| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017396255.1, is a part of gene, LOC108222026. |
| The genetic_marker, MK002731 K0175, is located in gene, LOC108222026. |
| 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_017396255.1 | XM_017396255.1 | mRNA | DCARv2_Chr1:25524977..25531100 |
TTGAACCCGAAATTTCACAAACGAAGATAATCTAGCATTAAACGACGGCG
CTTTACAGATACAAACAATCTCAGAAGTCAGAACTAGGAAGATAAACAGA
TAGACACAGTTGAAGGGCGGAGAGTTAACTCTATTGTCAGAAATGGCGAA
AACAAAGAAAGAGCTGCTGGCGTCAGCGCCATGGAGAGGACAAGAAGAGG
AGAAATTCAAAGACGCAAAGCTAAAGGCGACAAGAAACCAGTCAGGTTCA
ACCATGCATCTTCATCGCAAGAAAAACAATGGTGTTGAGAAAACATATGA
AGATGATTCAATCACTGAATTGGATCCTCAACTTCGTTACTCTTTTCAGC
GCAATTACCAGGTTGAAATTGACCCTTTTGCTTGTTTTTTGTTTATCTTG
TGTTTTCGAGATGACCCATTTGTTTGATTTGATTCATTTGGTGATTTTTC
TGTGGTGGGTTTGCTTGTTCGTGTTTGTGTTTGATTGTTAGTTGTTTATT
ACGTGTTTTTGAGATCGCCCTTTTGTTGAATTTAGTTTATTTTTGGATTT
TGTATCTTAATTAAGCTTTTGAGTGTGTGGTGGGATAGACTGTTTTATAT
TTGATCAGCTAGATCTTAGAATACAACTTTTTGTCACGATAATATGGCGC
CTAACTAGTACAGACTGAAGTTTCTAGTGCAGTTTAAATGTTGGGGGTTC
TTGTTTCAATTACCTTTAACGAGATTTTGTGTGTGTATAGAGATTCAAAC
ACAAGTTTGAGGATTCAATCATATGTATGTTTGCAGGATTAATAAAGCAC
GATGATTTGGATTTAGTTTGAATTTTTAGGATTACCAAATGACATCTTTT
CAGCACAATTACCAGGTTGAAATTGACCCTTTTGCTTGTTTTTTGTTTAT
CTTGTGCTTTCGAGATGACCCATTTGTTTGATTTGATTCATTTGGTGATT
TTTCTGTGGTGGGTTTGCTTGTTCGTATTTTTGTTTGATTGTTAGTTGTT
TATTACGTGTTTTCGAGATTGCCCATTTGTTGAATTTAGTTTATTTTTGG
ATTGTGTATGTTGGTTAAGCTTTTGTGTGTGTGGTGGATGGATAGTTTTA
TATTTGATCAGTTAGATTTTGGGCGTTGGCCCTCTCAGGCACCGTCCTAT
GGCCCAAAAAGGCACCCTGCCGTATAATGGCCCCAAGTTTCTCTATAAAA
CGTAACTTCGGTAAGCCTTAAGAGCAAAACGTGAGTTTAAGCAGCGTTGT
TTTTTTTTTTCTTCAAAAGAACAGGATGAAACGTCTCTTCAACAGACGTT
TTAGTGGATTATTTTAAAATTAAAACTATAAAACGTTACTTAGTCTAACG
TTTACGACATTTTTAAATTTCAAAAAACTCAAAACGCAACTTTAAATTGT
GTCTTATATTCTAAACGCTTTTTAAAGTTGCGTTTTGTATATTACTTTTT
TTAATTTTTTAACATTAATTTAGTTTTAAGTATAAATAAATCATTGTAAA
ACCCAAATATGAACCCTAAAATATTAAAAATTATTTATGGATGTTTTTAG
ATTTATTTTTTTAATTTGGTTCCTCGGCTTTAGGGCCTCACGGCCCTAAA
GCCTCGAATTAATTAGGGTTTAGGCTCGAGTGTTTAGGGACTAAAGGAAA
CAGTAAACCCTAAATGATAAAAAACGTAAAATATTTCTTTCTCCGGTTCC
ATGGCTTCCGGGCCTCCCGGCCCTGAAGCCTCGCATTAATTAGGGTTTAG
GGCCTAGAGATTAGGGCCTAAAGGCCCTAAACCCTCACCCCTAAACCCTA
ACCGGTCGTTGGTTACTGTAAAGTGTACGCGCATTATTCTAAAACCCAAA
