| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017366922.1, is a part of gene, LOC108199187. |
| The genetic_marker, MK018871 8_21356104, is located in gene, LOC108199187. |
| The genetic_marker, MK009815 8_21358264, is located in gene, LOC108199187. |
| The genetic_marker, MK010968 8_21358270, is located in gene, LOC108199187. |
| The genetic_marker, MK003317 K0761, is located in gene, LOC108199187. |
| The genetic_marker, MK007911 TP6304, is located in gene, LOC108199187. |
| 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_017366922.1 | XM_017366922.1 | mRNA | DCARv2_Chr8:21354992..21363478 |
CCTTGAAATAAAACCCTAACACAGTCCTGTAAGAACAATCACCTCTAACT
CCATCTCTACCGTCCATATTATCAATCCAACGGTCCAGATCTCTTCTCAG
ATCACGCTTATCAGTCTCTGTCCTGAGCTCACTCCTCTTTTTCACACACA
CTCGCACACTCTTAACTCTTTTCTCTATATAAAAATGTCATCTTCAGTCG
CCGATCATCGAGTATCCTCATCGCAAAATTAATGATATTACACACAAAAT
CAGCTGTATCTATATGTTTATGACACATTGTATCGATTCATGTATTTTGA
TCGGTGAACTAAGTGATTAAAGCTTAAAGTTTTGATTTTGATCGGTGAAT
TAAGTGATTTGAGGTTAAAGTTTTGATTTTGATCGGTGAATCAAGTGATT
TGAGGTTAAAGTTTCGATCTTTGATCGATTTCTGTTAAATTTGAGGTGTT
TGTGTTTGGGTTTAGGTGAAATGATTACGGATAGTTATTCGAAGATGATG
TCGGATATCGGAATGCGATCGATGATGCAGAATGAGGATTTAGGGTTTAT
GTTGAGGAATCAGGAGATTAGTGATAGGGAAAGNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNGGGAAAGAGATAGAGAGATAGATTTGAGTATG
TATCGAAGCGGTTCAGCTCCGCCGACGGTCGAAGGATCGTTGAATGCTGT
AGGTGGATTGTTGAGTGGTGGCGGCAGTGGTGTTAGTGAGGAGGAAATTA
GGTCTGATCCGGCTTACATTTCGTATTATTATGCGAATGTGAATATGAAC
CCTAGGTTGCCGCCGCCTTTGTTGTCGAAAGAGGATGGGAGGTTTGCGCA
GCGGATGCAGGGGGCTGGGAGTTCAGCTGCTATAGGTGATAGGAGGAAGA
TTGGGAGGGAGGATGGTGGTGATGGGAGTAGGTCGTTGTTTTCGGTGCAG
ATGGAGAAAGGACAGCAGCAAGGGAGTAATGGAGAGTGGAGTGGTGATGG
ACTTATCGGATTGCCTGGTTTGGGATTAGGTGGCCGGCAGAAGAGTATTG
CTGAACTTATTCAGGTGAATTTAGTTGGTAGTAATGAATTCTTTTATTTG
TGATTTGTTTCGTTATGTTTATTTATGTTATACACTGTTATCGATTTGTA
ACGTTGCTGATTGTTTGCGTGTTGGATTGAATTTATTACTAAGCAGTGTT
GATGTATTTTGGATCTGTCATACATTATGGTTTTGTTCTTCAGCAGGAAA
GTGTGGACTGTTAAGTTCATCTTCCTTTAAGTTATTACTTACACATATAA
CATATGTATATATTATTTTGATTGAGATTAAAAGGAATATTCTTTACTGC
TACTAATGTGATCTTTTCCTGATTTTCTTAAATAACCTGTTATAGATGTT
TTTGATTCAAATGTTCATCATTGATGGTTGATCTTGTTTATTTTAATTGT
TACTTGTTAGTTTGAATTTAATACTTAGCTTTGTTCATACTTTCGCTACA
TATTGAGTATATCAAATCCATGATATGTTATGTGCGAGTTTTGTTTGTGC
TTAGCGGAATAGTGTGGTTTTTTGAGTTCCTTTTCTCTCAATTACTACTT
