| NCBI Gene |  |
|---|
| Relationships |
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| The genetic_marker, MK006385 K3829, is located in gene, LOC108203744. |
| The genetic_marker, MK010787 1_49509029, is located in gene, LOC108203744. |
| The genetic_marker, MK008028 1_49513524, is located in gene, LOC108203744. |
| The mRNA, XM_017372880.1, is a part of gene, LOC108203744. |
| The genetic_marker, MK016924 1_49508986, is located in gene, LOC108203744. |
| The mRNA, XM_017372876.1, is a part of gene, LOC108203744. |
| The mRNA, XM_017372886.1, is a part of gene, LOC108203744. |
| 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_017372886.1 | XM_017372886.1 | mRNA | DCARv2_Chr1:49508526..49514548 |
| XM_017372876.1 | XM_017372876.1 | mRNA | DCARv2_Chr1:49508526..49514547 |
| XM_017372880.1 | XM_017372880.1 | mRNA | DCARv2_Chr1:49508526..49514295 |
TACTTTTACACAAAACAAAACAAGGAGAAGTCATCAAACACCCTTTACCC
AATTTCACCTTCTTTTCCTACCATTTAATTTGATTCCTCCGTTATTTTAA
CAAAATTTTTATCTACAAAAGACCCATTTGATTACAGAAAATGCCTAGCT
AAGAAGACCTATCAAACCCCATCATCTCTATTTGAGTTCTTTTGTTGCCA
TTTTCAGTTGTTTTTACTTTAAACAAGTGACTTTAAAGGTACAAAAGACT
TTTTGTGTCTCTTGGTTTTTTTCATTTCTGGGTCAGAATCTTTCTTTGAG
TCTGTTGCAGGGAAGAACAATACATACACATATTGTATGTATAATATGGC
CTAATAATATTGAAAGACTCATCAAAATTTGAACCTTAAAAGTTTTGTGT
CAAAAAGTTTTGATTTTAACATTTTTGCAAAAACTTGTTATATAAAATTT
GAATTTTTGTATTTGTTTCTGTTGTTGAAGTTTCTTGTTTGATAAAGAAG
TGCTGAGATATGGTAAAGCAAGGACCCTGCTGTCACTGTGGTGTTACAAG
TGAGCTCTTTTGTCTTTTAACCTGTCTTTGTATTTTCTTGTGATTAGTGT
TTTATTTGATTGATTGTTTTTAAGTTATGTTGTAGCTTAGCAAGATAATG
GGTTGTTGAGATTATAACAAATTTGTGATTTTTGTTGATCACTTAATTCA
TACGAGCGAGATATCCCGGGTATGTTTGTTTAACAATAATTATATTCTTG
ATGGAGTAGTTTTTACAATTTTGTCAGTCAAGGGATTGTCTAATGGCCTA
ATGGAATTTCTTTATTTGTTTTGAATGTTGGTTTCGGATCAGTACTCCAT
TTGGCACTCTTGTTAATTGTGCCGAGTATTGAAATTGCAGTTACGGAGTC
GTTTTTGTAAAATTTAGGAGTGTGCCAGCTTAATTATTTCTGATGATGAT
CAACAAGTGAGGCTCATCATTCTTGATAGTGCTTGTTTGATAGGAGAAAT
GAAGTTTTATCTGTCTCATACTATATGTAAAATGGATGCATTGTATCAGC
AATTCAAGTTGAATCTAGTGTCCTTTCTTGATCGTTTGGATTGTGGCTTA
TGGAAAAAGCTTACTTGTATGTTTATGTACTATATAAACGTGCAATATAT
CAGGCATTGTTTTCTTCTACCAACGGATTTTAGTTTGTGGTCTATCTAAG
TTTGGCTACCCATTATGCTAGACTGCAGCCGCGTGATTGCTACAATCTGT
TGATATTTCTATATATGACAAAGAAACAACTGAAAAGTGAGGAGTGGAGT
CGTGTCGAAGACATATCCATCACAAGATGAATATAACTTTCACTTCTCAC
TGATTTTTGATGTTTTTTTTCATGGAGACGGATGAAGCATCCCGAGCATT
