| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017397026.1, is a part of gene, LOC108223000. |
| The genetic_marker, MK007701 TP107616, is located in gene, LOC108223000. |
| The genetic_marker, MK008300 5_31936146, is located in gene, LOC108223000. |
| The genetic_marker, MK006399 K3843, is located in gene, LOC108223000. |
| The mRNA, XM_017397025.1, is a part of gene, LOC108223000. |
| 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_017397025.1 | XM_017397025.1 | mRNA | DCARv2_Chr5:31935554..31942239 |
| XM_017397026.1 | XM_017397026.1 | mRNA | DCARv2_Chr5:31935554..31941722 |
AATTTCCATGAAGAATTTATTAAACAGCTTTATTTATATCAATTTGTCTT
TTTAAGCTCCTTTTCTATTTTTCTGGGAAACTGGAAACAAAAGTCCTCTT
TCTTTCTCTCTTCCTAGTAATCTTGTGTTCTTGATTATCCATCCAGACCA
TAGTAACTCTTGTCTTTACACCTATACACACAGCCTTGTATCTATATATC
TATATATTGAACATAAATCAAGATTTTGTTTCTGGGTATTTTATTTTGAG
GAGAGATGATGATGTATCCATCTGCTGCGTCCTCATCTTCTGCAAATTCA
GCTTCTGTTCGTGTTGAGAAAGCTACAAGTGAATTTCTTAACGGCCCAGA
TTGGACCTTGAATATTGATATTTGTGATGCCATCAATCTCAATCATTGGT
TTGTACTTTACACCAATTTCCCCTTTTTTTTTCTTGTGTGTAATTGATTT
TTATATTGACTTTTCAAGAAAAAATAAACAAGAACAAGAAAAGTTGGGTT
TTTTTATACATGGGTATTGCTTTGTGGTTGATATGTGTGGATACAGAGAT
GCGTATGTGTGTGTGCATGCATGCTTTGAATTGGGTTTTTAATTTTTTTC
TTGGTTCTTGATGATAATTGATGTTATGTGTATATATATAGATGAATTGG
TTCTTGATGATAATTGAATCTTTTGGATTTATGTTATATGTATATATATA
GACAGGGTTGAGTGTGTTGCTTATTGGGTTTGTTGATGGTGATGAGAATT
GGTGATAATTTTGTCCTGACCGGAATTGTGTTGTTCGAATTTGGTATTTT
TTAAATTGCTGATTTGATTGTCGGATATGTGACCGCAGCTACGATTGAAT
TGTGTAATAATATGTTGATGTTGTAACCTTGACAGGCTAGCAAAAGATAT
TGTCAAAGCTTTGAAGAAAAGGTTGCAACACAAGAATTCTCATGTTCACC
TACTTGCCTTGACGGTATCTTTCCTGAATGCATTCAATACTGTGTCGTTT
AGCAATCCTTTACTAACGCGTATCTGTTGTGCTATTGGGCAACAATTTCT
TTGCTGTTCACTAGTATCTAAAAGTAATACCATGGTTTATAAAATGAGTT
ATAAGTCAATTCCCAGGATAATTTGATATATACTTGGTCTATTAATTAAG
AGCGAGACAGCTGAGGAGATTTGAGGTTCTACATACATGTAACTGGTCAC
CAACCGTATTACATATTTAGATGCACTGCCTTTATAACACGCTAATTTCT
GATCCACAGTGATTTAGATCACTACAACACAGAACATGTCCGTGTCACTA
GTAGTTTCTAATACTTTTTTGTATGCGATTTAGCTTTTGGAGACAATGGT
GAAGAACTGTGGTGATCCTGTGCATTCCCAAATTGTCGAGAGGAATATAC
TGCAGGACATGATTAAGATTGTAAAGAAGAAGGCAAGTTTCCCATTACAT
TGACAAGCAAGAAGTTGCTTGATATTTTCCATCAACTATATGTTTTTAAG
ATGTTTAGGCTCCAATAATCTCTTTTGCTAATCACTTGAGTTTTTCTTCT
CTTCTTTACCATTAGTCTTTTTATTTAGCTGTATTTCTAGTTTTGTATGT
AGGTACAAAGCATCTCCGGTTTGATCTCTTTCCTTAAACAGTCAACCTTT
TGTGTGCGATAATTTGTGATAAGTATATATGCATCTCAGCATACTATTTG
TCTGCTTGGCTTGATAAAATGACTGCAAGCTATTTGAATGAATATATGAA
AAGCCAAGATATGCCTCATCTCTTGAACTCCGATGTAAGGATGTAGTGAT
TATATGGAGGGCAATCAAGCTGAACTATGTTATTTTAGCGGCAAAAGCTT
