| NCBI Gene |  |
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| Relationships |
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| The ncRNA, XR_001806291.1, is a part of gene, LOC108218121. |
| The genetic_marker, MK001256 BSSR-099, is located in gene, LOC108218121. |
| The genetic_marker, MK001178 BSSR-021, is located in gene, LOC108218121. |
| 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. |
CATCCTCGTTATTCCCAAATTCACCACTCAGATCTAGCTTCATTGAAGAG
TTTGCAAGATACATACAACTATATTGAAGAGTTCGCAAGATACATAATAT
TCAGATTTCATCGGATATAACTTGGTAAGTCATTATCTAATTCGATCCGT
AGTCAATTTCCTTTATGTTTATTCCAAATGAAAAAAGTTGAAATCAATAT
GATTTGATATATTGTGTACACGTATACATTTATGTTGTTGTTTGATTTTA
AAAATTTTGATCGATTTAGATTTGATTGAAATTTTGGGTTTCAAATGAAT
CGCCGCTGTATCGAAACCTCGCGATTGAATTTGATTTTAGATATGTGGGT
TAGATTCATATTTATATCTTAATCGGTAACTGTTTTGTCATAAAATCCCC
CTGAGCTTATTTTATAGGCCATTAAGATATATGGGTCTGCTTGGATTGTT
TGGTAAAGGATATTGGGATTCGACCCTCGAGGGTGGAAACCCTAGGCTGT
ATAAAGAGACTTGCAGGCTTGTATTGGAGACCGTGGGAAGGCTTCCACAA
GGTTGGGGCTTCATTTGAGAACGTTCCTAGAGCTATCCTTGTCAGGTTTT
TCCACTGGGTGCATCTCGGGTTGTAGCTGTCACGGCTGCAGTTATGGGGT
TGCAGCTGGCAGCGCTTCGGTTATAGGGTTGCAGCTCTCTGGGCTGGCAG
ACTAGCAAGAATCCTAGCAGGAGTCTTCTTCCTACAATTTAGGAGGACGA
ATTAGAGGAGTATTGGGAGTGTATCTACTAGTACTTAGCTATCTAATGAA
GATAATTATCATAAATATGGAGATTATTACAATACATATACAAATCACAT
GGATATATTCAGATTTTACATGGGATTAGAAGGCTTCAAGTGACATACTT
GCAGTGAGACTCTTTGGAAGGTTGATGTATATCAGATTAAACACCAAATC
AGGTGGGATAAGGGCATATCCGCCCCTGGTTATATGTATCTCAAGAACTA
CATTGGACTTGATCCTTATAAATAGGGTATGTATGCACTTTGCAAAAGGT
TCGGACTCATAATTTCTACACTCTAGAAAGGCACGTATAACTTCTGTGAT
TACTTTTCGGGCACCATCAAGGCGGAGTAACATTATTTCGGCTTCCTTGT
CTGGTGGATTTCCATACTCAGCCCCAAAGCATCACCAAATCTCCATCTTT
TCCGGCAGTTGCAGCCCCTGTGCGCAGCCTATTATTCATACGAAAATCAC
GGATAACCCTATAATTACGACATATAATTCTAGAGGTGTTGTACCAAATG
CTCTCACAACAATATCCATCCTAAATATTTTGTTATTGTGAGAATCAGCC
AAATTACATGTTAATATTTTCAATTGTTGCAAAAAAGTATCAACACAAGT
TGTGATTTTATTGATTTTCTCGAAACTGCACATATCATGTGATGTACAAG
ATTTTGTACTTCATCTTTATGATTTTCTTATTTCAAAGTAACATATTAGA
TTTTTTTTTATTATGATTATTGATATAATAAATTTTTTATGATGCAGGAA
ACAATGAAGAAAGTGCTTCAAATAGTTGTGTTTTGGAGGGACTATGGGCA
GGTTATATTTTCATATTTACTGAAATTAAATAAAAGTTTCATATGTAGGA
CCTTTAACCTTATATATGTATGTAAATATGTTAACATGAAAAATATTTAT
AGGATCTTAAAATCTTCTTCCCAAAATATCATCAGAATACACATAGGTCC
TCAAAATATAAACAAATACACGCGACCTTAAATTTTCACTTTATTCATAT
ATATATACATATATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGT
GTGTGTGTATCTGTATACGTATATGTATATGTATATGTATCTGTATACGT
ATGTGTGTGTGTGTGGATACTATTTCACATTTAAGGTGATTCTATTTCTT
GTGTTATATGTAATATTTGTTATATGGGCTGATTTTGTGTAATATATGTT
