| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017387208.1, is a part of gene, LOC108214942. |
| The genetic_marker, MK008675 85036.22262, is located in gene, LOC108214942. |
| The genetic_marker, MK010045 3_49340232, is located in gene, LOC108214942. |
| The genetic_marker, MK003030 K0474, is located in gene, LOC108214942. |
| The mRNA, XM_017387207.1, is a part of gene, LOC108214942. |
| 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_017387207.1 | XM_017387207.1 | mRNA | DCARv2_Chr3:49338491..49345042 |
| XM_017387208.1 | XM_017387208.1 | mRNA | DCARv2_Chr3:49339589..49345041 |
GAGGATATATAAGAAAGGGTCCAAAGGGGGTCTAATAATTTATTTAATTC
CAATTTGATATACCATGCCCTCTTTTTTCTAGGTTTTCACTTTCCCCAAA
TTGAAAATCACAAACTGGGGGCATTTCATATCATAATCCAACACTCTAAT
CAATCTTCACCTACATGGGGTTTTAATTCATACATATAAATACACGTATA
CACACAAATTTCATCAAATTATGGCAGAGAGTTCCTGGGTTGATGATTCA
AACGCTGCCCAAGTTCATAGAAAGTAAAGTTTCTATCTTTTCTTGTTTTT
TTATTTGATTTGTGGTTATTTATGTTGGTTGATGATAATATTTTGTGGGG
TTTTGTTGGAATTGAGTTCTGGGGAATTCTCCAAATGTTGGAAATTTTGA
GATTTTTTGATGGATTTGTGGTGGCTTTGGATTGGAGTTGAGATTTTTGA
CTTATGAGCTTGGTATTATGATGAGGTTTTGATTTTGATTGGAATTCGAG
ATGGGGTATTGCTGTAGATGAACATTTCTTGGTAAAGATTAAATTTTAGA
CTGGATTATTGATTTTAAGAAACATATGGATGCCCTTTAAATTATTGTTA
GATATGTTGGCTATGCTATTGAGGGAAGATTTCTTATAATATTTAGATGG
ATGCTCTTTTTAACTTTTCTGGGTTTTTATTATTAAGAATTTAAGAATGA
GGTTTTTCATATGTCTTAAAGTTGTTTATAATTTGTGCACATGTTCATCA
AGAGCTGAAAGTTTGTGAAAAGTTCTGTTACTGGACCTGGTATAGTATTC
CCCTGCAAGATAAAATCAGATAACAGAGTTATAATTTGGTCTACCTATTG
ATGTGAGGGATATCTTACTCCTCATCTTTATTGGTTAAGATTTCCGTGCA
TGCTAAAGTCTTCTGGTCCATGTTTAATGCACTGCTTTCATCAATTCTTC
TGTATGCAGCCATCTGGTAATCTTGAAACCTTATCCTTTGTAACATTTTT
AAATATTTAGCTGTAGAAATGTCTTTCATATTTTGGCGCAAAGAGAGACG
ACTCCCAGGACAAAATGTTTGGCAAGAAAGCACTGGGGAGAAGCTTTTAA
ATCAGATGTTGAATCCTATTTGGAGCCCAAAGTTGAAAGATTAAAAGATG
CTAGGCGGGAACTTTTTTCCTGGTAAAAGTTTTGTGCCACTTGCTTGATT
TCTGATTTTATATTTCTCAAGGTGTATGGTAAATTATTTATGCTGTGTTA
AAATATGGTACCCTGAGGTGAATGTTTAGTTGTTTTAATAATTTAGGGTA
GAGGCGGAGTCTTTACAACACTTATCAGCCAAATATTGCTCTTTAGTGCC
TGCTCCAAGGTCAACTATTGCAGCAGCATTTAGCCCAGATGGAAAAACAA
TTGCTTCTACTCAGTACGTTGTACTTCTGATTTAGCTCTTATACTGAATT
CCAGATACTATTGTCATCTAACACCGTTCATATGATATTGGCAGCGGTGA
CCACACTGTGAAGTTAATTGACTGCAAAACTGGGAATTGTTTACAGGTGT
TAAATGGTCATCGAAGAACACCTTGGGTGGTGAGATATAGCTATCATCTT
TTGCCACTTGATTTATTAGAATTTACTTTGAAGCAATGAGTTTGATTGAT
GACTTTCTTTTTCTGTCTCGCTTCTTATTGTATTGGCAATGTTATTATCT
CTTAACTCTGGTTTAAGAAGAGAGGCGGTCCATATTGTGAACGTGTAATA
TTATCACTTATATGTAGGAGTTCTAGACCAGTAATATATTTATAGTGGTT