TATCATCGTTGAAATTTTATGAAGAAAATGATGGGAAAGGGGCTAAAACA
AAGGGAAATTTTCATGTGTTGTTAATTAATTTAAGACTGTAGATGTAGTG
TAGAGAAACTTGATACATATAATTCTTATATTTAGGGTCTAGTTATTTAG
AAAGTTATAGAGGATTATATTTTCTATATAAGATAAGCACAAGAGGGTAA
TTTGGTTGTTAGTACTGCCGTAGAAACAATAGATTCTGTAAGATCTATTA
AGAATTTAAGACGACGATAACTGTCTGATCATATGACTAAGCAAGAAAAA
CATACTGTTAGTAAAAGTGCGAAGTAATATTCCTTATTATTTATACTAAT
AGAGTACTAATTTCAAATATTAAGACAAAATAATTTAACCTATTAATAAC
ACAAAAATAAACTTAACTTATTTTTTGCACAACTATCTTCAAAATGTTAG
AACTAAAATAAATAAAGGTTGAACATTCTAAACACAAAAATGTCTGTAAA
CATGTCAACAACCAATACCATTAATCAATTCTATGTATAAAATACGAAGT
ATGGCAGAATTTTCTTAATTCCAATTGAGTAGGCGTGTTGTGATGATTCT
TTTCAGTAATATATACTGAGGCCTAAAGAATGGAATTAAATGCCTCCCCA
TTGTTTCTCTTTCTCTATAAATGAGCCCACTTGGGGTACTTGGTAGTGAT
TGGGATATAATTTATTGAGCAGAGCTGCGTACTTTGGAGTGATTTTGATA
CTGTCCATGTCAGAGGTCTAATTATCGTCGGGTCCTTGTCAACCTTGTCA
AGAGTCAACAAGGCAGACCGATACCCTATTGTTCGCCACCTTGGTCATAT
TCGCCTTCATATAAATTTGTTTACTGTATATATATGGTATACCTGATATT
TGCTATATCCGTACCATAAAATTAATAAATAAATTTGTGAATGGTTTTTG
CAGACAAACATGAGTGTCAGGGAGAAGATCTTGGTGTTGCTGGACTCTTG
GCAACAAGCATTTGGTGGAGCTGGAGGAAGATATCCTCAATATTACTGGG
CATACGAAGAACTAAGGGTTGGTGAATTTATGTGTGATTACAGTTAATTG
CATGGTTGACACTTATTTTTTGCTGGGAAACTCTGAATTCTAACTCTAAA
ACTATCAAACACTTTAGTTCAGTCTAATATAAGTTTGGTCAATCATGAGA
GATAGTAAGTTGTAAACTTACGAAAAGCTCTGGAATGGATCCTGTATTGC
AATTGCTAATATCTCTCCTAAAACCCTATATCTGATTTGTATTATGTATG
TCAGAGTTCTCTTGTGCTAAAGGGTGAACCACTGTGAGCCCAGTTTCTGA
TCTACATATCAACACAAGTGTCCAAATTAAGTCTATGGAAATAATTTGGT
CTTTGCTGTCTTGCTAGATCCAACTTGAGTAAATTTGGCATCTACACTAT
TATAAATGAAGTGTTAGAATTTGAGCCTAACACATGTGAAGTATTCTTAA
CAGTTAATATCTAGATGCATGATTTCCATGTTTTGTGTTAAAGAGAGAAC
TACTGAAAATGACAGTTTTTGTGGAAATCTCCTTTTGACATGAGGAATTT
GGCAAGTCATTAAATGGATCTTATATCTTTTTTAACTTTTCCCTCGCTCT
CGGGACTGAAGAGTATGTCATTAGGAGCCCATAAGCATAAACTTAGTTTT
CAAGTTGCATTTTTTAGATTATTGGGGGTAAGGGGACTTGAACTTGCGAC
CACTCAGTATGCGGAGCCCCATTACCATGTTAGGTGACCAACTAAAAATT
TAATTCCGGTACTAAAGTTAATATATAGTCCAGCTTCTAGTTTTATACTC
CTCTTGACACCAATTATGACCACTCTCTACTCTCAATTATCACTCTTTCA
GTTCTTTTCCCATAGAATGAAGCATCTTCCATATGGTTTAAATAAAATTA
ATTTCCTTACTGATTTGTTAGTAACAAGGCAGTCTGAAGAATTTATTTCC
ATCTGTTTTAGCCAAAAGGTATATACAGAGGATGTTCCATATGATGACTA
ATTTTGTATGTGTTAATTGTGGCAGCGTGGTGGTGTTGAATTTCCCCAAC
GTGCATCTGATTCAGCCCTGATTTTTACGCCTCCTGTAACACATTCAACA
GTTGGACATGCACATGCAGGTTATGGGATGCCAAGCAATTCTTCAACAAG
GCTTGATGAAGCTATGGCATCTGAAATAGAAACTTTAAGGTAACTATTAA
CTCATTATACATGTTGCGAATACTCCGCTGTGCTATACCCCACTTTCTAA
TTTTGTTTTAAACACTATACCCTACCTCTTTCTAATTTTGTTTTTTTTAA
CTTAAGTTTGTCAAGCATAAATTCAATGCAAGAAGTTCTGGATCTTTTAT
