| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017374420.1, is a part of gene, LOC108204800. |
| The genetic_marker, MK005514 K2958, is located in gene, LOC108204800. |
| The genetic_marker, MK016764 1_36161337, is located in gene, LOC108204800. |
| The genetic_marker, MK010711 1_36161359, is located in gene, LOC108204800. |
| The genetic_marker, MK016735 SSR0425, is located in gene, LOC108204800. |
| 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_017374420.1 | XM_017374420.1 | mRNA | DCARv2_Chr1:36159889..36168518 |
TCGGCTTAGCGGTGCCATAGCATTTGGAAAACAAGCAGAGTCTTGGAATA
GTTGGAAGTTGAATGGAGATCTGAACACTGAATTGAATTGAGAATGGCAG
ATTCCCAACACTCGGCCAGATCTTCGACGGTAACAGTTAATGACGGAGAT
GATGAAGTTTCCGGTGGCTTTCTCCCTCTCGCCTCCGGTCCTCAGCAACC
TTATGTCTCCGAACTCCTCTCTTTCACTCTCGATCGCCTCCACAAGGTCA
ATTACTCCCCCTCCCCATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
TCTCCCTCTCCCTCTCCCTCTCTCTCTCTCTCACCCGTTTTCGACAGCAC
ATATGTAAATTTAATATGTGTTTTGGTGATGTGATTGAATAACCGATTAT
TCCAAAATGAGCATGAGCTTCTAGTAGTGACTACTTAGACAATACCAATT
ATATTATGTATGTCTTAGTATGTGTTTCTATACCGATGTGATGGAATTTG
TAATGTCTTGTGTGTGTTAATAATGTGTGGCTCGATTGATGTGATCAAGT
AAATGATGTAAATGTGAGCTGGAGCCACTGACGGTGTCTTGTATATTTCT
TTGTTGATATGTGCTTCTATATTGATGTCTTTAAATTGAATAGGAGCCGG
AGCTTTTACGAGTAGATGCCGAGAGAATTGAGAAGCAGATGCAGGAGGTA
GCTGTTAGTAATTACCGCGCTTTTATTTCTGCTGCCGATGCATTGCTTGC
TGTTCGTCAAGAAGTTTCTTCCATTGACAAACATCTCACTTCTATGGTAG
TACTCTCAGCTCTTTTACTATATATTGGCTATATAATTTGTTTTTCTAAC
TGGATTGTAATTTCCACTAATTTTCATGTGATTCATGACTTCAGTGTTTG
ATCTAAACTTGTTACCTTTTGTGAACTATTTGGAAACTATATGCAGTGAT
GATGTAACTTTTGGCTTGTATTTGTAGCAACTGATTAGGGAGGAAACTGT
TTTCTTACCATGCAATTAAAATCTAAATAATTGAAACGAAATTTTTACTT
GAGAATATGTTTTGAAACTTCAAAGCAGAGCCTAAAGCATTCCTATTACA
GTGAACACGTCCAATTTTATCTTCAGTGCATCGACATGATTCCATATTTC
CATCTTTCGTTTCTTTAGTGTTGGTCATTCTAGTGATATAATGCTCTATT
GGTCTACGATATTTTAATTTGCACTTACATATATTTTCATTATGCAGATT
GCCGAGATCCCCAAGCTAACATCAGGCTGCACAGAGTTCATCGACTCGGC