TTGTGCTAATTTTATTAGTTTTATGTTCTATTTATTTTCACATTTTGATT
AACGTCTGTTATGTTATATGTTGGTATTGTTTAGTGTAGTATCGTGAGTT
GGGTTTGGGCCTTAGTTTCATTTCTTGCAAGTCTCCTGCTCCATCTCTCT
CATTTATCTCCTCTTGTGTTATTACTTAGTATTATATGTAGTATTTAACT
ATATATTTTTTATATATGGTTTTTAATGTAGTTCACTGTATTTTTTAACA
TAATTCTGAAAACATGGAAGACAAGTAGATATGGCCAATGAGCTTGCTTG
AAATTGATAGGATATTATAAGTAGTCAGTTGTCTTTGCATCACGGAAATA
GCCTTTTACGAAGAATGGATCCATNTTGGCTTGGCATCCATCCCTGGGGT
CCCTACACCAGTTATTAAGCAAGTTATTATACTTGATATGTAATCTGTGT
GAATCCTCAATCTTTATCTATATGGTCAATGAAATCTATCAATCTAAATA
AAAAAAGATTTTAATTATTAGCATGCTCTAAATGCAATGCAGACAGAGAA
ACAACTTTTAGGCATAGATCGAGATTCGGGAAAACAAATGCAAAGTTACA
GGTTTCTCCGATTAATTTATGTTTTTTAAGAACTAATCATTGTTCCAAGT
TATCTTGATCCCACCAGTAGTAAGAAGAAATACTTGCACAAATACAAAAA
ATAGCATATTTAGTAGTACTTTATGAGATGGAGAGTGTTCTGTGTCCGAG
AATTAAACCTAAGTAAATACGGAAAATTAATTTAAATTAGCACTTGGTTG
CTTTTAAAAGCTAAGGTTCTACATTGGTCAAATAACAAAATTGTACATCA
CCAATCAGAACAAAAGAAGAAGAACGTATTCAAGCAAATGTGCAGTTGTG
AGGTCCAAACAGGTTCCTTAGCCTTATTTCCAATATCAATATCAACAAAT
TTGTCATAAGCTTGGTTAATGCTATTACATATGTTAACTGTTAAAAATAG
ATGTTTCTCACCACTTAGCTTAACCTCACTATCTTCTAGTACCACAGGAT
GACGAGCAAATGCTTCTTGGAACACTTGCTTGAGTGAATCTTTTATAGGC
ATCCCTTTCCTTGTTTTTCCATAATTCACTGTACTGCCAGAGGTATCTCA
CGACATCAACCGTTATAGGCTTTAGCAAGTAAGCCGGTGCCCCGTTCATA
ACTCCCTTGCACACCATCTCAGGCTTGTCGTCGGCTGATATCACTGTTTA
TCACAAGTTCAATATTTGTTGATAGACTTCCAAGTTGACAAGGTATGTTT
TAATTATTTTGAGTCTGGTATCATTGAGATTGATGATTTTGTGGACAACA
ATTAATTTTGATTCAGATCTAATTAGAGCGGGCATGTTTTCATCTCTCAA
CCCTAACCTTGTTTTAATTATCTATACGCCTAGTCTCTTCCATATGTATC
TGCCTGCAAATTCATGTATTATACATGTTAACCCTCTTGATTTTGGTTGA
GAGATCCAATTTTGAACTTGAAAAAGATATTTAATATGAAAATTATGTAT
ATGTTTGTGTGATCTATGTGCACAATATCTGTTTGATTGATTAATAAGAT
TGTTGGTTATTGGTTTGAAAGAGTTTCAAAATATGATGAATTGATATAGA
TGTATAGTTTGTTGATTTGTTGAATTTTGTTGAATTTGGAGTGTTGGGAG
TTCCGATATTTTTTGGTTTTAGTTTTAGATTTGTTGGTAAAAAAAGGACT
AAACTAGTGAATTATTCATACCATTATTCTTCATATTCTTGAACCCTCTT
GAATTGAAAATCATATGGATCTTGAAAACCGTAATTAGATTTTAGTAAAC
TGTTTTGGAGATTAAAATTGTTATGTAAAATTTAATAGTATTAATTATTC
AATTTTTAAAATTGTCTACATTTAAATTCATTAATCTGTTTGACTGTAAT
AAATTCAAATTGTATGGTGAGATATAATATTAAGTAGTGATTGACTCCTT
AAATTGTATTGATTGATTGATGTCATAAATGTTTATAACGGTTTAAATAT
AAATTGTGTCTTGATTGAGGCAAACTTGTACCGTTCATGGGTGGCCATAA
GCGATGTCGTATATTTCGGCTTGTAAGAAGCAATTAACTTTGTTTTAATT
ACTTTAGTGTCTAACCAAAAATCCGTCTTTGGTTTAGACTTTATACGCAC
TTTTAAAAATAATTTATATTGGATATGTTATCCTTTATAATTATTATAAT
GTATATAAAATTTTTATATGAACTTTCTTATTTCGTTTGTCTTTGGCGGG
ATCCTTGGGAGAGATTTAAATGGGTCCAGAGATATCTTTACAAGTATTTC
GGTTAGATGGTAATCTTTTTTGAATGAATAAAATCTCTTGTAGAAGCTAT
TGTATATTGAGATACAACTCATCTACGAGTATGTACACCCTGAAAAAAAA
