| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017387638.1, is a part of gene, LOC108215234. |
| The genetic_marker, MK011139 3_27468363, is located in gene, LOC108215234. |
| The genetic_marker, MK006489 K3933, is located in gene, LOC108215234. |
| 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_017387638.1 | XM_017387638.1 | mRNA | DCARv2_Chr3:27467510..27473562 |
AATTTTATCCTGTGTTGAAGAGCGTATAATTACCACAGTAAACACCATTT
CTCACTCCCCCAGATAATTCTTCTTCTTAAACTTCCCCCAAATCTAGTTA
ATCTAGGGTTTCTCCATCTCCCCATGGCCGGAATTAGACTCCCTCCGGAA
GATTCCGACGTCTCCACGGCGCGCCCGCCGACCAACACTGATCTCATCTC
CGACGACGACCGCTCTGTAGCCGCCGATTCATGGTCTATTAAGAGCGATT
ACGGTAGTACACTCGATGATGATCAGCGTCACGCTGATGCTTCGGAAGTT
CTCTCCGCTGTTCCTTACCGTTCTGCCTCCGATTACAGGTTGTGTCTGTG
TGTTTAAGAAAAGAGATAGAGTTGCTAATAGTGTGATTAGTTTGATTTTA
TGAACTATTGCGTGTGAAAATAGGCTGAATTGTTTTGTTAATTTCTGACT
AATTAAATGCTGATTAACGGGTTTACTAATGTGTTTATATAAATAGATGA
TTGTGATTGGTAGCAGTTAGATCAGTTATCAGAGTGTATATAAGGGTTTA
ATTATGTTAGTAGTAGAAGAGAGAGAGACTGGTTGATCTTTCTTATTGTT
AGAAATGATTATTATGCCATTGTGTTATGATATATATTGATGGTCATGTG
TACTGATTGGATCAGTTACTCAAATTAATGCTTAGTTATTGGAGGAGCAG
TGGAAAGACTCGTGCTTTACTAACTTTAGATGTTGTATGTACAGTTCTGA
CAAGGAGGAGCCTGATGCTGAACCAGTTTCATCAATGTTAGGCTTTCAAA
GTTACTGGGATGCTGCTTATGCAGATGAGTTGGCAAATTTTCGTGAGCAT
GGCCACACTGGTGAAGTTTGGTACTTGTTCATACCTTTTTCTACTCATTT
TTGGTTGAAATTAAGTACATCATGCTGCAAGCAACAAGCCTGGTAGAGGG
AAAAACTTCTTATTCCCGGTCATTTTCTTAAATTTAAATCTATTTTATGT
GATAGGTTTGGGGCTGATGTTATGGAAATGGTCGCATCATGGACCAAAGG
CTTGTGCAATGACATAGCTCAAGGTCAAATGCTTAATCATGTGGCTGATG
ATACTTCAGTAACTCCCGAACAGGGTGAAAAGGATCTAACCGACTGGAGT
GTGCTTGATGTTGGGACTGGGAACGGTCTGCTGCTTCAAGAATTTGCTAA
GCAGGGGTACACTATAAAGCTTTCTACTATTTGTGTAGTATTTGCATGTT
TAACAGTTCGGTGTCCGGATGAATAACATCCCCCACTTTGACGCTGACTT
AATCAAATACTTGCAACTTTTAAAATGTCTTCGCAAGTCACTTCTTTACA
AAAGAAGTAAAAATATATATATATATATATATATAAGGCGCCATTATGGG
TTAGTGTTTAATACTTAATACTATGTTTGATCTGTTTATTTCTGTTCAGA
TTGACTGTGTTCAGACTTCAGACTGACTTTCATGTATTACTTCAATTTTC
AATACCATTTGGAAGCATGTAAAGATAGTATACATCAACTTGATAATGTT
AAAGAGCCTTTTGTGTAGTTTGGACTCACTTACTTAATTGGCTTTACTAT
TGGGGAACTACTTGCGCCAGAAATATAAAAAGAAATGTCATGTACGAACT
TGCCTCTGTGTTGTTTAGGCCTCAACTACTCACGCTGGGACTTGGGAGTA
AACAAAAAATATTAAGTATAAACATCTGTCTGAATTGGCTTTGATATTCT