AGAACAGATTTTAGAGAAGCGGAAGTTGAACCAAACTTTGCTATCTAATC
ATAGTACTTTGCTTGACTTGCTTGAAATTCCTCAGCTTATGGACACGTAT
GTGTTATTAATTTCCTAACAATCGCATGCAAATGTTAATTAATGCGGAAA
ATTTATATTGTGGGTTTATTGTTTAATCTTCTATCATTTACGCAATGATT
AGTAGGATAAAAGTTATCTGCCTTAAACAAATGGCCAGTACTTCACTGCT
TATATTCTTCTCTACTGTTTCATATTATGGCAACACAATCATTCTGGTCT
AGGTCTTCTAAAGAAGTCTTTTTCAACTTCTCATATATCTATAATTTTCA
AGTTCCCCTGGAGTTATTGTAGCAACTGCTGTCATTGCTTAGAGACATAC
ATCTTCTTACATTGATGTAGGTGTGTGAGAAACGGAAACTATGATGAAGC
TCTTGATCTTGAGACTTTTGTTGGCAAGCTTTCAACAATGCACCCAAAGT
AAGTTCATGTTTCTTCTTATTTTGGTTGCATCTCTTTCTTTTTTACAAAT
CTTTCTAACTGTCTTCTGATTATGCTCCAATATATTTATTTATATTGTGT
CTTTGCCGTAATAAGGTTGCCTGTTATTCAAGCACTTGCTGCAGAAGTTA
AGCACACCACCCAATCTCTACTTACACAGCTTCTCCAGAAACTCAGATCA
AACATTCAGGTATGCTACACATAATACATACTTGGCGNGCTGGAAAGACT
GGGTTCAAAGTCCTTGACAAACCTGCATATTTTATCTTGTATTGCAGTTG
CCAGAATGTCTCCGCATAATTGGATATTTACGTCGAATAGGAGTATACAG
TGAATACGAAATGCGCTTACAGGTGGTTTTTTGTAAGTTAATCTTGATTT
GTATAAACTATTTGCAAGCGTAGAAGATCCATGTAGTTGCTTACCTTAAC
ACTTAAGATATTAAGAGAGGTGGTCATCCAGCATCATATCGCAGCTCAGG
CACACCGAGAGGTTTTAAGTTTGGGCCTGGTACCCCACAAATTAAAAAAA
AGTAATCTAGACACTATAATTAATTTCTGGCCAAAAGATGGGCTTCAAGC
GAGGTAGCGCAGTAAAACTATATAGTAACACCTGGTACTTAGCTTACGAA
ACTGCAGGTTCTAAATGCTTTTTATATTTGCTTATACATGTGGTTAGTGA
CAAATACTTTTTTCAGTTTTTAAGATGCAGAGAAGCATGGTTAACTGGAA
TTCTCGATGACTTGGACCAGAGGAATGCATATGAGTACTTAAAAGGGATG
GTCAATTGTCACAGAATGCATCTTTTTGATGTTGTAAACCAATATCGAGC
AATATTCGCTGATGATACATCGGGAAGTGAGGAGAACCATGATGGCGGCC
TTCTTTTTAGCTGGGCCACCCATCAAATTACCTCTCACCTTAAAATGCTC
AAGGTTATGCTTCCCAAAATAGCAGAAGGCGGGTCATTGTCAAATATCCT
GGACCAGTGCATGGTAAGAAAATTTTTCTGCGGTGAAGTAGTAATAGAAG
ATTCTTTTTTTAATATTTAATTGGACATATGTAAATATGATTGATTTCTT
AATTTGTGGTGCCTTCTTATGGAAGAGGCTTGCATACAAATATATCTGTT
TAGTTTAGTTTTAGTTCTAAAGTGATAGCCTGAGTCTAAAGAAGTTTCTT
ACATCCAATACTCATTAAATATATCACTGTGGTGAATAACTAAAACATTA
AAGGCTCAATTTGGCCTGCAAGCCTCAGTAGCAGAGAAATTTGAAGTGCA
