| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017388814.1, is a part of gene, LOC108216131. |
| The genetic_marker, MK009330 1_1595663, is located in gene, LOC108216131. |
| 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_017388814.1 | XM_017388814.1 | mRNA | DCARv2_Chr1:1590239..1595837 |
ATGAAGCGGTGGGGGGAAACAATCACGGTGGTGGTACTGGCGGTGACAAT
GGTGATAGAATCGGCTATGTCAGATCCGCAAGCTAATAAGATAAGCAAAA
CTGGGCGAGAGTCCAGCGGGTTTGATGCTAGAAATCCATCAGAATTCTTC
AGAAATGTGAATGCCACTCTCGCGGACCTCAGACGACAGTTATCTGTAGA
AAAAAACACTTTGCCACCGCAGAGGCCAGTGCCGCGGAACCTGTGTACAC
TTTGTTCCAGTGCAGAGATTATCTATCCACTGCAGACTGCGTCGCTTGCT
TTAATGTAGCCACAGCTGATATTGGCAAAATTTGCAAGTTAAATAACGGC
GCTCGGGTCATATATGATGGTTGCTACCTGAGGTAAGCAAACTGATTATT
CCTCAGGTGAAGATGCCGGCTTGAATAATCTTGATTTACAGCTTGTCTGT
CTTAATCTCTGATCAAGGTACGAGGTGCGGTCCTTCTTTACAGAGATAGA
GCTTGGAACTTCATCTGAGGTATGCGCGGACAACAAGACTGTACCCGCAC
AAGCTGCTTTTACTTTAGTTGCAGTACAGTTGCTGAAGGATCTTGCAGAT
GCCACACCAAAGATAAAGAACTTCTTTGGAGCGGCGAAAAGGCAAGTGTT
TGATGGCGGTCCGTCAGCAAAAGCATCTGTTACAGTTTACGCTGTGGCAC
AATGTCTTGGCACCGTAAGCCAGGGTGATTGCGGAAAATGCTTGATGGGA
GGATACAGTAACATACAAACATGCCTTTCTCAATCAGGAGGAAGCTCGGG
AGGAGGAAGTTCAGCATCTGGTGGTTGTTTCCTGAGATACTCCGTGACGC
CTTTTTTTTCTGATAATGATATAACAAATATCATGCCTTACTTGCAAAAA
GGTAAGAATTCCATATATATACACATCAATCTTGAATCAATTTACTATGA
CCCTCTTTGACAATTAGCGGTTAGCATATCAAATTAGTTACTTTGGCAAT
TAGCGGTTAGCATATCAAATTAGTTACTTTGGCAATTAGCGGTTAGCATA
TCGAATTAGTTGTTTTGACTGACTGTTTTGACTAAAGGATTAAATTAGCT
AATTTGGATGAAACTGTTTGGTAAATAGCTGTTTGATCAACTTTTTGTAC
TTTAACTAGACACATATCAATCCTCTAACTATAAAAACTCCTCCAAATAG
CTTTTTCAGAATTAGATTTTTCAGTCCAAACTTCTATTTCAATCTGCTAA
TTGTCAAACACCAACATTAGATAATTCACATATCAAACCTCTAATATAGT
CTAAACCTCTACCGTTTTCTCAGAACTCTAACTTCCATACAAGGACATGC
ATTTCTTCTGCTCATTTCATTCCACCTCCTTGGAATTTCTAGTATACGCG
GAAGTAATAAACTATATGTGATTCTTGAGTTAACACATATCTAGCAGACT
AGAAAACTATGATTTGCACATCAGATTATGCAAACCGTGAATTATCCAGA
ATGCACTTGAGTTTTGGACTAGAAAGCGGGGATTCTTCATTCACCAAGCC
GCACCGTGCACTCAATTCTTGGGGATTCTTGTTAATAATTAATTCTGTAA
TTAGATGAATAATTTCACTTAATCATCAATATATATATATAAAGGAGGAT