CCAAATTGTACCGATAGTAATGCTGGAGGCGTAGAAAAATAATCCCATAG
TTTTATATATTGATTGTCATAATCATGGATAGACTCTTTTTATGTAGATA
AATCATACTTCGAACTGCTCATATTACTAACAAATTATATTTAAGAACAT
TATTACTTTTTAATGAACATATAAGATGACTAAATAAAATGCGTGGCCTA
TGAAATCTGATCTTAAAATAGAGTATACATGCAATTACTAATTGATAAGG
TTAATCATGCATGGATATATTGGTGTCTTAGCGGTTAATATTTTTTAGTT
TCCCGATATTCATCCTCCTCTGAATCATTATTAATCATATATATTATTGC
TATTCTGATGATAATATACAAATGCACGTAGAATTAATTGTATCTTAGCT
TTAACAGTTGTAGGAAAATCTACTGTTGTTTACAAAGTTGGCGAATGTGT
ACAAGATGTGTTAAAATTATGGAAGGAATTTGTATCCTCTCAAGCTGATA
AATCTTCTGCAAGCTTTCAGAACGGTCCTACTTTAGAAATCCGAATACCA
GTTGAGCATGTCACGGCGACAAATCGCCAAGTAAATTTTTTATATTTTAA
TGAGCATCAGACAATCACTAAACATGTAGCAAAAACTAAAAATAGTGAAG
AAGCATACAATAGTTTTCTTTCTTTTGGTTCATTTATGATTGGCAGTGTA
TCAGAAGTTTTGACTATTTTTTTGCTTCTACAGGTCAAAGATAACAAGCT
ACGGGGACTGACATATATACAGATGATTCTGGTCTCTTTGCTGGTATGTT
GTGTGATCAACAAATCGGGTTTGTGTGGATGTATATGGGAATATATAATT
GTGGCTTACAAGTGTTGTTTTTGTATTCTCAGTCCTTATGCACATAGGCT
ACTGTCGCACAACGACTTCTCCTCCCCCATCTGCTATGCAAGAGTTACGA
GCTGTGATTCGAGTCTTACCTCTACAAAATTGTATGTATATGAGCAATGA
ATTCCTGAAATTGGATGCCATTGTGCCAGTGTTTCATGTCCTAATATAAT
TTCGTCTAGATAATCAATACGGGGAATCTTTTGCATGGGGTACATGGTTA
AATAAAACTATCAGGGTCGCTATAGGTTATATCTATGTTTACATAAACAT
GCTGCAGCTGATGAGTAAAAATTTGATAAATGATGCTTTGATATTAACAC
AAGTAGAGGCAAAAAGCGCATGTTTATAGTCATTCAATCTTAATTTACTA
AAACTAAATTAACTTTTCATCAGGTAACTAATATGGAGTAAAATAAAATA
TTACATATATAAGTAATGTCATAATTATCTCACACATGAAGCCTAATTAT
TATTGTGGAATGTTTATACTCAGTCATGGATAGCCAATAGTATAATGATT
GTTTACCATGCAAAAGCTCATCAGTCTTTTACCAATCAACCTAAAAGTAA
AAATCGATCAAGTATGACATAGGTCTTCATCAAAAAAGTATGACATATGG
TCTGTTAGGAATAACAAAAATTCCTCATGAACTGTATTATGTAGGAAGAT
TCATTAATGCATCAAGAGATCATCACTATGAAGCGACAAGGAACAATGCA
GGCGACAGAAACTGAGATGCGGATCAGGAACTGATACGAGAGGATCACTA
TGCTTATACTTTTTCAATAACGAGAAATATCAGTATCTGGAGATTGAGTT
CATAAGGAAACAAAATAAGATTGATGCTAGATAGCTTGTTTGTAGGGAAA
TATTATATCTTACGTGATATGCGTGGAAACAGATAAATATTGGTAGAGAA
TATCTTGTAGTTGATAGATGTAACTGTGTAGTATATAAACACAGGTATTC
GGTTATACATACATATGTACAACACATGAGATATCGTTGTAATCTAGCAG
CTCTGAAGAACAAAGTTATTGAGAGAGTTTGTAATATTTCTTATAAATCA
ATAAGAGCAGTTGAGTTGATTTAGTTATTGGTTTTTTGTCTTCATCTTCA
TATTCTTTTCAAGCCAGAGATAGGTTATTCAATAATGTAAGAAGTCGATC
GTAGGTACTCGTAAGATTTTCATCAGTATTTGTCCCATACCTTTCATAAT
CGTGAACAAGAAGTGTTCTTCGATTCTTTTTAATTGCTTTAGTCCCTTGA
CATTGGAATTCCAACTCATCCCATATTTCTTTTGAACTTTTGCACGCTAT
TACTCGATTTGACATGATAGCGTCCAGACTGTTATGAAAATTATTTTTGA
CTTTTTCATCTTTGAGGAATTCAAGCTTTTCTTCTTGAGTCATCTCGGCC
TTCAGATTCTCCACATAGTGTTCTAGTGTTATTTAAATAAGTTGAGCTAA
TGACAATAAACAAGCGCTTGTTGGGAGGCAACCCGTGATTTTTATTGTAA
TTTTTGTATTATTTTTAGA