ACTAGTTTCTTAATGTAACATTTTTTATGTAAAGGTATATTTGAGATTAA
AAAAAATTAATTTTCCATGACCGAGTTTTTACAAATTCAGTACTAAGACT
CTAACTGGTCGTACTACACAATTAATATATTACTATCTAATTATATTCAT
TGTCAGGTTGTGGATGTTGCATAGATTTTGGGGCCTATAGGGTGGCTGTT
TATATTGTTTTCTCCTATCCCTTTAGTTAAACATAAACTTTGAATCAGTT
GGGATGATTTAGTTAATCAGATATGGGACTAATTAAACTTCAGTCCAAAA
TTGTTTATCTGTTTTTGCTGTAGAAACCATGGATTGAATTATTGTTTCTT
GTAAATTCTGTTTGACAACTCCTCTTTCTACCACTCTCCATTTTTGTTAT
TTCATATTAAAAAGTTGTTTGTCATATGCTTTTATGGGATGCTTTACTTC
TCTTTTGTCTCTCCATAACATCTTTACTTTCACCACCCTTGAAATTAACA
TGCTCTTCCATTCACAAGTTTAAAATCACTACAGTTTGCATATTATTATA
TACTTGAGGTTCCTTTAATCAAGAGGTTAAATCTTCATGCAGGATGATAC
TACTCATCAGACATCTGCTTCGGGGCACCCTTCTCGTCCAACAAGCCGTA
ATGCTTTTGACAATGGTGTTGAACCTTCTGAATCTCACTTTGCACAGTTT
AAGCAGGACTTGGCTTCACTGGATGCTGTGCATGCTTCTGCAAACATTCA
AGGCCTGTCTTCTACTCAGAATGTTAATTCCTCGGTTTCACATACTTATG
CTGCTGCATTAGGTGCTTCCTTGTCAAGAAGTACGACTCCAGATCCGCAG
CTTTTAGCTAGAGCTCCTAGTCCTCGAATCCCTTCTGCTAGAGGAGGCAG
AAGCTCTCTGGATTTACAAAATGTTAATGGGTCAATTTCATTCAATGGTG
CATCTGGGCGTGTGAGTCAGCAAGCAGATCTGGTTGCTGCTTTGTCAGAA
ATAACTCTATCAAACAACCTTCTGGATGAAGAGAACCATGCCAGGTCTAG
AATTCAGCAAGAGATCGATGACCATCAAAATTTATTCCATCTGCAGGGTG
ATCAGTACAATAATAAACAACATCCATACTTAAACAGGTCCGAACCTGGG
CATTTGCAATCTATATCCCAGTCAGGCAAAGGATCTTATGGCTATGGGGT
AAGGGCGGAACTGAACAACTCTTCTTTATTATCTGATGTGCAAGTCAATC
TTCACAAGCCTTCGCTGGCATCTGCAAACTCTTACTTGAAAGGGCCATCC
ACACCAACACACAATAGTGGAGGAAGTTCACCTTCTCAATATCGTAATGT
TGGTAGTCCGAATTCATCATTTTTAAACTATGGTCTAAATGGGCACAACA
TCAATCCTGGATCGCCGTCCATGCTTGGAAATCAGTTTGCAAGTGGAAGT
TTGCCACCTTTGTTCGAAAATGTTGCAGCTGCTACAGCTATGGGGGACTC
CAGAAGAATGGGTGGCTTGGCCCTGGGGCCCAATTTAATAGCTGCGGCAG
CAGAGTTGCAGAACCTCAGCAGAGCTGGAAATCAAAATGCATTGAATGGT
CTTCAGGTTCCACTTGTAGACCCATTATATCTTCAGTACTTGCAATCAAA
TGAGTTTGCTGCTGGCGAGGGTTTGAATAATTACATGGATCTTGCTGGAA
TCCAGAAAGCCTACTTAGGGGGTGTCCTTTCACCCCCCAAATCACAATAT
GGTCTTCCTTACCTCGGAAGTCCATCCAGTCTGACTCATGGTTACTATGG
TAACCAAGCATATGGACTCGGAATGTCATATCCTGGCAGCCCATTAGGTG
GCTCCCTTCTACCAAACTCTCCCTTCGGACCAGGTAGTCCTATCAGACAT
GGCGACAGGAGCCTTCGCTTTCCCTCAGGAATAAGAAACTTTGGTGGGGG
TGTAATGGGACCGTGGCACCCCGAAGCTGGTGGTATGTTAGATGAAACTT
TTGCATCCTCTCTCCTGGATGAGTTCAAGAACAACAAGGCTAGGTGTTTT
GAGCTTTCGGAAATTGCCGGGCATGTTGTGGAATTCAGGTATATCTCATT
GTATGCTTTGAAGGTGATGCAATTGTATATATGTATATTTATGCTTTCTT
CAGAGGGTCATTGGTTCTTAAAATTGTCTGAGCAGTGCGGATCAGTATGG
GAGTCGCTTCATACAACAGAAACTTGAAACTGCCACAAGTGAGGAGAAGA