GCGGGCGTCTCTAGAATTGTTCGATTCAGTCTTCTAATTTTTCTTAAATT
TCGGAGAGAAAATATAGTTATAATTCAAAAAACTAGGTTTAATACAATTC
TAAAGATAATATAATTCTTCTTATTGGATCCTAAAGGTAATACTCTAACT
AATATATAGAAAAAGAATTCCAAAAGTAATAAAACTCTTTTTCTTATTTA
GGAATCATAAAGCTAATACAATTCTAATTTTTAATATTGTTTTATACATT
AATATACAAATTATTAAAGAAGTACAATTCTTATTTTCAATGGTTATCAA
ATTTATAATTTTATTTTATTAAATTTGAAAATAAAATTTACAATTTTATT
TTATTGAAATTTTCCAAATTTATCATATAAATTTGTATCAAACATGTATA
AAAAAATCAATTTTTTACAAGACCGCATGAATTGATCGGGAGACATAGTT
TTGCAGCGTGTAATTTTACCATTGACCATTCTATAGCTTAACCTATCGAG
GCAAGCCCTTCGATTTTCATCCGCCGGCGAACACACACTATAGAGGAGGA
TATAGGGCGGTGACATGGAGTCTCTCAAATTTTTCGATTCATTCTTATAT
TTTTCTTAAATTTCGGATAATCTAAAATTATAATCTAAATATCAAGGTTC
AAGTATTGTATAGATAAAAAGATTGCAAAGATATTGCAATTCTTTTACTT
ATTTAGGAATCATAAAAAAGTAGAATTCTATTGTTTCATAATAACAATTA
TTGAACAAATATAATTAAAAAAATACAATTCTTATTCTCAAAAGTTATAA
ATTTATAATCTTATTTTATTAAAGTCTTTCAAATTATATATCTAAAAAGT
AAAAACCAGCGTCTTCCGGAATCTCAAATTGTCTAAACAGATTCGTAGCG
CTAAACTCAAGTCGTTCGATAATGATCAAAAAGATAGCATCCCTGTCATG
AAAACATCTTTAAGATCTTCGCAACCTCATTCAATTAGTATGCATGAACT
TACAACCAATCTCGACAATAGTTCGATCCAGTCTAATAATTTTCTTGAAA
TCAAATTTAAGGATCTTAAAGGCAATACAATTCTTTTTTTATTGGATTCT
AAAAATAATAAAATTCTTTTTTATAATTTTCTTAAATTTCGGATTGAAAA
TATAATTATAAAAAAAAAAATCAGGTTCAATAATTCCAAAAATTAATGCA
ATTCTTTTCTTTTTGGATTCTAAAGGTAATGCAATTCTTTTCTTATTTAG
AAATCCTAATAGTAATAGGATTATATTTATTTAAGATAACAATCATAAAT
AAAATGCAATTTATATTTAAGATTTGTAAGGTAATACGTATAATTTTTAT
TTTTGATTTAGTCTTCTAAATTTTCTTGAATTTCGGAGAGAAAATATAAT
TATAATTCAAAAAATCAGGTCCAAGAATTCTAAAAATAATACAATTTTTT
TCTTATTTAATTCTAAAGATGATACAGTTCTTTTCTTATTTGGTATTTCT
TATTAAATTCTAAAGATGATACAATAGTATTTCTTATAGAATTCTAACGA
TGATACAATTCTTTTCTTATTTAGTAATCCTAAAAGAAATAGGATTATAT
TTATTCAAACTAATAATAATAGATAAAATACAATTTATATTTAAGTTATG
TAAAGTAATATATACAATTCTTATTTTCGATAATATATAATATATTGAAG
ATATGTTTAACGGGAACACGACTGAAAATAACTTTTATGGAATTATAATA
TTATTTCGTATCAAAATTTATAAAAAAGATTATTTATTAGTATTGTGTTT
AAGGGGAGGACGGCCCAAATTAATTTTTACCTAAATAATAATATTTTTTT
TATTAGTATTATGTTTGACGGGAAAGTAACTACAACAATAATTTGTCTAA
ATTTATATAAAATTCATAACGCCGCCGCGAAGCGCGGCTTTTTCACTAGT
TATCTTATAATGTAATAGTTGTGTTAATAAATATTATATTTTAAATTATT
