAGAAGTACAAAGAAAAGGGTAGA
TCTCTCATGTTCAATTTGAAAGACAGGAACAATCCAGAACTACGCGAGAA
AGTTATGTCCGGCGACATTACTCCTGAAAAGTTGTGCTCCATGACGGCAG
AGGAACTTGCCTCTAAGGAGCTTTCTGAGTGGCGAACAGCAAAGGCTGAA
GAGCTCGCACAAATGATAGTCTTGCCTGAAGATGGTGATAGAAGACGTTT
GGTTAAAAAAACTCACAAGGGGGAATACCAAGTGGAAGTGGAGCAGGATG
ATGAAATTTCTGTTGAGGTATCTGTCGGGGCAACTACTCTGGGACAGTTC
CAAAGGAATGATAAGGAGAAACTACCTCCCTCCTCATCAGATAAGGATGA
ACTTAAAGATTCAAAAAAAGTCGAAAGTGAGAAGGGTAGTATGGAAACTA
TGGATCCATCATATAGTCTTACTATTCCAGCTGACGGGACTGATTTGATG
CAAGGGTTAATAGAGGACGAATTTAAAGATGCAGAATTTCTTCCTCCAAT
TGTCTCATTGGATGAATTTATGGAATCCCTCAACTCTGAGCCACCGTTTG
ACAATTTGGCAGCAGACACTCAAACAAAAACTCCTTTGGATAAGTTGTCA
GCTGAAACTGGTGAGAATTCGGAGTCTTCGAAATTAGCTTCCAAAGATGT
TGATAACAGGACAGGAAAGGCTACAGATCTTGATTCCAAAATGACAAAGC
AGGATGCAGAAGAGAAGTCTGGCGACTATGCAAAGGAGCAAAAACAATTG
AATCCTGACATGACATCAATGGCTGAACGTGTATGGGAGGGTGCATTACA
GCTACATATTTCTGCCCTTATTACAGTTATTGGCCTGTATAGAAGGTATT
TTCTTATTCACGTTATAGTTATGCAGGTTTTGTTTCTGGAGTTTTCCTTC
CTATTGGATAAAAGTTAATGATAGTTTAATTGTGCTGGATAAATCATCTT
GATCTTGAGGTTGTATAAATTGTTCATTGCCCTTATTTTCTGTTTAACCT
GCATTATTTAAATCGACATTATAATATATGTAATCTGCTGTTGATCCTAA
ATTTTGTATATAGTTACTACACTGACTGCCTTAATGTTGATTGCGGGAAA
ATCGTCACTTCTTGAAATTCTAGACATGCTTATTTTGCAATAAATATTAA
AATAGATGATAAAATGCAAAAGATTTTGTAGCTTCCTTTATTTCCAGCAA
CCTCAAAAAATTTGAATACCTAGTGAAGCAATTTATTTTATTTTGGTTCA
CCTATATTTTTCTCACTAGTTGACAATTTTTTCTGCTTTTGACAAATCTA
GTTACTTCTTGTCTGAGGAATTTTTTGTATTGATTTGTTACTCTTGATAG
TACATTGGTGGTCTGTTATGGTTTAACAGTGGCCAGACACATAAATTGGC
ATATGCCTCTTGCTATTCACATCTCAAAATTTGATAACTATCAGAGCTAC
TGTGTTGTCTTGGTTCATATTTATTCTTTTCACCAGCTTACAGTTTCCAT
TTTTTGAGAAATTTAGTTTTATACTTTTCTGGCATCTATATGTTCTGTAT
TAGTTCATTACTTGATTCACTTTCTTGTTTGTGTTTTAATGATCTGTTAC
TGCTTTACAGTGGTGAAAAAACGTCTACAAAGGAGTGGCCAAGTTCTCTT
GAAATAAAAGGAAGAGTTAGACTTGATGCATTTGAAAAATTTCTCCAAGA
GCTTCCCATGTCTCGAAGTCGTGCAGTCATGGTATATCAAGTTTCCTTAT
ATCTCATTGTATTTCAAAGTTGTGCTTAGGTGTTTTGTTAGTGTGTTGTT
TTGAGAATTACAGGGTGCCATTCTGTCATCGGTGGCAATTTACTTTTGTT
CAAGGTCATTGGTCGGAATTGACTTATTTCCCAGGAGGATTCATCGACTA
AATATTTTGGCGCAACGTATATATGGAGCAGACAGCAGATTTTTAACTAC
