| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017387221.1, is a part of gene, LOC108214950. |
| The genetic_marker, MK005765 K3209, is located in gene, LOC108214950. |
| 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_017387221.1 | XM_017387221.1 | mRNA | DCARv2_Chr3:34363406..34369312 |
CCATATTATACCAACACTACAACCACAAATATTTGTGCATCTCTCTCGCT
GGCGGCCCCTAAAATAATCCGATAACTAATCATCGAAACAAATTAGAGCC
ACCAATACATACAACATATACTTACACATCTCCTTCATACCCTAAGCTTC
CGCTTCGGAGATCTACGGTCAGTCTCTCTCTCTCTCTCTATCTCTCTCCC
CCGATGTAATCGATTCTTGACTTTTTCTTATTTCGCTTGATTTTGTATTT
ATTTTTTACATTTGTAAATCTGCTACTGTTGACTTGTTTACATTTAGGAT
CTGTATCTATTGCTACCTTATGTTTCGGATTTATTGCTTAATTTTACATT
TCATTTTTGTTTATTATATCTTGCTTTTGTGAATCTGATACGTGTGCGTC
TTTGAGTATACGCCAATGCTCTGTTTGGTTGGAGGAAATAAAATCAGCTA
AGAGTGATCTTGAACAAAAATAAAGTCTAAAGGGAACAGCGGAAGTAAAA
AACTTTTAATTACTCATTACACTAAGACTTGTGAAGGAGCCGGGTAGGAA
GTAGAAAAATGAACGGACAATATTTTTTGATTGGTGCCTGATTGTTTCAT
TGTTAATTTGTGTATTGATGGAATGGAGATTAGTAGATTACGAATATTTT
AGCTATTTACTTGCAGAAAAAAGTAAAATTTTCCTATAAATTTAACCTGA
TTTTATTCCTATTGGTAAAGTGGAATGCTATGGTGTGCAAATTTAAACTA
AAATGATATTACTATGTTGGGCTAGTGTTGTGTGTGTGTATAGTATCAGA
CTAAGTCAACAAGATAAATTTATTGTCCATTCACGCACCCTTAAAGCAGC
AAAAAAATTACATGAGAAATATTTTAGAATGTATGTACTTCTTTGACTGG
TAAGGCCCTTGGTGGATATATAATAAGAAATCAATGGGTCTTTAAGTGAA
TATTAAGGATGAGTAGTTGGAACTAAGTAGTGTCGAAAGACCTACAGGCA
ACTAGTTACACAAGTTAGCGGAACTATAATGAGTGATTGGGAATTATATG
AAAGATTTAGAATTTGCAGTAGTTAATATTAAAGATCTGGCTTACTGGTT
GCGATGAATTTCTTTTTTTCCTCTTGTTGTGCAAATTTTTTTTACCTACC
AAAAACTCTGTTCAGAATCCGAGTCCCTTCTTTGGATGTCTAGCTGGTTT
TTTTTTTTATGTTTATATCTGATCTCTATATTGGGCATAGTTAATAACTC
ATATCAATTTATTTTTTTGATGGCATCTTTGAAATGTTTAATCAAGTTCT
TTCGGGATTGGCCAATTAATTTGTTATTTTCCATTTCTTTCTTGTTGGAA
ATAACAGAGTAATTGACTAAAATGGTTGGGGGTGGAGCAATTCAACGATT
ACTCAAGACAAGACTTTTATCTCAATCAGCTGTAAGAACACTATCCTTCA
CTTTAAAATAGCATTTTCATATTTACAGTCTTTGTTAGTTGTGGTAGGGG
GGGAGAAGCACCTGTTCCTGACCTGAGGTACCTTTTTTTAAATACAGAAT
GGGACAGGAATAGAGAACCCATTACCCCCTACTAAGTTGGGAGGAATATG
GGACGACAATGGAATTTAACATAAACTATAGTTTATTCCAGAATACCCTG
CCCCATAATATTATATGTAATCTTGTGTGTGTCATGAAGTTGAGTTAAGT
ATGTACTTTATCTGAATAATAGTCTTTTATCTGTTTGAAAATTAGAAATG