CTGCCATGCTGCAGGCTGTGGATCCAAATGACCGCATGGTATGTACAGCA
TACTTTCCGTTTACTTACGTTTTTAGGTTGCTTAATATTATCTCTCTATT
TGCTTATAGGCCATAAAGGATGAAGTGATTGTTGATCTAGTTGAGCGGTG
CCGTTCCAATCATAAGAAGTTAATGCAGATGTTGACTACTACTAGGCAAG
TTCCTATCGTTATATTATCTGTTGTTTGATATTCCAACTCGTTTCTGGCC
CTTTATTTGTTCATCTTTATTACACCATGGAAGCTGGAAAAGGCTTTCTA
GTTCTCAATTACAATTAAAATGTTTAAATGCTGCTCTTACTTGACACAAT
TATATCTGAATAAATTTATTTTGGTACTGGCAGTGACGAAGAACTTCTAG
CCAAAGGACTGGAATTAAATGATTGCATACAAAATGAGCTTGCTAAACAT
GATGCCATAGCTGCTGGGCTCCCGTTGCCAGCTCAAGTGATGAGCCCTAA
ACCTCAGTTAACCGAAGTACCTAGTTCCAGCCTCAAAGTCGACGACGGTA
AAAAATTTAGCTCTTCTCCACCTGCTGCACCCTCTGCACCTTCAACTGTG
GTGATAAATGCTGCTGCTGAAGAAGAGGAAGAAGAAGATGAATTTGCGCA
ATTAGCTAGAAGGTTAGTCTAACACGTTTCACAATCATACAATGCAGTGC
AATGAAATGTGTACCACTTGGATCTTTATCATAAAATTCTTTTCTTATAC
TTCGTCTAAACTTTACATGTCATTGTTCTCTAGTAACAGATGAAAGCATA
TTTATATGCATGACACGAACATGTATATATGAATAACTATTGATTAGAAA
ACATACAGAATAGTTACAGTAATTTTAAACAGACAAATATGCAAAGCTTT
TGTTTTAGTATCATGTATGAAATATACAGAATAGTTTGATGATTATATGT
TTTATTACTTCAGGCATTCTAAAACTCAGTCAGCCACATCACAAAGCACA
TTTGCTGGAGCTAGTGAAACTGAACCTTCATTGAGCAATGCATTGGTTGT
ATCTGATCCTCCTGTTCCTGTAAAGACCACAAAGGAGCAAGACATGATTG
ACTTTTTGAGCCTCGCCTTGTCAACTACTGACACTCCTCCTCCCGCTCCG
GATTCATCTACTACGCAAAACATGCAGCAAGCACCTGTTTCACCTAATGG
CCAAGGAAGCCCCTATGCCCCGCAAACATATACTGGGAACCAGGGGAAGG
TAGCCTTTAGCAGTTATGTTGCTCCATGGGCTCAGCCCCAGCCTCAGATT
CAGCAACAAGCACAGCTCCATCAACAGCCTCTACCTCAGCAGCAACCACC
ATCTCAGGCTCAGGGTCAACCCAGGCAAGCACAATATCAACCACAAGTTC
AGTCTCCCCAGTTTTCTTCTGGCTATCCAACTGGTCAAACTCAACAACCT
CAATTTCAGTCTTCCCAGTTTTCTCCTGGCTATCCACTGGGTCAACCTCA
ATATCAAGCACAGGCTCAGTCTCCCCAGTTTTCTCCTGGCTATCCACCTG
GTCAAGGTCAACCTCAACAAGCACAGTATCAAACACATAGTCAACCTCAA
CAACCACAATACCAAACACATAGTCAACCTCAACAACCACAATACCAAAC
ACATGGTCAACCTCAACAACCACAATTTCAAACACAAAGGCAACCTCAAC
AAACCCAATTTCAAACACAAGGGAAACCACAACAACCACAAGCTCAATCT
TCCCAATATTCTTCTGCCTATCCTCCCCCACCATGGGCAGCAACTCCTGG
TTATTACACAAATCCAAGACAACAAGTAAATACGACAGCTTATAGGCCTA
TGCAAGGTGCTGGATCATTGCAACATGTAAACTCGGCTAATGGGTCAAAT
ATTGCTAGGGACGGACAATCGAGCTTGGGGCCAACAGGCAATGCTTCTGC
AGGAGGACAAAAAACCTTTGTTCCTACATACAGATTGTTTGAGGATCTAA
ATGTGCTTGGAAATGGAGATGGAAGGTCCAAGACAAACAACACATCCCCG
AGTTTATCAGGAACTACTCAAAGTATGGGAGGTGGATGGAAGTGATATGT
ATTATCCTCTTCCTACAGCAGCTATCTCGTTTGTTTGCAATGTGAACATC
GTCAATATGGTGTAACGATAGGTATTACCTTTTATTGTTTGCTTTTCAAC
ATCGGGTTGCAGCAACCCGATCTGGTAGATAAGAGTGGCCAACTTCCTGT
GTTTTTAGCTTAATATTTCGGAGGCATTGTTTTGTATGGTGACTTGGTTT
TATATAATTAGTATTCGCTGACGGAGAACTGTACAAATAGTATGACATTT
GATTGTGGGTGGAACTTGTACTTTGTTATATGTTGAAGATATTTCTATAA
CATTTTAATCCAGTCTCCATGCTTGGTTGTGGAAA