AGGAAACACTAAACCCTAAATGATAAAAAAGGCAAAATATTTCTTTCTCC
GGTTCCTCGGCTTCCGGGCCTCCCGGCCCTGAAGCCTCGCATTAATTAGG
GTTTAGGGCCGAGGGATTAGGGCCTAAAGGCCCTAAACCCTAACCGATCG
TCGGTTACTGTAAAGCGTACACGCATTATTCTAAAACTCAAAAGGAAACA
CTAAACCCTAAATGTTAAAAAACACAAAATATTTCTTGTTTCGGTTTCTC
GGCTTCCGGGCCTCCCGGCCCTGAAGCCTCGCATTAATTAGGGTTTAGGC
TCGAGTTTTTAGGTCCTAAAGGCCCTAAACTCTCAATCCTAAACCCTAAC
CGTCAGTCGATTTAATTTCAAGTATAAATAAATCATTTTAAAAACACAAA
TTGTGAACCCTAAAATGATAACAATTGTTAATGTCTAAGTTTTTTTGTTT
ATAAACTAAATTGCTAACGTGACTTCTTGTTACGTTTTGCATGTGCACAA
AAGTAAATCCTGGTAAACGTCAATGCGTGCTCCATTTTAATGTGTTATAG
TAAACGCCACTTTAAGTGGAGTTTTGAAGTGATTGTGGGGGCCTTTTTTC
TAGACAGTGACAATTTGGGGCATTGTGTACTCAAATTGTGCCTCTCAGGG
CCCTTTCTCTTAGATTTTAGAACAGAACTTTTTGTGACGATAATATGGCG
CCTAACTAGTACAGATTGAAGTTTCTAGTGCAGTTTAAATGTTGGGGGTT
CTTGTTTCAATTGCCTTTAACCAGATTTTGTGTGTGTATAGAGATTCAAA
CACAAGTTTGAGGATTCAATCATATGTATGTTTGCCGGATTAATAAAGCA
CGATGATTTGGATTTAGTTTGAATTTTTAGGATTACCATTATAATGACAT
CTATAAAGCTTATATTATTTGTATGGCTCGGGTTTATCTTTTTCTAGTGC
GTTTTAGATGGATGTCAGTTGAAAATCAGAGCACAAGTTGTTCCTGTAAG
ATATTTAATCCTTTAATCATACATACTCAACTTTGATGCAGAATTACTAA
AGCATGATTCAAATTTAGTTTGAATGTTGAGGATTACCATTGGAAGGACA
TCTACTAGTAAATTTTTTATACTTTTGCTTTAAGTAGTTAGTGATTTCAT
TTTTCCTTGTACCTCTAGAAACTAATCTTACTTGTTTTTCCTGTTAATAG
TATGTAATAATTTGCATGTGCACCTTTAATATCTAAATGTGTCTTGCTAA
TTGTTTATTTCATGCTTCAAACTCGCATGGTTCATTTGTTTGACAATGAT
AGTATGAAATTGTCCAATTGGGGCTTCTAGGTCTTTTTCTCCATATTCTG
AATTGCGGCACTGACCTATGCCTGTTTTTCTTTCACCATTTCACCAATTT
TCTTTGATGAACATTTAGTCTTTTTTCCTTTTATCAATTTTTATATTAAA
ATCAGTACATGGACCCTATGCTGGTCACTCGTATTCATATAGTGTTGTGT
GGGTCCTGAATTGGTAGTTGTGGTAAACAGAGCTATTGGCAGCATTCTTT
AGTTCAGCTTCTATGGAAATAGACACTTTGCGTTGCCTATTATCAAGTAT
CTAGCTTCCACATCTATTTTGTCCCTATCCTTCAATCTGCTAAAGATGCA
ACCAACTTGTTGCTGTAATAATAATTGATCAGCTCATACTAACAACCTTT
TAAATTGGATGTAATACTCCTAAAGCAAGTATTTGTTTTAGCTTATTTAA
ATGACTGGAAATTCTTGGCACTATATTACACCATTCCTTGTAAAACATAT
TTTGTAAAGCATCTGATGTGAATCTTTGCCTATGTTGGTTTGTATCACCT
TTGTGTAACACTGTCCAAATTGGAAGAACAAAGTTATACATTTTGCACCA
TAGTGTTCTGTTAAATCCTAATAATAGGCCAGCTTTAGAAATTCAAGATT
TAGAATCTCCATTAGTGATAAATTTTTATATACCATCCTGGGTTGTTAGG
CCCCCCCCCCCAGTCCTTATGTTCTGTAATGAGTGCGATTTATTTACTCT
TCTTGATTGGTATTAGTGATAGTTTTGTGTCTATTCTCGATGACAACTAC
CATTGATAGTTACTGGCGAAAAACTGTCATAGATTCCTGCAGCTTCTTAA
