| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017371913.1, is a part of gene, LOC108203152. |
| The genetic_marker, MK011475 9_17878533, is located in gene, LOC108203152. |
| The genetic_marker, MK005110 K2554, is located in gene, LOC108203152. |
| The mRNA, XM_017371914.1, is a part of gene, LOC108203152. |
| The mRNA, XM_017371915.1, is a part of gene, LOC108203152. |
| The mRNA, XM_017371916.1, is a part of gene, LOC108203152. |
| 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_017371913.1 | XM_017371913.1 | mRNA | DCARv2_Chr9:17872243..17879198 |
| XM_017371914.1 | XM_017371914.1 | mRNA | DCARv2_Chr9:17872243..17879198 |
| XM_017371915.1 | XM_017371915.1 | mRNA | DCARv2_Chr9:17872243..17879198 |
| XM_017371916.1 | XM_017371916.1 | mRNA | DCARv2_Chr9:17872243..17879198 |
AAACGATATATTTTTGATCTCGCAGCACCCAAAACCCTAAGATTACAATT
TACAACCCAGTAGAACAATAAGCTGCAAAACCCTCCCTTTCTCCCAAAAC
ACACACACACACACACACTTGCCGTAGACTCGAGATGTTGAGAAGACAAG
TGAGTTCACTCATCTCAATCTGCAAACAAAATGGATCCACGTATCTCCAG
AAGCCCATTGTCTCAACAAGTATGATTCCCCAACACCCACTTCAATTCTC
GAAATGGGGAAACTCAAAGATTGGATTTTTAGGCACAAGGGCATATAGTC
TGCTGAGTTTGAATGATTTGAGGGATAATAAAGGTGCAAGAAAACCAAAG
ACTAGAAAGGGTCGTGGGATTGGGTCTGGCAAGGGCAAAACTGCAGGTAG
AGGTCATAAGGGTCAGAAAGCTAGGGGGACTCATAAGTTTGGCTTTGAAG
GTGGTCAGACTCCGCTTCGTCGCAGACTCCCCAAAAGGGGATTTCATAAC
CCCTTTAGCCTCACTTTTCAGGTATCTTGTCATCTCTCTCATTCGAATGT
TACAATTTAATATAGTAATAATAATCCTGTGATATGCGAACAATGCTTGC
AAAGATACGACATAACAAATACACAATGGAATCAACTAATCAAGCCAATC
ACTGGATTGACATGGTCAAGAAATAGACATAATGATATAGCAATGACATT
TTAACTGACACTTCAGAGAAAAGCTAGTTGAACTCAAACATAAAAATTTA
AGCACAAAATGAGGCCTTGCATTTAGAAACTTTGAAAAGTTTGGTAACTA
CATTTCTGCATTGTATCTTTAATGTGAGCCGTGATGAATCTAATTGCTTC
TCGAATCTCTAAAGATCGCTTGGAAACTCCAAAGCTATGTTCAGAGGTTT
GTCTGATCTTCCTTTCTCCAGTAAAAGTATAGAGTGTGTTCTTAAATTTA
TGGTCTAACTACAATCATTAAGCCTCTTTTAGCCTTTACCGTTACTTCTA
GAGTTTCTTTTTTAGTCCTGTAGCCTGAAAGAGATTCTTTAATGATTCTT
CCTTGGTGCTTGTGTAAACTTGTGCTTATCCTAGAATGAAAGATATTATA
GTATCATGATGTTTGGGTCACTTTTTGTGGGATGTTAAAACTTGACTAGT
