| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017398242.1, is a part of gene, LOC108223816. |
| The genetic_marker, MK011216 5_15490812, is located in gene, LOC108223816. |
| The genetic_marker, MK004150 K1594, is located in gene, LOC108223816. |
| The genetic_marker, MK005184 K2628, is located in gene, LOC108223816. |
| 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_017398242.1 | XM_017398242.1 | mRNA | DCARv2_Chr5:15487776..15495588 |
CCAAAGGTGCACCAAAAGCAACTACACCGTCTATCTAAAACATACAGCTT
CAGCTTCGTCTCCTTTCACCCCGTCCCCATCTGTCATCACTAATCTCTCT
CTCTCTCTCTCTCTGAATCTCTCTCTCTCTCTCAGAAGACAACAAAATCT
CTGCGAGAATTTCACAAGACAGTATGAGATTAAGTGCATTGCAGTGACAA
CGACTTCAACTTCCGAAAACCTCAGGTATTTTTCACTGCTTTCACTTCCT
CAGCGCTTAACATTTATCACTTGGCATACAGTGCATCTAAGTTTTCACTA
TCATCTAGTGATTAATTAAGTAGCAAATCAGTCAGCGAATGCAGACAGAG
ACTGACAGTCTGTATTATAGGGGACCATTCCGCTATAATATTCAACTACT
TATTATATGGTTACAAAGCACTCAATTAAATAATGCGATGAAATTAGCAA
TTAATCCATGATTAGATTTGTTTGTTTCGTAGATAATGATTGTCCAATTT
GCTGGTCCCTATTGTCTCTACAAACTAAGCCAAGCATTACAATGTGAAGC
ATATGACTCTGATTAGTGTGTGCGTGTTTCTATATATTATATGTGTGTGT
GTTATTATTGAGGCGTATGTGTTGACGGTGGCATTGTAATTATTGTTAGT
TGAGAATGGGAGCGAGTGATGTTGGAGAGGAGGTAGGGATGGCAGGGGGA
CATGATGAGAAGATTTTCGTGACCGTCCGGTTGAGGCCTTTGAACCGGAA
GGAGATTGCGAGGAATGATGTGGCGGATTGGGATTGTATTAACGGCGACA
CTGTCATTTACAAGAATGCTAATCTTTCTATGCCCGATCGGTCTATGTAT
CCGTCTGCTTATACATTTGGTAAGCTTATATTTACTATTAGTTTTTCTTG
ATTTGTGTGTGATGTATGGTGTATGTTTCGGTTTGTTATGTACAATGGTA
CTTAATTGTCTTGTATGGACACGTTTTTAATGTTAAGCGCTGTTTTGTTT
CCTAGAGGTTTAATTTAAAGTGGAAATGAATCATTTTCGGGGAATGGGGA
TTATCTGATGCATTTTCCATTTGTGCTCGGCCGGTGGAGTACGAACGGGT
TTTAGATTTGGTTTATAGTCGGATATAGTTTTGTTTATGGTAATTCTTTT
CAATTGATGGTTCAAGTGTATATGTGTTGAAATGAGATGGAATGGAGTGC
ATGAGCATGACTATGTTTTTTCCATTAGACGTTTGTGGTTAAGCTTCAAT
GATTTTGATGTATACTAGTTATCATAAGAATAAGAAACTAACAACAATCA
CTGCAGTTGTGAATTGTCGAGTTTAACAGTATTTTTCTAAGATTGTTCTT
ATAATTTTGTTCATTCGTGGTGGGATTTTGGGGATCCAGATAAGGTATTT
GGTTGTGATTGCTCTACGAGGCAGGTGTATATGGAAGGAGCCAAGGAAGT
TGCTCTATCAGTTCTAACTGGTATCAATTGTGAGTATACGTCTCTATTCT
ATTTTATTCCCTTCTTTTTGTCATGAATTTTCTCTTGACTTTGTCGCAAA
TGTATACGACTCCAGCTAGTGTTTTTGCATATGGACAAACAAGTAGCGGA