ATTGCTTCTCCACCTCTCCCCAGGTTTCATCAACTGCCCGGACCAGTGTT
CTTTTGAGTCGTTCCTGGCTCCTAGGCATACGAAATTAGTGAATGAAGTT
GAGAGCTCAAGTTAAAGATGTTATGCTAGCTTAATCCTTGATCTCATGGC
TCCTTTGTTCTTACTTGTGTTACCTATTTCAAACTTAAACATAGTCAATT
TGGGTTTGCTGGTAAATAACCTTCCAGCCAAAGGGCTATCTGAAATCCTG
TAGTAGAGACTTTTGAATAAAACTCCAAAAAGTCATCTATAATTATAAAC
ATTGTCCCTAGAACGTCCTATACCATTTCCATACCATACAAAATACTTGG
ATAAACACTCCAACCAACCCCCTCTGTTACCAGTAACTCGAAGTTTATGT
AAGTAGATTTGCAACCCATCACACATGCATGCAGGGAGGAGCTTTATTTA
ATAAAGTGTGTATTTCATTAATTAATGATACCAGTTATACATGACGTCCA
AAAAGATTTTCCTCATATGTGGAGTTGAAGATAGGTTGCAATCTTGGTGC
CTGGTATTATAATCTTATTATTATTTTATAAATTTAAGATAAATAATGTC
CAGCTTAATGTTTTAATAATGAATATCTTTGTTGAAGCTCTTAGGCTTTT
TTATATTAATGGAAATAGCTTTTTGTTTCTTATGACATGTATATTAATAT
ATTTTGTTCTTCCTGAAGTTGTGGCAAATCCATTAGTATTCATTAATTCT
TTGTGATGATTTGTACTGTTATATTTTTTTGTAACTTACTGTATACCAGT
CTTACACTTTCTTTGCATGCTATCATTGTTCTCCTGTCGGTAATGTGATT
TTGAATTGTTATTTATATGTTACAAATTTATGTATTATCTGTCTGAAATG
CAGTTTCTTCAGAGCGTGTTCAGTATCGACACTATTGTCAAACCTCTTCC
TCCTGCAATGGCATATAATGTTTCTCGCAACTTGAGTTTCTTTACGCGCA
TCTTTACCCAGTTCTTCGGTATGATATCTACATATATATTATATTATGAT
ACCTTAGTTGTAATTGAATCACCTTCATATCAGGTATGAAAAATGAGGCT
CTAACTAATTCTCATGATCATATCATCATATAAATAGTTATAGATTACTA
ACCTATGATCATCCCCCTTTTTTTGCTATTTTTTCTTTTTTGGAAACACT
TTCTATTATTTTTTTATGCACATGGAGAAAAGCTGGGAAAGTGAACTCTA
GACATCTATTTTCAGTTACTGCTCTCTTTGTGGAGACCAGTTATCAGGAA
CACACATGATAATGTTTAATTTTGGGTCCGTTTGTTGCCGAAAAATACCG
GAAATTATTTTGAGAAAATATTTCTAGGAAATCATTTTCCTGGAAAATAT
TTTCCGTTATTTAACTATAGTGAAAAAAGTCATCGCAAATGATCAATTTG
AAAAATGGTTTCCTCTTTTGAAAAGGGGTAGTCAGTTCCAGAAAATCATC
TCATTTTAGAAGGAATTTTCCTCTAGATGTAAGCGGAAAGGATGTCATAA
CTGGACATGGTTTAAAAATATGAAATGCAAAATTATTGCACTAAGAAATC
TGAGAACTGGTACATAAAGAGCGGTATGTTTATCATGCAATCATGTGCTA
GACTCGATATTGTATTATATATCATGAAGACATGGACTATTTCCACATCC
TCAATACTCATTCTGTATTAATGGCGAAATATATTTGTTTGTACCTAAGT
TCTTTCTTCCATGCCAATCAGTTTTAACTATTTTATCTGCAGATCCAGAA
GGAATTTCAAATGCTCAAAAATCACTTGGACTGGGACAAGAAGAAAAAGT
CCGTCAAGTTCGTTAAAAAAAACTCAATATATTTTCCCAACCAGCTGTTA
ATTTGCTAAATCTGAACTTTGTATTGACCATGTATAACTGTTTCTGCATC
AGCTCATATATGAAGGATAAATATTTGGTCTAGAGACTGCTCTTTTCTTA
AAATTTATGATTTGAGTTGTTATCCTAGTCTGTGTTTTGACAGCTACATG
AACTTACAGGATACCTAAAACAGAGTTCTCCCAAATGTTTTTTCTAGATA
AAGTATGAATGTATGTTGCCGCA