TTTTGTAAGGTCTGTGTTTGAATACATCTTACCTAGACACCCCTTGGTAT
GTCATGTTTGTTTCGCTTGGTCTTTAATCTCCAACTCTATTTTATACTTC
AGTTGTACAGTGTATCAAATTTCTTTCATTTGTGTTGGGATTATACCTGC
TAAATGATCCCCTAAAAATATCCAGAGTATCAAAATATTTCATGTGAGTT
ATCTCTCCAGAGGTTTAAGTATCCGGTGACAAACATAACCATAGCGGCAG
GAATAGGGGTTGCAGTGAAAGCCAAAAGGTATTTTAAAGTATCCGTGGGT
AGGGCTGAGCAAACGGTCGGTTCGGTCGAAAACCGAACAAAATATTTCAT
GTGAGTTATCTCTCCAGAGGTTTAAGTATCCGGTGACAAACATAACCATA
GCGGCAGGAATAGGGGTTGCAGTGAAAGCCAAAAGGTATTTTAAAGTATC
CGTGGGTAGGGCTGAGCAAACGGTCGGTTCGGTCGAAAACCGAACCGAAC
TAACCGAAAACCGAACTTTTAAATTTATGAAAACCGAACCGAACCGTAAT
TGTCTTTCAAACCGAACCGAACCGAACCGAAAATAATTCGGCTTTTTTGG
TTCGGTTCGGTTAAAACCGAACTTTATATTGAAAAAAAGGCAATTTATTA
AAGTCTTCAAGAAAAAGCAATATTGCTAACATTTACCAACCCCAAATGCC
TGCCAGTTGATCTGAAACTCCAATATGCACTGGACTTACAAAGTCTATTC
ATGTTTAAACCAAGACAACCAAATCAGTAGATTACAGAGATCTAACACTT
GGGAACTCGACGATATGCGAACTAAATCGGAACCTGGAAGTAAAGCACTG
AAACTTGAATCAGATGTGAAGGGTGAAGGGTGCTTGAATCAGATATGAAG
GAAGGATAAAGCTTGGATCGGAACTTTGGAGAAGGAGCGGAGGGCGGAGG
CGCAAGACTGCGGGTGGGTATTATTTGGTTTAGGGATTCAGGGGAGTGAC
TGACATTAACATTGTTACTTATCTATTATTTGATTATTACTATAAGTATA
AATATTATTAATATTATATATAAATATATTTAAAAAAATATATAAATATA
AAACTTCGGTTATTTCGGTTAAACCGAAATTATATTTTTCAAAATCGGAC
CGAACCGAACTTTTAGTTCGGTTAAAACCGAAAACCGAACTAACCGGAAT
TTTAAAAAATTCCAAACCAAACCGAACCGAATTTCTACGGTTCGGTTCGG
TTATTTCGGTTCGGTTCGGTTTTGCTCAGCCCTATCCGTGGGTAGGGTTT
TGGGATTATAATAGCAACACTGTGGGGATATCTGAGTAAGTATGGGGTTT
TTTTTTACTTTGTTTTTTTTTTTTTGTGTCTGACGGGGTGGGGAGCATGG
AGTCTAAGGTTTCCATTCCATTTGATTCCTTAATAGTTGATACTTAGAAT
TTATAAATAATTTATGTAAGCATTGTGATGCTTGTCATCTTTCACACCTT
CAATATTTGCATAAGATTTGTAACAACGAGTTTACTTCGTATTGTTTCTA
TGTGTGTATTTATCATAGATACTTAAACTTCTAGTTAGTTTCAAGCTTGT
GCCAGATAAGCACTTTGCACTGAATTTAGGAAGTCCAACTCTGGCTCGCT
TAATGATTCTGTGATTTAATTATAGCGGTTGATTAAAAAATTTAGAAGTT
TTCTATTAGACCTGAACAAATATTATAAGGTCAAGTACTGCCTGATGCTT
GTCTGACATCCATTGTTTTTTTAATTCACAGGGCCGTCCAGTTCTGTCTT
CTCTTTTAGCTAAAAAAGATCAGGAGGAAGCTGGATCTGCTGGCATGAAG
TCTCTAAGAGCATTTGCACTTCTTGGAGCAGGTGTATCAGGACTTCTGGG
CTTTGCTACAGTAGCTTCTGCTGATGAGTCTGAGCATGGTTTGGAGTGTC
CTAGCTATCCGTGGCCTCATGCAGGAATTTTGAGTTCATATGATCACGCC
TCGTGAGTTTCTTTGACATGCCATATATTTTTTCCATTTTGTTTCTTTCT
TCTCAGTTGATTAAAGTCATATGCCTGAAGGTTTGTATGGTAGAGTTTTG
