| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017371180.1, is a part of gene, LOC108202669. |
| The genetic_marker, MK019098 9_7941335, is located in gene, LOC108202669. |
| The genetic_marker, MK006256 K3700, is located in gene, LOC108202669. |
| The mRNA, XM_017371181.1, is a part of gene, LOC108202669. |
| 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_017371181.1 | XM_017371181.1 | mRNA | DCARv2_Chr9:7939890..7945776 |
| XM_017371180.1 | XM_017371180.1 | mRNA | DCARv2_Chr9:7939890..7945776 |
ATAAATATAAATTATCACCGCTTCTAGGGTTTCACTCAATCAGATCCCCA
ATTATTTTTACACACACAAATTCATCAGCAACATGCCACCCAAGGCAGCG
AAGAGAGGGGCGGGAGGGCGAGGCAAGCGCGGCGGACGAGGCGGTCGTGT
CTCGAAAAGCGTGCCCAAAGAGGAGCCCAAGGAGGAGCCCAAGGAGATTG
AGGTTCCCAAAGAAGAAGTGAAGATTCAAGAGGAGGAAAAAGTTGAGGAG
GTCAGTAAAGAGGAGGTGAGAATTGAGGAGAATTATGAAGAAGATGAGGA
TCCTGAGGAGATTTTTGAGGAGGGAGCTGAGGAGATTCAGCAGAAACCGC
CTTCTTTTACAAGTGAGTGGATTTTTTTTGTGATTTTTTGATTGAATTTG
TTGTGGGGTTTGCTTTTTGTGTGTGATTGGTGATGGGTTGGGTTAAAAAT
TGGATCTTTTTGATGGGTTGTGGTGGAAAGTATATATATTGCCTATGTAA
ATATTTTGATGAAAATTGGATTTTCTTGGGGGAGGGGGTGGTTAAAGAAA
ATTCGATGTATTTGTGCTTGTTTAGATTGAAATTGGGTCTTTCTAAGGGG
TTTAAAGAATATTTGATTGGTTTATGTTTGAAGTTATGCTCATTACTTGA
AGTTGTATTGTCAATGTATTTGTGTGTTTGTTAGTTTACATGTGTTGGAA
ATATGTTCTTTTGGTGAATTTGTATTTGTATTTTTTTTTTTGTCTAGTTG
TGTGGTAGAATTCAGTATTGGTTTTAGGAAAAGAGAGTTTCGTTGTGGTT
ACGTCATGGAAATATGATATGTTAAGTGGTAACCGGCCGTGGTCACCTGG
TATAGGGGATTTTGTTTTGTCGCGTTGCTTGGGGAATTAGTTATGGGCTG
TGTTGCAATGAAATTGAATTCTCTTGATATTAAAATCGGATCCTGTTAAG
GTGTATCGAGGCTATTTAATATATATGTGAGTAGTTTTTTTTGGAAGATA
TACTTTTGTTGGTTCTTATGTGTTAAAGAATCTGTTTTTTTTTTTTGTTG
CGGCTAGGTAATAAATGTCTGAGGTCCCAAGTAAGATATGAATTTGGTGT
TCCCAGCTGTGCTTTAGAATTGGGAAAAAAAAGAATTTATTTATTGTGGG
ATATAAATTATACCGAATGTGTCAACTTATGGAGTTACAGGAAGCTTTTA
ACTAAGATCTTATCGCTACCTGGTTTAAGATGATTGAGTTGCGTCTTAAT
CATTGAGAAGATGAAAATGTTGAAGTAATACAACCTTGCAAGAGTTAGTG
TGTAACTTCCTGATGGTGGAAGACTTTAGATGCTAATGCTTTGAAGATAC
CGTTGCTCCTGTAATATATATTTTCTGATATATCGGCTAAATAAACAGGC
AAAAAAGGATGGTTCACAGTAAGTAAACTGGTTATCCTAATTTGTCTTAA
ACAGGCTTGAGATTTTTTCCTGGCCTTGCATAGTTAATGGTCACTGCACC
TATGAATGGAGATTTCACTACAACTTCTTGCGGTGGTACTGGTTTAGTTG
AAGTTTGCAGGATTTACTTTAATTCTGGTGATGTATTACCAATGGTTACA