AAAACGTTTACCATGACCGGCATTACTGAGTATACTATATCTGATATATA
TGACTATATACAGAAGGTAATTAAAGTCAAGTGCATCATTTTAATGATAC
AGTTTTAGTTCTGCATGTTGCATTCAGTGCCTTGGTTGATTTGCTAGACA
TATATGGTTGTGTTTTTTGTAGCACACAGAAAGAGAATTTCATTTGAAGT
TTTCTGCAATGGAGATCTATAATGAATCAGTTAGAGACCTCCTCAGCACT
GATAACACTCCCCTCAGGCTCTTAGATGATCCAGAGGTGTGAACTTTTTC
CTTACACAATACACCTATCAATGTGTTGTTGTAGCATGACAGTTGTTTGT
TTTGATAGAGAGGTACCATTGTTGAGAAACTCACGGAGGAAATATTGAGA
GACTGGGATCACGTAATGGAGCTTCTTTCTCTATGTGAAGGTAAGTTTCA
TCGAACCATTCTTCTGATAGAGGACTACTGAATAAGGTCTAATATTTTGT
GCTGCACTTTTGCAGCTCAGAGACAGATTGGGGAGACCTCTCTGAATGAA
ACAAGCTCCAGATCACATCAAATCATAAGAATGGTACAACTGCCGAGCCT
AGTATATTATTTTATGATTTGTTTTGGGTGTAGAACCAGATGGGATTGTT
ATGTCAATTATATTATTTCATTTGTTAATATTACAGACTGTGGAAAGTTC
TACCCGTGAGCTTTTAAGCAAGGATAACTCGAGCACCCTCGTGGCATCTG
TGGTATGCTTTCGTTCAAGTTTCCATTAATTTTGTTCAAAATTGGTAAAT
GATATGTTTGAGAATATTGGACTAAATATTGTGTTTGTTTAGTGATATTG
ATGAAAATTAGTGTTCTTTGAATTTAGAATTTTGTCGATCTTGCTGGAAG
TGAGCGTGCATCCCAGTCATTATCAGCTGGTACAAGGTTAAAGGAAGGCT
GCCATATCAACCGCAGTTTGCTTACCCTTGGGACTGTAATCCGCAAACTA
AGGTCAGTCTCTCTATCCTTTTTCCCCCATCCAATTACTTATAAAATTTT
AGTCATTATTTCACTAATTGATAGATCTTTTGATGTTTGAGAATAATGTA
TATTCTGCTATTCTTTATTTGTGATAGAAACTTTAGTCACAAATCATCTT
CAAGGACTTGCAACTGTTTCCATTTGAGGCATGGTTCTTGTGGGTACATA
AGTACATAACTAAGTTTGCTTAATTATTTTTACGAGATATATAAAAGGCT
TTTGATATTATGACAATATGACATGACAGGCTGGCAAATTATCTGCTGCT
CTCCTATCACACTCACCCACCCCCCACCCACACACACATCTCCCCTAAAC
TACCCTTCCCATGTTTGAACTTTACCTTGCCCAGCTGCCCTCTGTTGGTT
ATGATAAACTAAAGAAGGCTTATACAGTGCAACGTGCGAAAATTTTATTT
GTGGTAGTTGTCAAAATATTAACCCACTTTTGTAAATGGTTGCAGCAAGG
GAAGAAATGGTCATATTCCTTTCAGAGATTCAAAGCTAACCCGTATACTG
CAATCCTCATTGGGAGGCAATGCTAGAACTGCCATAATATGTACAATGAG
CCCTGCACGAGTTCATGTTGAGCAATCAAGAAATACACTGTTGTTCGCAA
GTTGTGCCAAAGAAGTATCAACTAATGCGCAAGTTAACGTGATAATATCA
GATAAGGCTTTGGTAAAACATTTGCAGAGAGAGTTAACTAGATTGGAGAG
TGAGTTAAGTACAGGATCTACTTATGTTGCATCGAAGTATTCTGCACTTC
TTCGCGAGAAAGAACTGCAAATTGAAAAGGTACGACTCAAGTTCCAAAAT
TAAATTTGTTAGTCTTGATATATTCTTTTAGAGACTATTCAATGCTCAGT
GTCAGTAACTAGTTCTGCTGTTAAAATTACTCATTATGTATTATATCTGA
AGTGCTTAATTACGGATTCAACAATATTAATGCAACTGAGGTAGTATCCC
TTAAGTAATACATTGTTGCTGAAATATTTATAGTCCTTCTATATCCACAG
GATTCTTTCCTTGATAGCACAATAGGGTTTAGCAAACTTTTCACCTGTTT