ATCTCAGCTCGAATAAATATTCGAGTAGCTCGAACTCGAGCTCTCCTTGA
TTATTGTCGATCCGAATTTAAATATTTTACGAGCCGAACTCAAATAGCTC
ATGAACAGTTGACTCATTTACACCCCTAGGTCTTTTTACGTGAAACCTGC
TAAGTGGATGGAATAATGATTAATAGAGCATGGAATGTTGCTAGATGAAC
GTTTGACTTGCACAAAAAACGTTTATAAAATTTTCTTAAGTGTTAGATGC
TGTACTAGGATCTGGTAAATGATTGCCAAAGTTGTAAATGAATATTCTTG
TCTGATATTGTAGGTAAGCATTTCCCTGCCCCTTTCTTGTTACTGCTAGT
AGTCAGCTGACTCAGCTCCCTCTTAGATCTGTGTCGTGATGATGTTAATT
AATGTAATGTATACCTGAGGCTTTAAGTTATTTTGTATATATGTATTCTC
GCGGTGAAATCCAAAGACGGAATTTATGCTCTCTATTTTTGTTGTTGACA
GTATTGTGCCATGGGTCTTGGATGGGTTGGACTAGACTTCCGTGGCTTGC
TTCCACCACTTTTCGAAGAGTAAGTAAAATTTATCATTCTTGCTCTTCCA
TGCCAACACTTTTAAAACTTGTTGGTAATATCTGTTTGTTTTATGGGGTT
TTACAGAGCAGTCCTCAACTTATTTTCAAAGAACATGGGTACAGCTGTGG
AGAATTTTCAGGTATGCTACCATATAGTATTATTTTACACCTGTGTTATT
TGATCTTGAAATTCCTAAATTTTATTGTAAAACACTTATTTGACTTGATA
ATTTTTGGTAAAAAGCCATCTTTTTCTTTAATCCAGTCATCTTCTCTGAT
ATATAGTATGCAAATATGTTTATTTTCATGCAGTTAGTTTTAGACTCTCA
TCGCTGGGTACCGCTCCCAGCAGTTGGTTTCTCAGCCAATAGCTTTGGTG
ATGAAAACCAGGAAGACGTTACTCCTCCTCCAAATCTAATGGATCATCCA
CCTCTTGCTGTATTTGTAAATGGTAAGTTTTCATGAAGCTGGGAAATTTA
CGTGCTACTTCCATTTCTTTTAGTTCTAACAAAAATAGATAGGGGGTATA
AATAATGACTTTAGATTGTTTAGGTGTATATGTCAATTTTTTTAAGGACT
TCAATTGTTGTATAAGAATTAAATCGTTTACATATAGTTTAATAAGCAAC
ATGACAAATCCATCTACCTTTTGCGTCTGCCCCACCTTAATGTGAGTGCA
CTTGGTAATAGCAGTTCCTATCAGGAAATTTCACATCTTAGTAGGAGCTT
TTAAAGGGAACATAGAGATAAGGGAATGTTGATATTAATGAAATTGGAAC
ACTTGCCTCTTACTTATCTTTTCCTGTTCGAGTTTGCTTTCGCTCCTATT
TCATTTTAGAGAATGTGAAAGGGAGGTTCCAGCTATTTCTAGTCTGTTCC
CATTTGTACCTTCCTAGGGATTTTAACACCATTGGTCTCACTTTTGTTAT
TTCTATCTTAGATGTTTCATTCACCATAAAATCTGTTGTCCATTGACAGT
TTTATTGCTATCCTATTTGAACCAGTCTCAATTTCCGGGTTTTGTAGTTA
GTGGTAACTTTTAAAGGCACTTGCAAGGTTCGATCTGAATTAGCCGTCTT
CTACAAAGATCGGTGGAGATATTTGGCTGTTGTTTCCTTTATTCCATTTT
TGACTATGTTGGTAATGGCCTTCGATGAGAGCAAGGCTGAATGATGTCGA
GAGATAGACTGATGTGTAGATTCAATTTCCATGCACCGCACTTGTTTTTA
AAAAAGTCGTCTAATAATATAAACCTTTTTTATGTATTATTAAAATGCTT