TATTAAGCTCCGTGGGGCGTCAAGGTTCTTAGGAAGAATTAAACGACCGA
ACAGGACCCATTATTCGGTAAGTTTGCTAACTAAAGTGAGATTTCTAAAG
TAGTATTTTATTTTTGGCTGAAGCTAGAAATAGGTGTAGCCTTGTTCTGC
TATGCCCTTTAGAGATGGGTCAATTTAGGTTCAGAACCAGTACTTAGCCT
TGGTGCTGGCTGCTCCATGCAGAGGGCTGCCTGCATGTGGCCACTATTGT
ATAGAGGATGTTTGCGAATTCATCTATACTTGCTTATATAAAATCCTATG
TCACTTGACTCGGTACTATTTTTTACATAGCACCACCTCTTTCTGTTGCT
TGTTAATAAGATTTCCCAGAAGAAGTAAAAGTTCAGTGAATAATTATATG
CTACTCCTATTTGAGTATTACTTGTTTATGATCCTAAAGTTGTATGTGTG
CATAATTTTATGCGTTACTGCGACGAGGGCGCTTCGTTGACATGACTTTG
GAAAATACTGCTGCATGAGAAATGTGTGCATCTGTCAAAGCATGCTAGGA
TTGGATCGCTGACCAGAAGGAATTAACTTTTGACTGTCAATTCATAACTA
GATCTTAAGAGGGAATTGATTATATACTAGATCTTATGCGGAAAATGATT
GTGTACAAAATCTGGTGTTAAATAAATTGCATAGCCAAGAGTCCAGACTT
GATAAATTTAAAAGAAGGGTGGAGACCAGACTCATCTCAGTATACTTACA
ACTGAATAACTTCTGACCATAGTTTCTTTTTCCTTGATTTCTTTATCATG
CCGGTAGCCTTATTGTCTTTTGATTCCGATCTACATGGGGCTTACTTCTC
TCTGTTATAACTATTTTGTCTGACTAGTTCATCTGCTTTTACCTTGTAAT
ATGTGTACATAATTACTGGTAATCATGTACCCAAACCCAACAACCACAAA
TTGTGCTGCCCAGTCTGACCAGATTGGAACCGATAGACAGTTTATGGTTT
TAAATCTAGGGTCGAGAAGAGAGTCCGGTGTTTCTTGATTTTGGTTCTGT
TATTTAACTTAATTGTTTCAATCACAAATGACAATATTATATAATATGTG
TTCTATATTATATTTCTCTACCAGTTAGTTTCTATTAGTTTTAACTTTTA
CCTGTATACCAAGTAACTAAGTATTTATGTACACATATATTTGATAAAAA
TTCCAAATATGTTGTTTGTTCTGATAATCTTAATACCTAATTTCTCGCAT
TAAGGTATCTGTAATCTATGGCATAAAATTAGAGGTATTTTGATCATAAA
CAATATATAAGAATCTTTATGCATGTGACACATCTCTCTGGAAATCTTAC
TTTGAAACAAGAAAGAGCAACGCTTTAAGCGCTGAAGGCTTGGTTTTAGA
TTAACTAAATAACACTGAACCAAGTCGAACCACAGTTACAACAGCAGTGC
TAATACTAGATCTTACTAATTATTTAGCTGTTTGGGTTTACCAAGTCAGT
TGCATATAATGTGTCACACTTTAACTTTAGTCTTATACGGATATTTAATG
TACACACATATAATTGGAGTTCAATCGATGGGCTTCCGATATAAGTGAAC
ATGTCGTATTCTGAATTGCGCTAATGCTGAAGATAACTTTTGTCCTTTGA
CGCATAACTTGCACTTGGCAATTATGTATGATCCTCTTGTTTACCATATT
TAATTCTGCATTGAGCTTTATGCATTACCTCAATCGCCAAAATTGTTTTA
TCCCCATTTATAGTGATATGACTAAAGGTCTGAACCAACCAGTTGTGTTA
CTGGTGTAGGTTCACAGATCTTACTGGAACTGATTACAGTGAAGGAGCAA
TTGATCTTGCTAGAAGCCTTGCTGATCGTGATGGGTTTTCCGGTCTTAAA
TTCTTGGTATGGTAACCATACAAACTACAAAGCCAGCTGTAAACTTCGGC
TATTTCACATATATCTAATCTTTCACACTTATTTATTGTCAATCTGTGTA
GGGAGAACTGCTTGCCCTTTTGCATTTAATTTTGAAATTTTTTAGTTGTA
GTTCCTTAAGTTATAAGCTATCTTTTGTTACACTAATGGAATTTGCGGAC
CTGCTAGTTTGTGCAAAACTGAGCAAAATTTCTTATTTTCTATCTGCCTC