GATTCTCGTCAAGATAAGACAAGAATAGAGAACCAAATGGATTTCTTGGT
GCATACCGCCATACATGCAAGTGCATGCTACATGGCTTTTTTGTACCCTG
CTGCAATATTCTGTGGACAGATTTTGCATATTTTTTTACGTTGTAGAAAG
TGATCCATGATCTTAGACCACTGGTAGACGACAGAAGGTCGTCTTTATAA
TTCTTTATGGCATATAACTATCATGATAAGCTGGACCTCAAAGAATTTAG
AACTGTTTGTGGAATACTTTTAAGTTTCAATTCTTTTATGTTGGTACTAT
TATGGTTGTTGCAATAAACTATCTGTTGATCGCATCGGACATATCTTATT
ATTGCCTGGCAGACCAAGAGGAGGTAAAAGAGTCTGTTGAGGAATATGAG
AGAGGTGAGCGGTTAGATTTGGAGGACAATGAGCCAGAAGACGAAGCTGA
AGAATATGGTGGGGTGGACTATGATGAGAAGGAACCTGAACATGATGATT
TTCAAGAGGTTGAGGAAATAGAAGAAGACTCTGAAGGGGCTATTGTTGGC
GAGGAAGAGGGTGAGGAAGTTGAAGAAATAAATGACGGTCACGAGGAACT
TGGAGAGGAGGATTTAGAGCATGGCGGCGAGGGCCCTACTGATTTGGCTG
ATGCTGAGGAACAGGAGCATCATGACGTTTTCAAAGAGAGGCGAAAAAGG
AAAGAGTTTGAGATTTTTGTTGGTGGCTTGGACAAGGATGCTTCTGAGGC
TGATTTGAGGAAAGTCTTCAGTGAAGTTGGAGAAGTAACTGAAGTCAGAC
TTATGATGAATCCTCAGACCAACAAAAATAAGGGATTTGCATTCCTGCGT
TTTGCGACTGTAGAACAAGCTAAAAGAGCATGTTCTGATCTTAAAAACCC
TGTGGTATTTTCTGTGATCCTGTCATAGCTGTCATGGAAATTGATATTTC
TTTTATCCTGAATCATAATTTCTACCAAATTCCAGGTTAATGGGAAAAAA
TGTGGTGTTACTCAGAGCCAAGACAGCGACACCCTTTTCTTAGGTAACAT
ATGCAAGGCATGGACGAAGGAAGCTGTAAGTAGACTAGGAACTTTCTGTG
TCTTCATCAAGTTATTTATCTATCTAGCTAAATATTTAAGCAGATGTCGG
GGTTGTTATTCATTCTCCCTCTAAATTGACGTCTAATATTATCATAATCC
TTTAGATCATGGGTACTCAAGGATAAAATATTAAATATGTATGTTTCACA
CTTGTGTCCTTTTTCTCTTGTGTGTTTCATGTTGTCTATCTATATATATA
TATATATGTATAAGATTAATCAGAGTTGCTTTGCTATTTGACATTTTGGC
ACTACTGACTAATTGGTTGTACTTCCAGCTGAAAGATAAGTTGAAGCATT
ACGGAGTTGATAACATTGAGGATTTGACTTTAGTTGAAGATAGTAACAAT
GATGGTATGAACCGTGGATTTGCTTTTCTGGAGTTCTCTTCCCGTTCAGA
TGCAATGGATTCTTTTAGGCGATTGCAGAAAAGAGATGTTGTGTTTGGGG
TTGATAGACCTGCCAAGGTCTCGTTTGCAGATTCCTTCATCGACCCTGGT
GATGAAATAATGGCTCAGGTACGCATCGGAATAGCCTTTGCGTTATTAAG
ATCCGTGGTTTGTTACACTATGGTACTCTGTATTACCATTTATCTGGACA
TTACAATTAGCATGATGCATGGATTTGATTCCAAGTCAAATGCTTTTTTA
TTTTTTTTTTTGTGTTACTGTGCTGAGTAATGCACTTCCTTCTACTTCAA
TCCCAAATTAAGCTTAAGGTTTTTAAAGATCTTTTTACTCTGATTTGTTG
AAGCAAAACCTTTTGTGTTATTGATATCGCTTGAAATAAAATTTGAAAAA
CAGTGGACTGAGTTCTTGGAAATCATTTACTGTCTTCTGCGGTGCCACCA
ATAATTTTGTGCCCTATTATATGTGTTTCTATTGCATTGAAGATATTTAC
TTATACTTGTACATCTTTACGAGTTCTTTTTAAGATATTTACTTATACAT
GTCATATTTTACATGTTCAGGTCAAAAAGGTTTTTGTTGATGGCTTGCCT
GCCTCATGGGATGAGGATCGTGTAAGGGATCTTCTCAAGAAGTACGGAAA