GACAAATACTGTATCGAAGTTGTCAGTGACCAAGTCATGACACCGGTATA
ATTATGTGATGGTTAAATAGATAAAATTATAAACATGACCTGATTAGTTG
ACTAGTTTCTGAAAATAAATATTATATTTCTTTCCAAACGAGACTTTTAC
TTTTATAGTGTATGAAATTGACCTTCTGTTGTTTAGCATTGTCACTTCCT
TATACCAATCCTTGTATACTTTTGGTGAGTATGCAAGTGGTCGAACAACT
CACTTATGCAAAGCCTTTCCGGATATCGAAATTCTGGAATAGAGTATCAA
GGCATCGAGACTGTCTTTGTCTCTTTCGTTAAAATAATTTACTCTAGGTT
CTATAGTTGTAGATTAGTGTTTTTTGGTCATGTAGATTCTTGCATGTTGT
AAAGCATAGATTCTATGTTTGCCATCTGCAGAAATAGTCCCTTAGTTCCA
TATATTAGAGCCTCTCCAGCCCTTACACTAAATTTGGTGTAGTTTTTAGA
CCGTAAAAGTCACACCAAACTTAAAGTCTCTCCAACCCATTCACACCAAA
GTTTACACTAAAAGGACTCTTTTTTGTACTATATAGGTTATTTTATTGTT
AAAATACAAAATTAATAAAGTTTGTGGGACATAAAAGGAGATGAAATTGT
TTTAGGTAAGAAGTATAAGAGTAGTGTTGGAATTTACAAAAACTCCAAAT
TTGGTGTAATTTTTGGCATGACACCACATTTGGTGTAACTTTTGGTTGTG
ATGCCAAATTTGGCGAAACTTTTAAAGTTTGGTTGGAGATGAATTTACAC
CAAATTTGGTGTAAAAGCACACTTTTAGAGTTTGATGGAGACTGTCTTAG
AATAGCAGATTTTAAAACATGACCAGGAAGTGTCATTGAATCGGTCTTTC
TTGGGTGATAATTTGGGCTACAACATCGTTTGGAGTGTTAAATATCTCTA
TATCATCATTAATCTATGACAGGTCAGGTTTCATCCCTTGCATCCGGAGG
TTCTCGCTAGCGGGAGCTTGGATCATGAAGTTCGCTTATGGAATGCTAAT
ACGTCAGAATGCATTGGATCTCGTGATTTCTGTAATTTCCTCTCTACCCA
GTTAGCATCTTCTTGAACATTAATTTGGTTCTGAACTTTCTATATTGTCC
TTTTAGAGTTGATCAATGTACTCCTCTTATTACTTTGTAGATCGTCCTAT
CGCTTCCATTGCTTTCCATGCTGAAGGGGAACTCCTTGCTGTCGCTTCAG
GTCACAAGGTTTTGAAATCTAACCAGCTTTAATATTGTTCTGACTTCTAA
AATGATTTATTCTATAGATCAGTAACAATCAGTATTTGTATGGGTCAAGA
CTGTTGTCTCTCGTAATTTATTATACTGACTCGCGGAATCTAATTTCAGC
TTTATTTATGGAACTACAATAGAAGTGGTGAGCATTCGTCACCCACTATT
GTATTAAAAACAAGGCGTTCTCTTCGAGCTGTGCATTTCCATCCACATGG
TGCTCCATTGCTCTTGACTGCAGAGGTGAACTATATTTCTGAAAGGAATC
TATGTTGTTTTGGGCCTGTCTCTTATAGGTCACTCTATTGAACTAATATG
CAGGTAAATGATCTTGACTCTTCAGATTCTGCTGTTGCACGTCCCACGTC
TCTTGGATCATTGTATTATCCACCTCCGTCTATATTTTTGGCTAACGTGC
ATCGCAGCGATAGTATTAGTTTGGCTGCCGAGCTTCCTTTGATGTCCTCA
CCTTCATCATATGTTCCTATAATTGCAAGGGATGATTCTGAGACAGATTT
ACAGCTTGGAAATCCACCTGTTGATTCAAGTAGCATACAGGCTGAATTTT
CTGCCCCTGTGCAATTTGAGATAGACCTAAATGCAATTGGACACTTTGAT
CATAGAGCGCTTCCTGCAGAGACGTCAACTGCTTTACATTCTAATGTACA
ATCCACGGCAGCGGACACCTTACCAAGTTATAATCCTAGTAGAGTGCCCA
ATCTTGTTCATGATGGTAGTAACAATATAGCAGATGTGCAACTTGGAGAG
GCTAACCTTTCTAATGTGGATCCATATGGTGCTAACAGTAGTGCGCAGCC
ATATACTCCTCAGCATGCTGTTGAATCTGGATTTAGTGTTACTCGGCCGA
TCAGGGTTCCTGCAGATTTAAGAACGCAGTTGTTACCTTCTACAAACCCA
ACATCTTGGGAGCTGCCTTTCCTGCAAGGATGGATTATGGGTCAACGTCA
AGCTGTTATGCATCCAGAGCTACCTCATGTTGGTAGGAGACAAGAAGGTT
CATCTGCTTATCCACGGGTGGGTTTTTATGCTTTATTGTCGTCTTATTTG