TGTCATTAATATCATAATAAGAATACCAAAGTTCACCTTTCTTTCCATTT
TTTACAATCTCCGAAGTGAATATCTGATAGTGTCATTACTTAGATCGGTG
GGCTGTACACCTGTACATCATCCCATTGCAGAGAAGTGTTCTCAGCGAGT
GAATACTTTGATCTCACACCATTGGATGAAAGAAGCACTGCTATATTCCT
CCTTGTAGACATGCCTGATGAGATCTGGAGTCTCCATAGTTATATATGCA
GTTGCTGAGAACCTTGATTTGGATTCTGGAACTTCAGAAATGATCATTTT
GGTTTTGGATGTGAATTGGATAAATGGATAGATTTGTCATCTCATTTGTA
AATGAGTATCAAGTAAAATTGGTTTATAAATTCATTTCACATGATGCTTG
GAAAATCTAATTTAGAAGGGTAAACATATTTAATGATGACTTGAACCATT
TCAAGAAATTTTCAGATATGTGGGAACCACATTGTAAATGAACAGGCTCT
GGCAGAGAAACACAAAAAGCTCATCATCTTAATGAAAGTTCCTGTACAAT
AACTTGTTAAGATTTCTGGTTTTTGACTGGTAAAAGTAAACATTCCTGTA
GGCATTAAGGAGCAAAATGCTAACTGTTATCTATACATCTGCTAATGGTC
TCTACTTGCTACAAATTGATATCTGGAGTTATCATCTTAAGAACTTTCTT
CTTTGCTGCAGGTGATACACTTTGTCTTGAAGGCAGATTCGTCTGCAGAT
GACCGAGCAAGTCTTCGTGAGGTGACCTCTACACTTTTCAATTCTTTTGT
CATACCATACTATTAGAGCCTTTTTGGTCTAAAGTTATACGGCTTGGTTT
GTTTCTTGGGACAGGCTATAGATTCTTATGTTCTGGATGAGAGGCTAGGA
TTTGCAGAACCTGCATCAGGAATGGAGCTTTATCTCTGCCCACCACACCC
AAAGATACTCGAACTGCTTGGCAAACATCTCTCCAAGGACCAGACCGAGC
TAATTAATTCGACAGATAATGGTTTAATTGGTGTAGTTGTATGGCGTAAG
GCTCATTTAAGTTCTACAATCTCACCTAACTCAACCTCACACCATAAACA
TAGCTCAAAAAAGCAACAAAACTTTCGGAGACAGGAAAAGAACAATAATG
TTAATGCTAATATGACCCCAAGAACTCCTGTACCTTCAACTCAAGCTCCC
ATCAGATCTGGAACTTTACCATCCGGTAATGATGATGATGATATTCCACC
TGGGTTTGGTCCGGGAAATGCTCGGGATGACGATGATTTGCCTGAATTCA
GCTTTTCTGGCAGTTCTAACCCAACTCAGTCTTCAAGGCTGTCCTCAAAC
CCATCACGGCCCGTAGACCAAATTAGAGAGCTTATTCAGAAATATGGAAA
ACCTGCAGAAAGTCAGAGCACTAAGAATTGGCAGGGTAAAAGAAGTGCTG
GCCTTGCAGTGCAAGCATGGGATGATGATGATGACGACGACATTCCAGAG
TGGCGCCCTGATGCTCCCCTGACCCATGTACAGACTCGTCCTCCTGCTCG
TGGCTTTCACCAAGCAGTGCAGCCTCCCTTGGTTAATCAAACTGCAACTA
CACAGCATGTTCTGTCACCACAGGTGGCTATGCCTCCGATGACCATGATA
CAAAACAACCCCTCATCTTGGCAGCAAGGTAATGGGAGATGGGTGGCACA
GCCGCCAGGTTTTCAGCAGAGTAGTTTAGCAAGTCAGCCTAACATAGGGC
AGTTCCAAGGTGGGCCCGTGGCTCAGGCTGGGCAGCCACCGCCTGGTAAC
TGGAGGAGAGATGCACCTAGAAGTAGGGGTTTTTGATTAATGTTTCATGT
ATATCCTAGTATAAAATGTGGGTTTAGCAGCAGCAGATTGTACACCTAAA
TGTTTTACACTTTTTTCGTAGGTTTTTTTTATCTTAAACTTAATGGATTC
CCCTGCAACGTTTAATTGAAACTTGAACTTCAGTAA