TGTGAGGAATTTATAGCTTTTAAAGTTAATGTGATGTTGTCAAATTGTTT
GATTTGTACTTAATTTTATGACTTACACACTCTTCTATGCTATATGTTTT
CTCAGTCGTGTTTATGCAGTTTTCTATTCTCTAATTGCTTAATTGATAGT
TTGAAGAAGTTTTGACACGTTATCGTGGCTTGCCTATTTATGAATTGATG
TCCTAATGATCATTTGGCAGACACAAGACATTTGCTTGCTGACACTTATA
TTGTAATACAGGTACCCCTCTATGGCGCAATGGACCTCCAGAGAAACCAG
TACTGTGTAACGCATGTGGATCACGGTGGAGAACTAAAGGATCACTCTCA
AACTACACACCTCTTCATTCCAGGGGAGAACCAGATGAGTTGGAGTACAG
GGTCAGAATGAAGGCCATGTCCTTAAAACATAAAGAAGCAAAGGTGCTAA
AACGAAAGCAGAATCATGGTGTGGATGTAGTCTCTAGAGTTGCCCCTGAT
ACTGCTTCCCAAAAGGGTGTTCGGGATGCTCTTCACTACAATCAGGGATA
CTTAAAGACCCTTGATGAAGATACAAGTAATAGATCAAGTTCTGGCTCAG
CAATATCACCCTCTGGGAGCTGTGTGCATCTTGGTAGTGCAGATGCAAGT
GATTTGACAGGTTGGATGACCACTCATTTGCGTTTTACCCATATAATGTC
TTTGTAGTTTAAAACTTCCAATCACTATATTTATTTTTAACTTACTGTCT
TCATTGTTTCTCTTCATCTTATAGTTGTGCATCCCATAGTGAGATACTGC
TGGCTGTATACCTAAATTTTATCGAGGCTTATTAAGTGGTGTAGTTTCTG
ACTTTTCGGCATGATGTTTCTGTGCCCCATGCAGGTGCAACCCAATCCAT
TGTGTGGGATAGTACTGTACCCTCAAGGAAGAGGACCTGTGTTGGTCGCG
CAAAGCCATCTTCGGTTGAGAAGCTTACAAAAGATTTATATACCATTCTA
CAAGAACAGCAGTCATACTTCTCTGGATCTACTGAGGAAGATGTGCTTTT
GGAGTGTGATACTCCAGTAGTCTCTGTAGAGATAGGACATGGAAGTGTGC
TTATCCGGCATCCAAATTCAGTAGCCCGTGATGAGGAATCGGAAGCTAGC
TCCTTTTCAGTATATAACAAGCCACATCCTGCTAATGAAGCTTGTTCAGA
GTTTATTACCCTGCGTAACCATACTTTAAACAGGTTCAACAATTTTTCGT
CGGCTGAAATTGAGGGAAAGAAGCAGCCTGGACATGAAAAGGAGCATGAG
CTATATAAAAGGTACCTCTTCTATTTGCTATGGAACTTGGAATTGTCAGA
TACAAGATACAGAGTATTTTGCTTCCCAGTCTGACAAGGATACAGAGGTA
CAATGCACAAAATAGGTTTGACAATCTTTTTCACAAAGCTGAGTTAACAT
GCAAACAGAAGACACCTCGCTATGATACATGCATAAGCTCTCTTCAACAC
AGTCGTGAGGAGACAGTTTTCGGGAATATAAATGATGCCGTAATATTTTG
AAAAAAATTGTATAAATGCTTTAGAGATGTGAGTCGGTTATGACTTATGA
AAGACAACTGTAACTGAAATTGGATAGCAAGTCTCCTCAGTCTACTTCGT
TCATAAAACAGTTAAGAGTCTTGAACATATTTTAGTACTGCATGGATGGA
GAGAGATGAATAAATTGAATAAGTCCTTTAAATTGAAAAATGCGAGTTTG
GAAGGAAGATAATCACTAATATGTCCCATGCATCTCTGTTTCTTTTCTAT
ACAAACTTACTTTTTACCATCAAGTTACTCATATGGTCAACCTAACTAGC
TGCTACGCAACTGGAGATTATTAAGTCTATCGGCATAAATAATATACTTG
TAGGGTTTGGAAGTAAGATAAATACACATTAGAGAGATGAATAAGTCTTG
ATCTTCAATCTTTTTCCACTGGCTATATGCACCTACAGTAAGCTCTATAC
GTGATTGATATCAAGAAAAAATGAAAAATCTAACTATTGAAACTATATTG
ACCTAGCTAGGGACATGTTTATTTAGTGATTTGTTGAGTAATTGTGCTTT
ACTTATGCTAACTGTTCGGATTTCAGAAAGGACCAGCAAGAAAATCTAGA
GACTGTTGGGAATCACAAATCACCAATATTTTCCATAGAACTAAATGTAA
GTTCCAAATATACACATTTCCTCTGCGAAGTAAGTTGAAGCACAAATGTC