TTTACTTATGGTAAACTGAAAGATTTTCCTTGCATGATCATGCTCCACGT
GCACATTTTCAGTCACATGTAGAGGAGGACCACCACTCTCGTTCAAGTCT
CAATAATGGGATTGGAGCAACTTCCTTTTCCCTAATTAGTAGAATACAGT
CTGAGCTTGCTGCATCAATATCTGCCACTGCAGCTACGGAGTTGCCTTGT
ACAGTGAAGTTAAGAATCTGGCTTCATAGTTTAAAAAATCCATGTTCCGT
GCTCGATAATGAAAGGTGTCTCCTCACTATACCACATGCAGTGCTTTGCA
GGTATGGATGAGCTCCAACTCTGTGACATTAATCAATATTATAGTCATAT
GTAAAAGAGCATCAGTAAAGAAGCGTCAGTTGGGGCCTTTTGCTATTAAT
TAAAAAAAAAAAAAAACCCTTCTGCTTTCTTATTAATGCATTAGTAAGGG
CCGTCTTCAGCTATAAATGGAACACTATTCTCCTCTTTCTTATCATGCTT
AAGTGTCTTGCATGCATTTTATTTTCACATTATCTTTGAGAAGTTAAATT
AATAAGATTTGTACTGCATGTTGCAGTGAGATGGGGGCCCATTTTTCACC
TTGTGGGAGATTTCTTGCTGCTTGTGTTGCATGCGTGCTTCCTGAATCTG
AAGCAGATCCTGGATTACTTACCCAATTCTATCACAACGGAACAGGGGCT
GCAACTTCTCCAACCCGACATCCAATATCAGCTCGGCAGATAATGTATGA
GCTTCGCATATATTCGCTCGAGTACGCGACGTGAGTCCGGTTCCGCTGTT
GGTCTTTTTTATTTTCTTGATTTTTTAACCTTTTTGATGGTGGGAACTTC
ATTTTAAGTTCATTTATCCCAACCCTAATCTATACAGTCATTCTGTAGAT
TTGGTTCTGTACTTGTTTCGAGGGCAATAAGAGCTGCTCATTGTCTAACT
TCAATTCAGGCAAGTGTTTTCAGAATGTCATGTGGAAAAGATAATGTGAT
AATGACTGATCGTATTATGTAACTAAATTTTATTAAAAGTTAGGAGAAGT
TAAGTGCTATCAGTTGCAGTGATCTGTGAATATCTTTTATATTTTTTACA
ATATAAGTTATCTTCGCTTTTTCGTTTTTACGAAGTTACTTTTTACATTG
TTATATGGGTAAACCCAGTATATCCTTAAGATTAAATTTTTTTCATTATA
ACGTTACTTGTTTGTGCAGTTCTCACCTACTTCAGAGCACATATTGCTTG
CTTATGGTCGTCGGCATAGTTCTCTTTTAAAAAGCATTGTTGTCAATGGG
GAGACATCCTTACCGATATACACAGTGCTAGAGGTAAAATTTTTGGTCCT
TCTGATTTGATAATTTCCCATGCCATATTTGTTACACCCTCCGCCCCCTT
TTACTAGTCCATTTTGGTTTTTAAGAAGTCAAATTAACCAATTTTTCATT
AAACATTACAAATTATCTATAAAATATTTTTAAAATCTGAAAGTTATATA
TTAAAATAGACTAAATATACTTTCTAATGATATAATTTTTATTATTTTTT
TCAGTTATATGATACATATAAATTTCAGTCAAGATATATAGTCAATTTGA
CTGGTCAAAAATCAAAATGGACATTAAAAGGGGACGGAGGGAGTATCTTT
TTATTTATTTTTTTCCATTTTAATCTTCAATGAATAATTTAGGGGCAATG
AATGATTGTTTTTTAGTGTTCTTGACTTGAAAGATGGAAGATGGAACATA
TACAAGTAACGATGCATGAACAATAGAAGTAAAACATGAAACATAGGACT
AATTCAGATATTTATGCATCAGAAGTTGTTTATGGGATAGTGGTACATGA
TTACTGTGTGCAGGTTTATAGAGTTTCCGACTTGGAAGTTGTCAGCATGC
TTCCAAGTGCAGAAGATGAGGTTAATGTTGCATGCTTTCACCCTTTCGCA
GGAGGTGGCCTTGCATATGGAACCAAGGTGTGAGCCTGAATATTCTGATT
TATTTTTACTGCCAATTTTTTTGAATAGTAGTATAGAAACAAAGCTTTTG
ATAATTCATAGGCTTACACAAATACATTGTGCGGTCAATCGCAGGAAGGT
AGGCTTAGAGTGTTGGAGTGTGATAGGGTTCATGATCATCAGAATCTGGC
TAGGCCAGATATTATATCACCTGAAGACATGGTTGAGGTAGAACAACTCT
TCTAGGTTTTACGGATGCTCTGTACATTTGTAAAACTGCATCCTTTTGTA
ACCATGTACTTTCTGTATCTTTTGTGTGCATGAGGTCTTTTGTGTGCATG
GGATTGGGCTAATGATAAATCGTAACTGTGCCACTTGTTTGTTTTTATAA
CTGTTAACCCCGACTTGAAAGCAGCTCTAGATTCATCTTGCCAAGCGCCA
A