GTTGCATGATATTCTTGTATGTTTCTGTGTACTTTGACCATTAGTTTTAA
TATTCATCTTTCTTTGTGTCGTATGAATTGCTATGATCACGGCAGCCTGT
GGGGTTAGGAAAGATTGCAAAGCTAATAAATGCAGGGAGGATAGACTCTT
CAGAATTAATCACCATGAAAACTCTCAAGGTAATTGCGATTTTTTCTATG
ATTTCTAGGTTCAGATTTGTACTAGTGTTGCCTTGGCTGACAGTCAGATA
GTGGGCGCCATAATATTGTAGGAAGCTGGTGCAATTGGAAAGCAAATACG
TGATGGGGTTAGGTTGATGGGACGAGGTGCTGAACATATCGAGTGGCCTA
TTCATCTTGAGGTGATTTTTAATTAATACTTCTTACAGATCCCTTTTGTG
GCAGCAACAATATATTCTTCTTCTTCTTCTTCTTCTTTTGGTGCTGAACA
TATCGAGTGGCCTATACTTATATTTATGTTTATTCTCTCTTTATTTCCTT
TCTCTTACTGTAGTAAGTATGGTTTGTTACTTCGTTTTACTTATTCTTTT
GGTGTTGCATTTATATATTTTGGTCACTCTCCTGAGTACACTGTTCTGAA
TACAAACTAGGTGTATGCAAAAGAAATCCAGAAAAATGAAAAGTGCTCAG
GGAAAACTAAAACTGAGAGAAACAGAAACAAAAGGTTTAGTTACAGTTTA
GGTCATATCCATACTAGAAAGGTTCGAAACTATGCTTTTGCTTATGTATA
GTCATGGCTAAATGTGTTCTCCTTTATTGTATCTTGTATTATTTGTAGAG
TGGAGGGAGTAGGTACAGTCAAAATCTTTAGAAGCAACAAAGTGAATGAA
ATTTAACCATTAGGAACACAAACAAATTAGTTTAGCTATAGAATAGTTAT
AGAAGTACCCTTAACTGCATACTTAGCCCAAACCACATCGAAATTAGCTT
TTGTACTTCGCTTGAAATAGTTGAAGTGCCTTCTATAAAGCAGAGAAACC
AGACAACACTTATTTGCCAAGGGAAGGCACAAAACAGATTTGAAGAGCAG
TCTTGACCAATTTTGACATAAATATCACTTTGGCTGTCATTTATTTATTT
AAGATTATTAACAGAATCCCTAGGAGGTTAATGACTTTATTCTACTGGCC
TTGGCAACATGATAATGCTATTGAGAATATTTTCACATCATTGATCGTGA
ATTTTCCATGAGGCAATTGTTCGGCTCTTCCTCTACCAAATTTAAACAAT
CACTTAATCTGGTATAAACAATAAAATTTACAAGTTAATTACGACAACTG
ACTCCATTTAATTTCAAAAGCTTCATCCATGCTCTTACCTATCATTCTAC
TCTGTTTTATCAACATCTTAGCATTGCCTTCCTTGAAAGTTAAAAGTAAT
GTTTATGCGTATTGAAGGTATGAAGGTTCATAGAGGTGACTTTAGGGAAT
TTCTTGAAGTCATTGTAACTAAAGTAACCTTTTTTATGATTTTTGTGCTA
AATAAAAATTATATTAGAATTAAGGAATGTACAAGATAGAATGTGCAACC
CTTCAATGTTGAATACATCAATGCAACACAGTAAATCTAACACTAGATTC
TAAGTATCAGTAACAGAGTTAACTGTACTACAAACTAAGTCAATAAGCAA
AAAAGAGGGGGTTCCCCTTGAGCTGCCCTTTGAAATCTTGGACAGGATAA
CACTCTCACTCGCACAAGGACTGCACTTTTCTTAATCACTGCTGCACTGT
TGCTAACTCCAGGGTTGTGAATACGTCTGTTTCTTTCAGCCCAAAGACAA
TTAACAATTACTCCTAAGCAGTGTTGTGAAAAGCGCGCCTAGGCGAGCGC
CTAGGCGCAAAGCGAAGCAAAGCGCACCCTTAGCGCCTCATATATGTCGA
GGCGAAGGAACTTAAATGAAGCGCACGCTTTTAGCCTTGTAGCACAAAGC