GATTGAAAAGATTGAGCTTGCTCGTAACATGCCATCAGCTAAGAGGAAGG
ACTTTGGATTTATTACCTTTGATACCCATGATTCTGCTGTGACATGTGCT
AAAAACATCAACAATACAGAGTTAGGGGAAGGTGAAAGCAAGGTTAGCAT
AGTTAATTGGATTTTTTTAATTTTTTTTTTGGATATGTTGCTGGATATCT
TTAATGGTTTGTTTCGAAGCAGGCTAAAGTCCGAGCCAGATTATCGAGGC
CAGTTCCAAGAGGCAAAGGCAAGCGTAATTCTCGCGGTGATTTTTATCCT
GCACATGGGGCCTCACATGGCTTTAAGGCTCCTTGGGGACGTTCAATTCC
GCCACGTAGTCTTCCTGTCCGTGAAGCAAGAGGTGTTAGAAGTAACCTGC
CACCTATCAATCGTGGTCTAAGGAGGCCTCCTGCTTTTAGGGACAGGCGA
GAAGTTATCGCGAAGCCACCAAGGGGAAGGACAATGTTAGCTCCCATTCC
CAGGTCTCCCATTTCAAGGTCTCCCATTTCAAGGTCTTATGATAGGAGAC
CTCCTCCGGGTATGTATAGTTCCTTTTCAGCTTTTTTACTTCTATGATGT
GGTTTCATCTTTTACATAACCTGCGAATAGTTTACACTTAATGATTGTTA
CATAATTTGCGTGTAGTTCCTTCATACCCAAAGAGCAGCTCGAGGAAAGA
TTATGGAAGGCGGGAGGAACTGCCTCCTAGGAGTAGGCCTGCTGTAGATT
ATGGCCCCCGGGTTGCTCCACCAGAAAGACGTCCATCTTACCGGGATGAA
TACCCCCCTCGAGGATCTGGATACACCGATGTGCCCCGAAGTGCAGCTCG
TCCTGCATCAAGGAGAGCTTATGTTGATGATGGCTATGGTCAAAGATTTG
AAAGGCCACCTCCAAGTTACCGTGAAGGACGGCCTCGTGATTATGACTCA
ATTTCTGGGTCGAAACGTCCATATGGTGCCCTGGTTAGTGAAGTTCTTAC
TCTACCCTCTCAATTGGTCTTGCAGTTTTATCCTTGGTCAAGTCATAAGA
CTTTGTGTCCCTTTTACATTTTAGGATGATGTTCATCCCCATTATGCTGA
GCCAGTGCTCCGCCAATCACGTCCTCGTTTGGAGTATGAACCCCGTGGCA
GCGCTTCCCAGTATGGGGATAGTTATAGTGAGAGGTACAAAGTTTTGAAT
TAGTTTTTCTAATTTTAGGATGCACATTTCAGGATTTAATATGCCTTTCC
TGACTCTTTTTAGTGCCAGAATCGGAAGATCTGAAATCGGATACAGTAGC
AGAAGTTCAATTCCCAGTCAGGATTCTCGTGCTCTTTATAGTCGTCGTCA
AATCATGGATTATGGCGGAGGTACGTATTTGTCAACGTGTTCAAGCTCTG
ATGCATAAAATATATGGATCCAAACTTTATCTTAAATGATAGTTGTCAAC
AAATTTTAATTGCAGGTTCTTATAGTGGAAGTGATGTTGGTGATGGAATG
TATTCTTCAAGCTATAGTGATTATATGTCTCGTGGGGGTGATGTATGTTC
TCTTTCACATTGCTATCTCTCTAAGGATTTTTGATACAGTATTTGTTCCT
TACCATGTGTATGTAATTTTATTGAAGGTTCCTAGTAGATCTTATTCTTC
GCTCTATCCTGGTTCTGGTCGTGGCTTGGGAGGAAGCAGTTACATGGGAA
GCAGTGGTAGTGGATCGTACTATTGAGGTAGACCATTTCGCAGTCCATAT
ATTTCTTCAAAATTTATACAATTATTAGAAGCAGTGGTGGTGTTTATGAC
CATGAGTTAGTAGCTTGCGTGGCGGCTTGCACACATAGTGTCACTGATTT
ATAATTTGTTCCCGTCTCAGATCTGAAATGCGGACAATGGAGAGCTCTAG
GACGTGGATGCGAGGCTCATACCTAGTTATTAAGTCCACAAACAGAGTTT
CTCTTTGTTGCAGTTTGGTCTAGTGGAATAGTTTCTTCCGAGCCTGAATA
TTTGGCATATTAGGATTTTCTATATTCGAGTACATATTTGATGTTTGTTA
AGACTATTTTAATAATTCAGAGTTTGCTCGTGACAACTGTGTTGAATTCC
TTTGTGTTTATTTATGCCTTTTTATTTAATCCATCA