ACATGGTTTTTGATGAAATCACGCCACAAGCACTTTCACTGATGACTGAT
GTGTTTGGCAATTATGTCATTCAGAAGGTAACTTGCTTGCATAGTAATTT
GCAAGTATTTTTTTTCTTCGTTTAGTTAATTTTTTATGTTTCCTTAATAA
TGTACCTAAAACAATCATCATTAAGTTTCAGCCTTAGTTGCAATTTTCTC
CTTTTTTGATCTAGTTTTTCGAACATGGAACTGCAACACAAATAAGAGAA
CTGGCTGATCAACTCAATGGGCATGTTTTGAACCTCAGCCTTCAAATGTA
TGGTTGCCGAGTGATTCAGAAGGTAAATATACTTTGCAACGTAATCAACA
TTGGTCTAATATATGTTTCATTTTGGGACGTGGCTCTTGGGTTTCATATC
ATTATCTGCTAGCCTTTTTCATACACTAAATACAGCAGAATGCATAGGAA
TTCAGATACATAGCATATGGTGATAATCCTGAGAGGAATTTCATCCTCTC
TAATATTTAGTGGATTGGTTTTATGTATTTCATTGAAAATATTACAAAAC
TATATCTCAACTGCAGACTATATTATTTACTTGCTAAGCTTCTAAGATTT
ATGAGCTTAGTAGAAAGGGGTGACTTTTAATATACTTTTAGGAGGTCTTT
GCAGAAGGAAACTAACCAGTTAACTTCTATGTCAAAGATATGTAATCTAT
AAGCAGAGATATAACTATATCTACCACTTGCAATAGTTGGATTATCATCA
CTCATGTCGAAGGTTCTGAATACTGTTTTTTGTGAAAAATGTTCACTATG
CTTAAACTTTTGTTTTGGTTTTAATTTGTCAATAGTTTTTCTGCTATGTG
TGTAACCTTGCTGTATTTATCCAGGCCATTGAAGTTGTTGATCTGGACCA
GCAAACTAAAATGGTTGCAGAACTTGATGGCCACATCATGCGCTGTGTAC
GAGATCAGAATGGAAATCATGTTATTCAGAAATGTATTGAATGCATCCCT
GAAGATGCAATTCAGTTTATCATTTCTATATTTTATGATCAAGTGGTGAC
ATTGTCCACCCATCCTTATGGTTGCCGTGTAATACAGGTATTTAAGCAAA
ACTTATCATAGCCACCTTTTTCATCAACTTTGAAATGCTTGAAACATGCA
AATATGTGTATAAGTGTATTTGACTGTGTATATGTTTATTTTCATGTGAC
AGAGGGTTCTGGAGCATTGCAGTGACCCAAAAACTCAACAGGTAGTGATG
GACGAAATTATGCGGTCTGTCTGCATGCTGGCTCAAGATCAGTATGGAAA
TTACGTTGTTCAGGTTTGTAAGCTTTTCAATAAACATTCCTTTTTCTTTC
AGTTATTATTATTATTAATATATTTCTAAATGATATTGTAATCTTCGTAT
TTTAAATTTCAAATTGGCTATATGGAGTTCTTTTAAGAAAGAAAGTATGA
GTATGCAAATTCTTGTTCACTCTACTAGATGCTAGCATATTTAGTCAACT
TCTTCCAGCTCTTGTTTTTGTGGTGCATATGCAAACCACTCGAATTAGTT
TTATTGCTGCAAAATATGTACAGTAATATTTACAAAGCAGTATTCTACTA
CAATGATTCTATTGACTAAAAAGTACCGTAGTTAGTCTTATGTTCCTCCC
TTTACTTCTTGTGATTGCCCTTTAAACTAGGTATCTGGATTTGTGTTGTC
TGCACATTCTACTTTAGTATTTCGGTTGTTGGCAATGTTTTATTAGATTT
GTTTATCCATGGAACTTGCAGTATTTCCGTAGTTAGTCTTATGGAGCACC
TTTCCTTGTTGATGGTTTTCTATTTTGCAGCGTATGGTTAGTGATGTATA
TTTGTTTCTCAAAGTAGTGAGTCATAAGATTTCTTTGTCCCAAGTCACGT
ATGCTTCTGGTTCAATACTATACTGGCGTTTAGCAGCTTGATTGTTCATC
TTTGGCTGCTACGACATGCATGCAAGATATTACCACTGTATTGCATTGTT
TTTGTTTCAATTTGTTTGTCATAAAGCTGTGGTGCAACCTCGTCTGTATG
CTGACTAGTCTTTGTGATTCCCTTGGCAGCATGTGCTGGAGCATGGGAAG
CCTCATGAACGTACTTGTATAATTAATAAATTGATAGGCCAGATAGTTCA
GATGAGCCAGCAGAAATTTGCTTCCAATGTTGTGGAAAAGTGTTTGACTT
TTGGTACTCCAGAAGAGCGCCAATCCCTAGTTGACGAGATGCTGGGAACC