GCGCTTAAGCACGAAGCGGTAGAAAAGCGCGCTTTAGCGAAGCTAAGCGC
ATAGTAAGATATTTAATGTTATTGGGCCACTTTTAAGGCCCAAAAGTACT
AACCCATAACAAAAAAAAGAATTTTGGGTCACTTTTAAGGCCCAAAAGTA
CCAACCCATAACAAAAAAAAAGAATTTTAGGCCCAAATAAAAAGTACTAG
CCTGGAATTCTGCCTATGAAACATAAATTTTGAATTTTAATATTTAATTT
TAGGATTGTTTTTCCCTCTAAAAGTATTATTTAATATATTATAAAGGATA
CATTAAGTTATTTTTGGCTTAAAGTGTGATTTAATATATTATGAAGTATA
AATTATGTTATGAACCTATATACATATATCCTAAATAATAAATAAAAAAA
ATTGTAAAACATGCGCCTAGCTTCAAAGAAGCGCGCGCCTCGCTTTTGCG
CTTTGCGCCTAGGCTCCAGAGAGTTTTGCGCCTCGATGCGCTTAATGCTT
TCGATAACACTGCTCCTAAGTAAAGAAAATTAATCTGGCTCTCGAGTGAG
TGAACTGCACTAAATGTGTGCGCAGTCCAGTTGTGAGAAATATCAATAGA
GCATCTTTGCGAAATGTCCAGGGTGAATGTACAGTCCATGAGAAAATGAT
TTGGAGTTAGAGTGTTGTTGGCGCGTAATAGGTGGGTCTGGCCTGTTTGC
ATTTAAAAAATTAACATTCTGTCTTCCATCAACAACCTCTTTTTTAATGG
TAACCAAAAGGTGAAGGAGCACCAGGGTATAGGCATAATATGCCAGACCC
AGGAGTGCCAATGCACCTGTGGCCTGGTTACGAATGGTGTTCCATATCAG
ACTAGTCGAGGACTATTGACCTGAGATTTGTCATGTTAAAAGTCCACTCA
CCATTACATATAATGGAGCTGACTTTGGCCTGGAAGTAGGATTTCATAAT
GGAGATAATTGAATAATGAAATCTGTCTAGAAAGGGAGTCTTAGAAGCCC
AAGGATCATGCCGAAGCAGGGTCTGGTTCCCAGAGCAGACCCGAGCAAAG
ATGCGCCTCAGAGCCAGAGGTCTGTGACGTCTGTCGTTGAATATTTTTCT
AATTTCCAGGAACATTTTCTTGGTTTGTTCCTAGTCCAAAATTTCTTTCA
CCTGAGCACTGTTTCCATATTGAGCTTTGCTTATTCGTGACAATATGCAC
TAGATGCTTTAACATAGCTGCCAGATGTCACTCAAAATTTTTTAAATGCC
AAGTCCTAATTTAGGCAAGCAACACTCAACCCAAGAGACTTTATAATGAC
ATTTCCCAACTTCCCCTCCCAAGGAATTTTTCAAGAACAGATTGGGTAGA
TTTAAGCATATACCTACAGGCATAAATAAATTGTCTATCCAGTACATGAT
GCTACCATATAACACTGCTTTTCTTAATCAGTTGGAGATGACCTGCAAAA
TTCAAGTAATTGCTAGTCCAGGTTCAAATTTGGTCGCATATTCTTGCTAC
TAAAGGACTACAGTCTTGTCTGGTTAACTTGGTGGGGAAAAGAGGTCACC
CAAGTATCTTGTAGGCAATTCACCCCAGCTGATTTTCGTAGTGGCAAGAA
TTTGCTGGATTTGGTCCAACGGCATGCTACTAAAGAAGCAGGTGCATTTA
TTTGGTTTTGGACAAAGTCCAGAAATCTTGGAGAAATGATCAACTCCATT
CATTATAGCTAGTACAAAATCGACATCTCCATAAGAGAACAGCAGAATAT
CATCTGCAAACACCAAGGGGGTTAAATTAATGGCAGCTGCTCTTGTATAG
AATTTGAACTCAGGCCTCACCGAAGCTTTTTGCAGCATTGAATTAAGAAC
TTAATGGCAGCTGCTCTTGTATAGAATTTGAACTCAGGCCTCACCGAAGC