AAAGAATAATAAACAAAAATTGATAGCCCATTAGGACATTTGTATGAAAT
GATGTTTTCCTAGTTTGATTTCATGAGGATAGTACTAAATAGAGAATGTA
AAGATAAACTAATTTAAACATCTTTGATCTGCCACACGAGGGGAAATAGT
TTTGTTGCTTGTATCTGTAATACATTCATGGTATAATTGTTAATACATTA
TGGTACAAGTTTTATACATAACTAGCCTTAAACCCGTGTGAAACATGCCT
AATTCGATATTTATTACTTAAAAGTTAATTTTTAACAGCATTTTAATAGT
AGTATTGTTGGATGCGCACATATTTTTGCATGAAGAATTCTATGATAATG
TATTGAAGTTTAATTAAATATTATTAATCGATTGATTATGGTTTCACTTG
GAGATTTAGCTTTTACAATGTTTTTGTCATATGGTAAACGGGTAGTAGAA
ACAATAGACTTTTTTTATCATCTATGTGTAAATGTTTTCCTAATATTAAT
GTTTTTTGATTAATTTTAAATCATACTTTTAATGTGTTTTTTGATTAACT
TTTAATCATATTTTTCATGTGCTTTTTGATTAATTTTAGATCATATTTTC
ATATTTCTTTTTTTTTTTCATTTATGAGGAAAATATTTTTATAAAATTTA
TATTGGCTTCCTATTTGTCTTGAACTAGAATACGTTAGAACTAAGAATAG
TTACATGATCACTCGTGTTTGTCTTGTAGTCTCTTATTGTTTATATAATT
TTTCGATTTATTATTTGAAAAAGGCAAAGAAAAGGGTGATTTAGGAATGA
CCAAACATATAACCAAACTACAAGTTATCCTTATGTTCAGTTATTATAGT
TTAGTATAGATAGATGAATATAAACAGCTCGGTGTAAATGACTTCATAAT
CACAAAGCATTTTGTTGCAGACTGTGTATACTCAATTTGCCAAAGTTGTC
GTTAAATTTTTTACGAGGAAGTAGTTTGTTGGGTTTGCACAGTGTATATA
ATCTGTAAACTACCCCCAGCCCCCCTTAAGATGTAAACATTTTATACTAT
ATTTCTTTTTCTAATTTTCTTCAACAACTAATATTAGGTTATCATTTACT
ATTGGTTATGTTCATTTACCAGTTTAATTTTTGATATGGTTTTCAGGTGG
ATGATGTTCTTGATACAAAAATAGAGAGAAAGTTTCAGCTTGTTATTGAT
AAAGGAACTTTAGATGCCATCGGTTTGCATCCTGATGGTCCTATTAAAAG
GTATGGCACCAAGTTATAGAATGTGAATAGGTTGTTAGTCTTCATTTATT
TTCTTGCGTGCATTTATCATGTGTTCTTTCTTCCTTAAGTCTGAACTCTG
AACCTTTATTTAGTTTTGATCGGATTGAGAACATAGTACTAAAATCAACT
ACAAATTGCAGGATCATGTATTGGGATTCCATCTCAAAGCTTGTAGCTAC
TGGTGGACTGCTGGTAAGTAATCTCAATATCTCATGACAAACTTTTGTGA
TCTGAGAGTTTGACACTCTTGTCCATATGTTTGGTACAAATTTCTGCTTG
ATGTTTGCATCATAACATTATTCATCGTTTTCTGTTCTCACTGTAGGTAA
TAACATCGTGTAACAGTACGAAAGATGAGTTGGTGCAAGAAGTTGATAAT
TATAATCACAGACGGGTTGCTGCATCGCAGGAGTCTGAGACTTCTGTGAG
CCAAGAAGCTGGCAGTAATTCTCCGTTGTTCAGCTACCTTGATCACATCC
GTTCATACCCGACATTTATGTTTGGAGGATCAGTTGGATCGCGGGTTGCT
ACAGTAGCTTTTGTGCGAAAATGAAGTATGATATATGTTTCTGTCGTATT
TGTAGCAGAGTTTGCTCAGCCCAAGTATGTTTGTTCGTATTTTTGGGGAT
GGAGATGAAGGAAATGTGCATGCATGACCTGTGGAAGAATGTTAATTTAG
TGAAAGATGCTGATGTTATTGGTCTTGTTAGGAAATATTATGTCTTTCAT
CTTACTGTGTAGATGTATGTTGTTTCCAGATCATGAATTGGAACTTCTGA
CTGTTGATTATACTACTTAAACCACTTGTAATGGAACTCTTCAAACAAGT
GTAGGCACACAATTTTTTTTTTATCAAGTCTGTTGCCCCTTTGTTTCCTT
CA