CCTATAAGTTCTCTTCCCTTTAGCATTAAGAATTTACTGTCTTGCAAATG
ATTGACCCCCACGAAATAGGTAATTTATGGTCTTGATCAATTTAAAATCT
AACCTCTTCTTAACCAGCCCTCTATCTTTCAAGAAAAACTCAGAATGCTT
CAATATCTTTGTGGAGGTTTATGCTAAATCTATTAATTGCGTAAGGTCAC
CTTTTTTCCCCTTCTGCATAAATATTAGGTAATTTTTTTTAAAGGATTAA
GAGGTTATTTGCTTCACTTTTAGAAATCAATGTTTGTACTTCAGTGTATC
AGAGGAGATTTAAGTCGATTTCAGATTGGACATAAATTTAAGCCCTTTAA
TTATAAAAGTTGGTGTCAGTATCACAGCCAATGTCTTTGCAGCAGTTAAT
CAATGAACCAACCCTATGTATCTTCCTTAAAGCCTCCCTCTCTTAAACAA
CCACATATAATAATTACAGAAAAATTAGCAATATTGTTACTGATATAAAT
GAGGTAGAGATGCTGCAATTTTCCCTCAAAAGGGTTTATTTTCTGAACCC
AGATTACTACCATTGCATTTAATCGAAAATATAAGGTTCTACTTGTGTGC
ACCCTTCTATTTGTATTCATGTCTTCAAAGATCGTTCTCTTTGTGCAATT
TTTGAGCTTGTTTTAATTGGTTAAATTTTAGATGTATTCTTTACTCAAAT
ATCTTACATGCTCTGTATATGAACCTTACATATAGCTGCTATATCAGATA
TTGCTGTCATCTTGAATGTGCTTAATAAAACTGTGGTTAACCTATATTCT
CTATGGTGTAGCTGGAAAGAGAGGTAAAGGACCTGACTCTGCAACGAGAT
TCTGCTAAATCTCAAATTCAGGAAATGCTAAGATGTATTGGAAATGATGG
GCATCCATTGACAAGGGTAAACATTGTTTTCATTCATATGGGACTCACTG
AAGTTTCTCTTCTATCTTGACCCGTATCCATTGTTAAGTTCTAATTCTAT
GTTCCAACCTTCCAGGTAGTTCATAATCACTACCCCCACTTGCGAGTTCA
GGATTCACCAGATGCCGGATACCGAGTAGAGAATAATTACTTAACAGCAG
TTCCTCACTCTATGGACGTTGCTTCCAAAACATTATGCACATCTCCCTTT
TCTGATAGACAGGATGTTAATGCACTAAATTATAACCACAGTTTTTTCCC
TGGTTCTTCTGAAGATTTGCACCCAGACCCATGCCGAAGACCGCTGACCA
GTACTTCACAGATCAGTGAAAGTGATTTAAGCCAGGATCTGGATGATTAT
GATGGTAAGAGTAATTGTACATCTGAAGATATATGCAAGGAAGTTCGGTG
CATCGAAACAGAAGATTTCAGTAAGAATAATCATCCGGAATCCAGTCAAT
TATCTAATGCCCATGACATTGGAATATCCGCTACTATTGTTTTGAAAAAT
GGAGAGACTGCAAATGAGGAATGGGTATCACCTATGTCAAAGTCAGATGA
GGTATTAGTCTCTTTGCTTTCGAAAGAAGAAACAGAATCTATTGCACCCT
CTTTAAAGACGAATAGAGAAGCTCTAACATTTCCATGTAGTGAAGATAGA
CAAGTGGCATTACCATATATAGAGGATAGTAAAATAAATTGCATTTATGA
TACTCCTTCACCTGAAAAACGATCTCCATCTTATGACCTGGTCAAGGAGT
TTTCCAGGTCCAGGAGCCCGAGTTCAACAACAAGCAGGAGCTATGAATCT
GGTATTTCGGCAACCTTATCTTCCCCGAGGCTGCAGGAGGCAGTACACCT
TGATGACACTCCACCAAATGGCTGTGAGGAATACCACACTCAAAAACCTC
ATGCTTCTCAGAGTGAAAATTCTAGACTAAACTATGGTTCTGATGTTGTG
ATCTCATCTAGCAATGGCTCGCAGTCGCCTAACAAGAATGGTGTTGACAT
TGAGCTTGACACACAAGAGCAGGGAAAATTATCTGCTGAAATTATTAGCG
ATGGCAATACATGCATTGCAAAACTGGAAACTATGTCTGAACCTCATGAT