AAGGATATTGAACTTATTTATTGGATTATTTGTTTTACATATTAATACAA
CTCTTGCATACATGCATAATATATATTTTAAATATATTAATATTTGTTGA
ATCCCCCCCACCCGAATCCCGATATTTTTAAATTTGTTTAATTCCCATAT
CTCCGTACCGCGCACCCCGTATCAGCACCCGCACTCATGCTTCCTAGGTT
TCGGATATATAGAAGACCAAAGAGTAATATTTTAATTTCCAGGTAGCTCC
AGCAAGAAGACGGCCATCATTGCTGGTGGAGTTGGAGCTGTAAGCCTTCT
CTTGCTCACGATTGCCTTACTTCTATGGTATCGATCATCACAAAAGCGTA
GAACAGCTAATAGAGGTAATTAGGCCTTATCTGTCCTGGATGCTTGCATA
TAAATGTTTTGAGTTATTCTACATAACACATCTGTTCATCTTCCATTTAC
CATAGGCCATAGAGTTTCATTAATTCTTTTCACGGTTTCCAGGTGATATA
CTAGGGGTAACTAAGTTGCAGGGACCAACTATATACAGATACAAAGATTT
GAAGTCAGCTACCAAGAATTTCAGTGAAGAATGCAAAATAGGAGAAGGCG
GCTTTGGAGATGTATACAAGGTGATCTCATATTTTCTATCATCTCCTACT
CACCGGAATGCATATGGTTAAGTATAAGGCTAAATTGATAATGTCATAAA
CAGGGCATTATATCAAATGGAAATATAGTTGCAGTGAAGAAACATGCTGT
GAGGACAAGCAAAGAAATGGCAGATTTTGAGAGTGAAGTTAGGCTTATAG
CTAATGTTCATCATCGAAATATCATCCGTCTCCTAGGATGCAGTGGCAAA
GGACCGGTTCAAATTCTGGTCTATGAATATATGGAGAACGGAAGCCTAGA
TACATTCTTATATGGTGAGTTAGCCTTAAACTTCCAGCTTGAAAGCTTCA
TGTTTTATATGAAGTACATTCACATTTGCAGGAAATAAACGCGGAACTCT
CAGCTGGAAACAACGGATTGACATAATCCTCGGTATTGCTAGAGGTCTTG
CCTATCTCCACGAACAATTTCATGTATGTATCATACATCGAGATGTGAAA
TCTAGCAATATCTTACTGGATGACGATTTCCAACCCAAGATCGCTGATTT
TGGGTTGGCAAGACTTTTACCAACGGATCCAAGTCATCTTACCACTAGAT
TTGCAGGGACTTTGTAAGTCATTCTTCTTACAGATTTTATCCGAGATATA
TGTTCATAGAGTACTGATGGGATATTTAATTTTTGTGATACTCAAGGGGT
TACACAGCACCAGAGTACGCAATCAACGGGCACTTGTCTGAGAAAGTGGA
TACCTACGGGTTCGGAGTCGTGGTCCTCGAAGTTTTAAGTGGTCAAAACT
GCAATAAGATGAAGAATGAGCTTCTAACCCAATCTCTTCTTGAATATGTA
AGTGTGCCCTTTAAATATATCAAGAACTTAGCATCTGATTATCGGAACTT
ATATGGTCACATGACATCACAATGATAACAGGCATGGAAATCATATAATA
ATGGCACGCATGAGGATTTGATAGATGAGACAATAGATTCGAGTGAATAT
AATGTCGAAAATGCCAAGAAGATGATAGAGATTGCTTTGAAGTGCACTCA
GTCACCGGTTTCTTTGAGGCCAACAATGTCTGAAGTTGTAGTGATGCTTG
TGAATGATGCATCCCCAGAACCTAAGCAGACAAACTAGGGTCCAGTCTAA
TAACAATATTAACGAGGATGTCCAATATATTGGATGATCCTCCTGCTACA
GATATAAGTTACGGTATAATCATATTATATTTTTAAGTTTACAATAACCT
TCTGTCTAAAACTTTCCGGTACAGAACTGATCTTGATAGTTCACGAATTA
TCAGTGAAGAAATAAATAAATTTTGGAAATTTAGTTAGTTTGATCTTA