| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017389208.1, is a part of gene, LOC108216442. |
| The genetic_marker, MK001005 GSSR-006, is located in gene, LOC108216442. |
| The genetic_marker, MK018120 4_31059104, is located in gene, LOC108216442. |
| 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_017389208.1 | XM_017389208.1 | mRNA | DCARv2_Chr4:31055790..31059596 |
ATATTTTTTAAAGTTAATTAATTAGCAGTATTTTAGTTAAACAAACCAGA
AAAATATGTAAATGGCATCTGACTGTCAAATTGACGGCAAGCGCGTGAGC
CAGCAGGGCCACACGGCTACAACACCAATAAGCAGTTTAATTAAATCCGA
AAACGATGACAATTCAAATTGACGAAAATGCCCTTTTAATGTGGAAACTA
AAACGAGGGGCAGATTGGTAAGACAAGTCAACAAGGTCAGAAAATATGAC
CGTTGGAAAGGTTTCCAATAAGCGTAAGCGTTTCTCTTTATTAATGAAGC
CATGAAATCTCATCATATCTCCTCATAAATCATAATTAATAGATCCAGCT
CCCCCAAACTCTAGATTGTTGTTAAATCTTCTAAATCTGATAAACACAAC
AATGCAATTCACACTGTAAGTGTAACCCCCTTCACAGAGAGAGAGAGAGA
GATAAAGAGAGTGAGAGAGGGAGATTTCTTCAACATTCTCTATTATTCCC
TCTTCGAAGCTGAAATCAGTAATGGCGAAGAAGAATCAAGAAGAGATCGC
GAAAGAAACGGCACTGGTTTTGAAAGAGATTAATAATGATAATAAACAAA
ATCAAGATTCTACAGCAGATGCTGATGCTAATGCTGCTGATCCATCATCA
CAATCATCTACTTGTGCTGTATCGAACAATAATGAAGATGAGAATGATCA
TCATCCATACGCGTTTCATGTTTCGGGGCCTCGCAATGTTTCTTCTCCCA
GTTGGAGAGAAATCATCAAATCTAGCTGGTATCTCTTTTGCTTTTTATTA
TATGCCCTTTTAATCTCCTTTAAATTGTTCAATCGTACACCAAATTTCTT
AATTTGTTTAGTTGTGTAAGTACTAAAATATTACTTGATAGAGACTTGTC
AGCCTTTGTTTACCGGTATTTACTTGTTTTTGGGTATGTGATTGCTTAGG
CTTAGAATCCTGGATTGGAGTTTTGTACAATATTTGTCTAGCAATTTATC
TTGGCTGGTTCATGGTTACAATAAAGTCGAAAAAATTTGCAAAGTAAAGC
CATCCTTGTTTTCTTAAGAATTCATAAGTTCTCGCCTTATTGGTTGGGTA
GTCCCATTGACTCCTCTTCAAGTTGTATAGAGATTAGTTTGTATATTGAA
TTGGAAGAAAGAGTACGTATATTAGCCTCTTATTTGTCTTGGGAGGTTGG
GATTTGATAGTTTCACAAATAATCTAATAAATCTCTACATTGCCCAATGG
TTATTCGTCCAATGGTGGAAGCTGTTTTTTTCCCTGTAAAATCTTGTAAA
ATATATGTGCTTAATTGTTTCGTCCAACAGAGGAAGCTGTTTTGTCTTGG
TAAAATCTTGTAAAATATATGTGCTTAATTGTTCATATTCCCTTTTGTTC
GCAACAATACTTGGTTTGATAAACCATATGATATTGTAGTCAATCAATTG
TTTTATTACAAATCTATAACATTTCTGACCAGTAAGTTTAAATATGAGCA
CATACAGCCATTTTTATACCGAGGTAGAAATAAGTACTGCTGAATTGTTT
CTTTGTCTAGATATATATATAAACACATTAGTGTTACATATGAAATTGCA
TTGATGTTGTTTAATTTCTCATACTTTCCGATGTGATTTTGCAGTTCTTA
CATTTTCTCGCTCTTTAGGGAAATAGCTATTGTTTCTCTGTTTGACATGG