TCGTAATTCCGATCAACAAAATTTGCTTAATTTTAATAAATACTCCCTCT
GTCTCAACTCTTGCCCAATTCTTTACATTGGGGTTGGGCACAGAGGTTAA
GAAAAATGTATAAAGTAGTGCGAAAAAGTAAGAAAAGTGGGTAAGTGGTG
GGTCCCATTAATATTTAATTAATAGACTGGGAGAGATTGATGAAAGTGTG
GGCGATATTAGCTTTTATATTATAAAAAAATATTATTTTTAGAAAGTTTT
GAAATGTAAAGAATTGAAATGGACATCTCAAAAAGGAAAGAGTAAAGAAA
TGGATGTGACGGAGGGAGTAATAAAATGAAACAAAATAACAAAATATATC
TTAAAAGTAGGTAATAGTTGTAGCTTACTGTTATTATGGAATTTGGCACT
AGAAGCTTTACACCTAGCGACAAACATCACATTGTAGCTTCTGTATACTG
GATAATAGTAGTCTTGACAAAGTACAATGCAACAGAGCATTTAAAAGGTC
CAAGGACGCTTGGTTGGACCAAGACAAGCAGTGTCCAAACCCAAGAAGTT
TCACAGTCCAACCAAGTGTAAGATTCTGGTTAATTAAAATTGTTTGTTCT
ATAACTTTTTTCTTTTTATGTTAATAGAATGTAGATCATTGCTAGGAGAT
CTAGAATGAAAATCAGTTACAGTTTTGACTGGAAAATTGAAGTAGTGTAT
TGGTGATGTGGCTTGTATTAAAACTTAAGATTAGTAATATTGTAATTCTG
AGTTCATTGCATGGTTACTTTCCTCAATCCATATTATGAATTTATTCTGG
TCCCCACTGTCAATAATACGAGTGTATGGGTTATTCAAGAAATCCATTTT
CAAATTTTGATGAACAAACGAAGTTCCAAAGGCTAGTAATAGTATGCCTT
CAATGGCAGTCAAAACTGTTAATAATAGTTAGTTTCCTACAGGGGATATT
GACTATTTTGCTATAGTCTCATACACTTTCAAACTTGACACAGGAGGAGG
CCAGTTGCAACTTTAAAAAGGTAAAAAGCAGATGAAGAGGAAGTCAAATA
ACGACTCTAAATTTTTTTTAAGAAGGAAAGCAAGTAAAAATTTATATGCT
TTCCTCCCAAACTTAATCGAACAATGGGATGAGAGGATAGCAAGTAGGAG
AGGTAAATTAAAAATGACGTGATAGTACCAGTATACCCCTTGCTACTACA
TTCTCACTTTTTAAAAGGAAGGATAATATCGTTCTCTGATGTTAAGTGAC
CAATTCATCGTATAGTATTTTAATATTTCACCTTCACTCAAAAGCCCATT
TTTGGGTCGAGAATGGATCACGGGCGCCCATCTTTGTGGCATAACTTTGC
CTTTGTGTCCGTAATTAAATATGAGAATATTGGGGGTCGCAGGTAGTTTG
AACCCAATTCCCTAGCGAACCTAAGCTCTGATACCATGTTAAGTGACCAG
TTCTCTCAAAACCTCAAGGTTTTGGGATGGCTTACCATGATCATATTGTA
TTCTAACATCTAACAATTAGTTATATGCTTTCCTTCCAACTAGGAAGCAC
AATAATGTAGGTAATTTCATTTCATATCCTATTTAAACTTGGTAGAAAAT
GAGTGAAATTCATTCCATTCATTTACATCTGTATATATTACTCTGTTTTC
TGCCCTTCATACACTCAGGAGCAGGCACTAGTCCTATAAAATGATTCAGT
TTCCTTCATCCTAGTAGGTTCTGCAATAAAGCTTATCTTGACTGATTTAG
CTTTGCAAGTTTTGCTAACCCTGGTATTAGGATGATAACTTAAAGATTTA
GTGAGGGTCGGGAAAGAAAATGATATATATGGGATTGAAGCGCGTAAAAA