CTTTGTATCATTTAGGTACAATCTGGCCAGGAAAAATATTATTAGATGAG
AGGAGTTTCACCTTGATAATATGTTTGCCCCTATGTATAGTAACATTGGG
TCATTATGGGTATTTTCTGCTGCCTGGATCAGTGGACTAAATTATGTTAT
TGCTGGTCTTTGTGCACTGTTCTCAACTTTACTGCACAGGATTCGTCGTG
GTCATCAGGTGTACCAACAAGTCTGTGCATCCTGCCATTCAATGTCCCTA
GTTTCATATCGTGACTTGGTGGGTGTGGCCTATACAGAGGAGGAAACAAA
GGCTATGGCTGCTGAAATTGAGGTTGTTGATGGTCCTAATGATGAGGGTG
AGATGTTCACCCGACCCGGGAAACTGAGTGATAAATTTCCTGAACCATAT
CCAAATGAGCAGGCAGCTAGATTTGCCAATGGAGGGGCTTATCCTCCTGA
TCTAAGTGTTATCACTAAGGTAATTACTTTCTTTTGGTTTTATTGTCTTT
TATAACATCTATATATAACAGTTGCACTCTCTGACTCTTCTCTCCGTTTA
GGCTCGTCACAATGGTCAGAATTACGTATTTTCCCTTCTAACTGGTTATC
GTGAACCACCTGCTGGAGTTTCTGTAAGTTTTTTGTTATATTAACTCTTC
TTGAACTTGGTCCCTATTATTTGTAAATAGAATAAAATCCAAAGGTGGAT
AGCTTACCACTTACGATATCCCGCCTACTTAAATTTTTGTATCTGTAAGA
TACCTTGGCAGCTTGGCTACTGCTGCATGTAGCAAGTTTACCTTTTCACT
ACTTTGAACTGGAGGCTTTTTCCATCTACATATTTCTCATGCTTACAACA
TTGCAATATAAGCTGCTACATTTGTAAGTGTATAACATGATACACTGTTT
GCTGGTTCTTCTTTTGTTTTTTATTTGATTGAATGTACATCTTCTTTAAA
ACAAGATTGATGTAGGAGCACAATTACACAACCTATATTCGTGAAAATAA
GGCTGATAGGTGTGTGATATATAGTGAGGCAGCAGTCTAAATGATATAGT
GAAATCAAAAGTTAACTGCAGAGATAAATATTATAGTTGCAGACCAAGGG
GGTGTTGGGTCTTTCATGGGAATCGGAACGGGGAATGGAATGAACTTGAA
TCTTTAATATCTCCTGAAGCTGTAAAATAAATCTGTTTTAATGAAAAAAC
ATGTACTTCATTCCGTTGACCCATCTCATCTGCAATGTTGCTGGTATGTA
GGTCAGAGAAGGACTGCACTATAATCCATACTTCCCTGGTGGGGCTATTG
CTATGCCTAAAATGCTTAATGATGGCGCTGTTGAGTATGAAGATGGTACT
CCGGCTACAGAAGCCCAGGTTGGATTTTCTCCCTTTCTACCTTTAAGAAT
AACTGGAGGTTTATAGGAGTTCTGCATTATTGAATTTTGTATCATACTGT
TGTTAACTCAGTGTTCTCCATCATTGTCATTGCAGATGGGTAAAGATATT
GTCAGCTTTCTATCTTGGGCTGCAGAACCAGAGATGGAAGAGAGAAAACT
GGTATGGACTCTGCTGCTACAATTCTTAGTCTCTGTAACTGATAGTTAGC
CGCTAATCCATTGTATTTTACTGCAGATGGGGTTCAAGTGGATATTAGTA
CTCTCCCTGGCCTTTCTTCAAGCAGGATACTACAGGCGCATGAAGTGGTC
TGTTCTCAAGTCCCGGAAGGTGATTGTTGATGTTGTTAATTAATTCCACC
TCCATCCAGGTTTTCTAGCCTCCTAACTTTATAGGGGGAACATGTGTTGG
CACGCGGCAGTAATTACTTTGCAGGACAAGGCTTTCTCATTTTGGCTGTT
GTGCTTATTATAATTGTACTATAGTCATATTAAATGATTTAGTCGTCCAT
TTATAAGGGGGAATAAGAGCCCAGTAGATGTGCATACTCTATATCCTTGT
CTGCAATATGTGCTGTTTGGAACTTGTTACTAAATGAGCAGTCCCGGATT
TTTTTGGTGTGTTAATAAAGCATTTAGCACCGGTTACTATACCCTCATTT
CTGAAA