AAGATTGGAAGTTATATAAGAGTTGTACAGTTTTTGCTATAGATAGTATA
GTCTGACTTTACCCTTGTCCTCTAACTTATTGACTCCTCTTAAAGTCATA
TTGGGATTAGCTTTTATTTAATTTGGCAAAAATAATCTGTATATTGGCCA
CTTATTTGTCTTAAGATGTGATAGTTGACAGATTAAAAATTCATCTATCT
GCATCAGATCTAACTTTAAGGTCTTTTATAGGATCCATCAGATTTCAGTA
GATTGAAATTTTATCTCCTGCCTGTTGGCTATACAACTGAATAACGGCTT
AACAGAGTGAAAGTGATTGACGATATATGTAATTTGACATATTGATCAGC
TTATATGTTGGACAACTTTATTGTAACAACCAAGTTTAAGGTCCAAAAGG
AATAATGCATTTATATGGATAACGTTTTTGTTGCTTGAAAAAATTATATG
AAATAAAGTAGCTGGTCATTGTCATAAAATATGAATTCTCCAGAGGATTG
TCTGAGTTGTGAGCTCCTTGAGAATGAAAGATCAGCTTACTGGCATTCTT
TTTTCTCAATAAAGGTGAAGAGATATGGTTTGCATGGTAATAAGAATCTA
TATCAATTGCTTCCAATCACCCTTGCTTATAGTATAAATCCGTCCCTGAG
TATAAGAATATATGTATGATATTGGCACAGATAATCCTTGATGCCAACTA
ATATCTACATGAATGTAGATGTCTATATATGATGAAAATGTGTTAGGTCA
ATGCACTCCTCAATCACAATTTACCTATGTATAATTTGAAGTTTTTTGGA
GAGTGAGATTTGTATTTGTCTATTTTCCATCCTAAGAAATATCATTCACT
TACACTACATTGATTAATTTTTGCAGGAAGAATGGGAACTACAAAAGGAC
AGTTATTGCATGTTTCATACAAGCAGTTTACCTTCTCGAACTTGACAGAC
AGGAAAATAAGACTGAAGAAAATGCTCTTGCTCCAAAGTGGTGGATACCT
TTTAAGTACAAGCTGTCCCAAACCCTAATTGACGAGAGAGATGGATCCAT
ATATGGTGCTATACTAGAATGGGATCGTTCTGCTGCTTTAGCAGACTTCA
TCCTTATCAGACCAAGTGGTGCTCCTAGGGCTGTCTTAGTACTACGAGGT
ACATTACTTAAAAGCCAAACAATTAGACGTGACATACAAGATGACCTCCG
TTTTCTAGCTTGGGAAAGCCTAAAGGGTTCTGTCAGATTCAATGGAGCTC
TAGAGGCTCTGAAATTGATTGCAGATAAGTATGGAGGGGGCAATGTATGT
GTTGCTGGCCATTCTTTAGGAGCAGGATTTGCACTACAAGTGGGAAAAGC
ATTAGCTAAACAAGGTGTCTTTGTGGAGACTCATCTGTTTAATCCACCTT
CCGTCTCACTGGCAATGAGCTTGAAGAACATTGGCGAGAAAGCTGGTTTT
GCTTGGAAGAGGCTTAAATCAATGCTTCCATCTAGCAATGAAACCCCCGC
TATCAGTGAAGTTGGGCAAAACGCGAGCATTCCTAGTAGTGGACTAAAGA
ATTGGGTACCTCATTTATATGTGAACAACAGTGACTATATCTGCTGCTAT
TACACTGATCCTGCTGGCGGAGGAAACCAGGAAGTAGAAAACAAGGAGAA
TGCTGGTCCGAAAAATGGACAAGCTGCGGCAAAGCTTTTTGTGTTATCAA
AAGGCAAGCAGAAATTTCTAGAGGCACATGGATTGGAGCAGTGGTGGGGT
GATGATTTGGAACTTCAACAGGCTCTCAGTAACAGCAAGCTCATAAGCAA
GCAGCTGAAGTCCTTGTATACACTACCAGCAGCTCCTAAACAAACTCAAG
CTAAATAGTAGAAGGCACTTTGGTTCTCTGTCTGAGCCTTGTTCAGATGA
CCTTCATTATAAATATTTTATCATTCTTTATTTTATTTTAATTTATTGCA
AGACATTTCATAAATCTGGGACAATTCCCGGACATTTTTTTTACTGCCAG
TTAGGCAGTTATAGATAACTGAAATTGGAATTTGTTAATATGACATACAT
TCTCTTTGGCTCTGAGCCTCTGAAAATTTGATAAAACTGCATGATTCTGT
GAGTTA