ACTGATGAAAATGAGCCTCTCCAGGTTCGATCAGTTTCTCATTTCACTTA
TATAGTTAAAGAAGCTCAATCTAAGACTCGTTTTTTAATCTAGTACACGT
AACATTCCTATTTCCTGGTGATCCTTTTCTACCTCTGGAATTTTCTTTGA
CTTGGAATAACATATCTACAGACTACAGTAATTGAGTTAATCTACCAGTT
TCTGAATTTTTTCGCATGTACTGTAAAGCATCTTTTTTGTGCTTCTGTTG
TCGTGGTATATTCCTGGTTTATTGTGTCATTGAACTTGATTTTGCAACAT
TTATAGAAATGTAGCGACATGCAATTAATTAAAGGAGTTTTTTTTTCGGG
ACAAACCAATCAACTAAAGGAGTTGCTCTGCATTTTTGTTCTTTTTACGT
CAGTGCGAGGCAATATTCTACCGGCTCACCAAGTGAAGTTTATAAAATTT
ATTGGAACCTGTATCACTCTAGCTGATGATTTATGTATAGTGCACTAGAG
AGAAGTTGGTTTTTTGTTGGGTCACTTGGATGCTCCTTTTTCACATGATG
TGCAAGTATATCTGTATGAAGTGTAAATTAATGGTGTTTACAATTTAAGG
AACACTATAAAAGTCATAGGTGTCCTGGAAACGACTGTAAAGTGTATTGT
TCGTATATTATGACATTTAGAATCAAGCTTATTCATAATTTCGTACTAGG
AACCCCAGTTTGGGGTTTGCACTGAGTGTCATGCTTTCCCTTATCACAAG
TCCATACAGGAGAAATAATTAATCACATTTACAGAACGAAAAGTGTATCA
TTTGTATATTATGACATTTAGAATTAAGCTTATTCATTCTAGGAAACCCA
GTTTGGAGTTTGCTAAACACCTTAGCACTGAGTGTCTTGCACTCGTGCTT
TCCCTTATCGCCAGTCCATACAGGAGCAATAAAATAATCCATCACATCTA
CAAACTAAAAATAAGGATGGCACTATTCTCTGAATCATATATACATAAAT
AACTACAGGTAATGTTTTTGTTTGAAGTAGAGCTATAGTATTGGCAAGCT
CTCTCATAGCTCCTGTTATATAATGACTTTAGTTATATATCTGAGATCTA
ATTATGTTTGCCATTTCTGACTTCAGGCAATGATGAAAGATCAGTTTGCA
AACTACGTTGTACAGAAAGTGCTGGAGACTTGTGATGACCAGCAGCTTGA
GCTTATACTTAACCGTATTAAGGTTCATCTTAATGCACTGAAAAAATATA
CATACGGAAAACATATAGTTGCGCGTGTAGAGAAACTCGTTGCTGCTGGA
GGTATTTTAAATATCCCTTGATCCTACTTTTACTTTTTATACGTTTTTCT
ATGAGTTGGTCTTAATGAGCTGAAATTATTCAACTTGTCATATATAACAA
AAATGTAAACTGTGCCTCGTATCTTGATCTTGTGTTAATAATTGCTTATA
ATCTGTATATACAGAATTGTATAATTTTACAAAGTTATGAAATTTGATAT
AATTATCTCCCACTTATTTACAATTTGTCATGCATAATGGTTGTATAACA
ATATTTTGATGGCTGAATTGTGAGTGGTTTATTGCATCATCAATAGAGTA
CAAAGAAATTTTTAGGGGTGATTATTATCCAGAATTTCTTGTTGTTGGTA
AACTTGAGTCGGTTATGTATTTTACCCTTTCATATCTACTGCAAGACTTT
TGACCCGTTTTAAAATTTAAAATCTTGCAGAAAGGAGAATTGGCGTGCTG
GCTTCATATTCTGCTGCTGCCGCCGCAGCCGCCGCAGCCGCTACCTAGCC
TACAAAGAAGCTGTACAGCTAACTTGGTTTAATATAATTGCCTTTCTAGT
CTATGTTTTCACGTTTAGCTGTGTATTGGCTCAATTTATCTGTTTATTAA
GATAAATAAGAGCCAGTTGCAAATAAAATCTGTTCTTTGTAAAATGTACA
TTGTTAGTTTTGAGGATATACCTAGAATCAGGGTGGCTTAGCTGAGGCTA
AGATGGTGAAACACACCCAATGCCCCTGCAGAGGAGATTTAAAAAAGGGT
CACTGTACACAGTGGTGTAAGAAAGTGGGAGAAAGATGTAGAAGTTTGTC
ATCGTGACTGTACAAATGTTGTTGGGTGCATAGCATAGCCTTTGATGTTT
AGAAGTGGCCAGAATTTTTCCTTAATATATGTATGAATTTGTTTAAGTTT
CCCTTAATTATAGAACCTTTTCCGGTTTTCCCTGAA