AGGTGTGGTCTGTTGCCTGTTCGAGATGTAAACTAACTCAATTCTAGTGT
TTGTGTCAATTATGGGCTTTGCTTGCTTATCAGTGAGTGAGTCTTAATAA
TAGTACTATACCTCCCATATCTTTGTAGATATAAGAAGGGATCTTTTCTT
ATTTTGCCAACTAGAAGTTATGATCTACATTACTGACAAAAAGAAAACAC
GATAACATATTTTCTTTTGGCAGTCCAATCCTTATTATAAACCGTCTCTT
GCCTGCTTCGTTCTGTGAATGTTCCCTGCTGGATAAAACTGTAATGTATC
TGATCTTTATCATATAGTACTTCAGGTGATCTCTTGCTGCCTGAATGTAT
TTGGATTTTTTATTCTTTGGATTTTGTTTCTATGTGTTCTCTGTTTTTAC
TTTTAGACTTGCTTGTCTCCTTTGCAGCCTGTGTAACTAGTTCTTAGAGC
ATCTGTGACAGAGATAGCTGAACAAGTTGCCAACTATTGACAAGTCACTA
TTCACGCTTTTTTTATCATCTCTCATCCACATCACCATTGGGCCTTGGCG
ACTTTTGTTTGAAATTAAGTCCTGTTGGCAACCCCAAAAGTTGTCAATAT
GGTCCCATAACATGAGACAATACAAAAATAGTTCTACTTAAATATAATTT
TGGACAATTATATAGGTTTTTACTAGTTTATGAAGTTGCCATGGCAATCT
CTTGACAACCATACAACTCCATAGTTGGCAACCAAAGTTGTCATGCCACA
TTAGCATTGACAACCTCTTGGCAACCCCCCGGTGGAGATGCTTTTATAAG
ACGGCTTGGATTCTATATATTGTAGTCGCTTTTTGTTTTTCTTCTGTCTC
TGTAGATATTGGAGTGTTTTTTTTTGGCAGTATATTTATCTGGATGGCGG
ACTAATACTTTTTGTCCATTACCAAGGTTGTATAAAATCAGATTATGAAG
TGTTTATGAATGTATAATCTTTTCCTACGTCTCTCTTTGTTGTAGGTGTA
TCAGCAGCAATGAACGAATTACGTCCGTGTGCCCCAATACGTTTGAAGTA
TATAATTGCGCAAGAATTGATTAAGGGACTGCGTGCCGTTTCAGATTCTT
TGCTCAGGTACAATACTACTAGGATGCTGAGGGAGAATGAGTCTGTGCTT
TTCCTTTCTCTTTGCCGCTCATTCACTGAGGTAAGAACATACTACACACT
TAAAGTAATGTTGTTTTTATTGCTAGTTATACCTTATAATCTCCAAGATC
TCATGCAAACCTTTTTCTTACTGTGCAGGTTGCTTTTCCACATTGCGCTA
CATGCTTTGGTCGTTGTTATGTAGGTGGAGCTTCTCTTATCACAGATTCC
AAGGGTTTATTTGATGGAATTAACCGTCTTGTAGCAGCATCAATCTCTAG
AGACTTGCCTAAACCGGTCAATAACTCAGAGAATAAGAACACAACAGAAA
ATGGGGAAGCACCACCAGCTGAAAATGGGGTTATAGATAATGGAGGACAA
ACAGAAAGCCTCGGTGCAGTTGAAAAGGAGGAGCATGACACCAGTCCACA
AACTGAGGAGAAACCTGTCAATGATGATGCTACAAGAGCTTAAGTTGTAC
AAACCCGTGTAACTTAAAAAGAATCCTTGAATGTTGATCAATGTTATGTC
GAGAGGTATGTAAATGTATTCATAATTCATCGGAAGTATAAAGAATTTTG
TCAAGGGACAGGAGGGATTTGGAATTTTCCAGTCAAAAGTCTGAAATAGT
GGATTATACAGTGTAATCAACAATCTTGATGTATCGGTGTATGAGTTTAT
CAATGAAAAGAAACAATCAATTTGTTAAA