GAGCACCAAGGTTTTGACACTCTTGTAAGTCTTATCTTAGCCTCAGTTTT
CAAATAGATTCCTAAGATCTTCTAAGGGCCAGTGCATTTTATCTGTTTAT
ACAAGTGAAGTGCAGAGTCATTGTTATTAGTATATATCCTACCATCTAAT
TTTGTCATCGTTACTGCATACTAAAAGAAAATTTGAGTGTGCTGAAGGCT
TTAATGGGTTCTCCTCAATCGCTAGATAAGTAGAAAGAACTTTTGCTGCA
TCGACAACTTTCTTTTAGGGGAATTGCATAAGATTATTTCCTGCATCATG
CACTTGTATAATGATAGTGGGAACTGCATATATCACATGAATTCATTGCA
AGACCTCAACATGCATGCATGTTATCTAATATATTGTGTGTTTATGTAGA
CATTTGTGCAGATATGTATGTTTGTGAGTGTGATGTGTGTACATGGATGG
ACAAACATATATCCTGGCCGGACGTAGTGCAATATTTGTTACCTATTTCA
ATAATTTTTTTTTGGGATAAATGTTTGAGAAACAGTAGGTGCTCTTGTTT
CGTAAGTGCACAAGAAACATGTTGGCAGCAACTACCCATCCTTATATAAC
TCTGCAATGTTATCCTTTTGAGGTCATTAAGCAAGATAACAAATGTTTTT
CTATCCTTATTTTTATATATGTAAACTAGCTGTTTTTCTAATCAATTTTG
TTGTAAATTCTTTTAGGCAAATGAGACAAAAACGATGTCCAATATGTGTT
TGAAGAGTGTAAAAGATGTCGGCTTAGATCCAATGGAATATGATCTCAGT
AGTCCTTCAAATTGGCCATCAGAATTTAAAAGACTCCAGAAAGATATAAT
AGAATTATGGCATACTTGCAATGTATCTTTAGTGCACAGAACACATTTCT
TCTTGCTATTCAATGGTGACCCAACTGACTCCATATACATGGAGGTTGAA
CTTCGGAGGTTGTTTTTTCTGAAGGAGACATTTTCTCAGGGTAATCAGAC
TGTGGAAGACGGAAGGACTCTTACAATTGCTTCCAGGTGAGAGATGTTTT
TTCTTTTATTTGTTTTATTAAGGAAGATATTTTTACTTCAAGTTATTATA
GTGCAGATTATCGCAGTCAACTCACTTTATTGCTTTGTTCTTTCGGTAAA
ATCATGGTAGATAAGTTCTGTAGGCATGCATGTACTTCGGAAATAATGGC
ACTGTTCTGGTTGTAAGTTGCAAAAATTTGACGTTTAATTACAAAGGTTA
TAATTAGAAATAGCAGCTGATACTTTTGTACTCTGATTAATGAAGAGATC
TCCAATACACCACCTCTATATCACTTGTCTTTTATTACTTGTAGCTTCAT
TAATTACTTTATTAACTCTCTGTCCATTGCTGTTATGTTTCCTTCTGTAA
TAGTCTCAAGGCTATTCGTCATGAGAGGCACATGCTCAGCATCCAAATGC
ACAAGCAACTCCCCCAAATAGAGAGAAAGAGTCTCTACCTTAAATGGAAC
ATTCCTTTGAATAGTAAACATAGGAGAGTTCAGCTGGCCAATCTCCTATG
GACGAATTCAGGAGATTTGGACCACATTGCAGACAGTGCCTTTGTCGTAG
CTAAACTTATTGGGCTTACAGAGCCCGGAAAGGCTTCTAAGGAGATGTTT
GGTCTGAAGTTTGCTCCCTGGAGCTCCAGAAGATCGTATAGTGTTAAGCG
CAGCCTGATATCAATATTGTAAGATTGCTGCAGATGGCAAGGGAGAAAGT
GTGGTAACAATGTGGTACCCAGGGGGCTCCATTTACTTAGATATTTATAA
TATATGTATAATTGCTACCTTAAACTTTCTAGTATAATTTTAGAGGCTGG
TACATTGCTCAGGGGTTTGTAAAACAGTAGCTAACCTATAAGCCTCAAGT
ACTTGTTTTTTTTTTTTTTTTTCTTAATTTTTAATTTTTAATTTAGTACT
AATACCTTGTGTATTGCTTAGTATTTCTTAGTAATGAAGAAACTTAACTG
GAATTCCCTGCATAAGTTTTCTTCTTTGTTCCTATGGAATGACGTTTGGT
TGGTGCACTCAA