TTTTTGCAGCATTGAATTAAGAACTTCCATGGCTAACCAAATAGCTTGGG
CAAGAGGGGCCCGTCCTGTTGAAGCCCAGATCTGCCTTGAAATTAACCCT
CAAGCGAGAACATTGGTGTCCTGAAGCACTTTTTTAACCAGATTAGAGAA
CTGAACATAACATCGAGGGATCCCTTCTTTTTTGCTAGCTCCGTTGCGCT
TGGCTGGACATAGCATGAATCTGATGAATCTTGTTGGTACTTGCCATAAA
TATTTATAATTTTTTGCATATACTACCTCTCTTTGATGAAATTCACGCTT
TGCTTCGTGCTTAAACTACCTCATTTCGGTCGCTAACGTTTTAAACCCGA
TTGACTTTGTTGGTCTCTGTATCGTCCATTTCAACTCTTATGAGCTTTTT
CTCGTCAAATTTGTAACAATTAGATAGCATTTTTGTGCTAATTAATACTC
CCTCCGTCCTACTCATTTTAAGGTGTATATAAAATATATTTTCATAACTT
ATATTTGGAAAACTTCCATTCTTGAAGAAAAATTTAAACTTTATATTTAT
ATTCAGAAGGATTTTTTTTTTGAAACTATATTTTATAGATTTCTTGAAAT
GCGTGTCAAGCTCCCCATCCCAAATGTAAAGAACCTGAAGGGACAGGGGG
AGTAGGTTGTTTTATAACTTGTTACTCGAATGAGTAATTTTGCGTTTAAC
TCTGATTAGCATTCCCTCATCTATTAATATTGTATAACAGTTTCGTTAGC
ATTTTATGCTAATTAATATGTAGTTTTATCTCTAAACTACTGCTGTAAAA
AAAGTTTTCCTTATTACTCTAGTGAGTACTTTGCATATTTCTAATTCGTT
AGTAGTAAGTTAGTAACAAGTTTTTACTACTAACTAATTAGTCTTTGTTT
GTGTGTGTAAACAATAATCATATGCGATTAATGCTTTATGGTTGGACCCC
CCTGTATAATGGTAAGTCCATCAGATGTTTATTTTGTTACTTAGCTTGTT
AAAGTCTTTATATAGCATTAGCATTACTCAAAACAGAAATTAAAACTGTA
TGCGGTAAACCTAAATTGAATAGTTGTCGTGTTGATATCTTTTCTCATGG
TTAGTAATTGAATATGTCAGTTTTGCAGTAAACTAGTGAGATCAGATAAA
GTTTGTTTAAAAAGCTTACTTTCGGAACAAAGCATGTAAAGTTTTACTAA
TGACATAAAATTTCTGAATTATACTGTTGCAGGTTAGTAGAGTGACAGTA
AGGGCAAAGGCAGCTGTTGAAGCAGCAGGTGGATCTGTGAGGAGAGTTTA
TTACAACAAATTAGGTTTCCGGGCTCTCCTTAAGCCGGAGTGGTTTGAAA
AGAAGGGAAGATTGCTTCCAAGAGCAGCAAGACCTCCACCTAAGCAGGCA
GATAAAGTGGATAGCATAGGACGTCTTCCTGCCCCAACAAAGCCAATTCC
TTTTACAGCCGAGGAGAAAGAGGCAATGTCCTCCCCAGCCATTTAAGGTT
TTTTTCTTTTTGCTATTCTTGGATAAGTTATGAAACAACAGGTAATGTCT
TTTTTGTTATTGCCATCTCTCTTCAGACATAAAATTGACAAGGGAGGATT
TGATGGATTTTTCTCTTTCCTGATCGTGTTCAGAAGGAAATCTCAATATC
ACGTATGGCCTAAAGGTTCAAGGCTGTGAAATCATGCTCCCTTCTGCTTA
TTTGTAGATTCTTGTACAAGCAAGTCTCCTAATCAGTTTCCATGTTGCAC
AGCTTTGAGCTTTGCAACATGATCTTGGTTATTAGTGCGGGTTTAGAATA
AAGTGGTGGTTTGATTATGCCATTAGTGAAAAACAACTTGCTTAGTGCTT
TAATGAAATGAAATAGCATGAGTGCTTTAGGTTATTCGAATTATGAATGG
ATTATGTTATTGCAGAGTTGAGGCAAGTTCACACATGATTTGCCTAATTA
GATTA