AGTCCAAATCCTGTTCAAGTGAAATAGTTATAAATGTTCCCAGAGATAAA
AACTGTAAACAAAGACACCTTGGTCATGTACTTGTGCTTCTTTAAATGTA
TTATTTCCTATTTTTGTTGAATCTGGGAGTATCTAGCTAAAGGCTGCTCC
TGCATTTGTAGTAAACTATCTTGCACTCTATGGTACAAAGTAAATACTTA
TATGTATACATAATTTATATGCTTTTTTTTCTTAAAAAAGGGTTCATCTG
TGCTCAAATTTAACATAGCTATGGTTGATTCAACTTGTATTTTGACTTGC
ATGCTTAAAAACACGTTTTCTTTATACATTATTCTAGTGCACATGTTGTG
CCCATTCCAGATGTGGAATTTGTAGTCTGCATCTTGTTATGGTTACCTTA
AAGGTTATTTAAAGTTTCTTGAACTATGTTCAAAACGTTAAACTTCACAA
CTAAAGCTCCTATCACTACGTCAAATGCTCTTGAACTTCAGTTCCCTGAT
TTGTTATGGTTAGGGATCCACTTATCTTGTATACCTGCGCTAATTGTTGC
GTATATTTTGCATAGGATGTGCTAAACTATGAGGAGTTCAGGAGGCACAT
AACCAACCATGAACTGCAAGAATTACTAAATTTGTTGCCTTCCACTGATA
TTCTTGGACTCCCAGACAGGTATTATGACTGCTCCAACTATCATCTTATT
TACAAAGATAACTTCAGAAGCTAAAGTTAACTATTTGTTTTGGTCATTAA
ATCAACAGCCTCAAACTTATGTTTGAAAGCCCACAGTTCAAGGAAAATGT
ATCAGCTTTCCAGAAACTTATTGCAGATGGTGTTTTTGATCTATCCTCAG
CAGAGGTTAACAATGAATGCAATAGTACATTGACGAGGCTCTTACTTCAC
ACATTGACAAAATCATGTTGGGTGGAGCAATATAATATACTAAAGGTTGT
ACTCTAAGAACTAATTACCTTTCATTAATATGTTTGTTACTAGTTTATGC
AATACTGATGATACGTTTCTTGCTCTAGGATACAAATTGTGGAAGTACCG
TTGGTGGTTCTTCTGATGCCAGGGAACATGCAGCTGTTGCATCTGCTCAG
TCACTGGAGATAAAAAGATCCCGTGTTGGTCAACCTCAGAATATTCCAGG
TTAGTTGAAGTCCTCTTGATATATAAACAGATAGAAATGGATATATACGT
TCACTATACTTAAAGAAACTATATGCCAAAGCAATGCATGTGCAAATATG
GATGATGCATTAAATAGTCTGTTTGATTTCTTGCTACTGTAAAAATTTAT
GAGAACACTGAACTATTACAATTCTCTTAGTCACAAGCATCTGGTGTTTC
TAAATCAATTATAAGAAATTTACCTTGAGCATGTATGCTACATATGGGTC
GTGGATTAGCTTTATGAATGCAAGTGTTTAAGCACAATGAAGTGTAATTT
TTTTATGTATCAGCTTGACATTTTCCTTACCACGCCATAATTGCTTTTAA
ATCTAACAATGGAGATTTGTGGTCAGCTAATCCGTCTTTTTCTTACATGC
ATATTGTTGTGTTATAATGAGTATTGGATCTTGTAGATTATAAACTTGCT
CCACAAAAATACTCTTAACATAAATGAAGATGCAACAAAAAATTTGCTTT
GTTAGATCTCTAAGCATTTTGTGTTGTGCCCTGCTGTTATATAGTCTAAT
CTATGTTACGTATGACATGGAAATATTTTGAAGCTAAAAACCTTTCATAT
ACGTGGTTCAAGTTTCAGGAGGGAAAAAAGCTGTGAAGACTAACTATGGA
CTAAAGGCACCAATGGACAAAGAAGCTACTTTCTTCAGTCCAAAAACCCG
ACTTGTGCAGCCTCCTGATAATACTTCTCTTATGCCGGATTGTTTTCAGT
TTGGAGATGAAAGTTCTGATCATGATCTTTTACTTAACATACCATCCCAC
AGTTCTTTCCCGCAGGCAGAGCTGCTTTTGCCAACTCAGGGTTTTGGTGC
TCAAGCTAGTACTAGTAGCTCAATATACCATAACCATGTTCTGCATTGAT
TTCAAACAAAACCTCATTAGGCCCAACTTTTGGTCACCAGTTTCGAACTG
TCGTTTCGGATGAATTCTTGTACTGGCTCATTATATTTAAAACACTGGAG
ATGTAAAGGTCTGCTAAAGAGGCTTACTTGATGCCCTTTGTGTACCTTGT
TTAAACTTAAAAATAAGGCCAACTCCTACAGGTGAGGACTCTGAGGACAG
TGGATATATACATGTAATTTTGTATAGGTTAAAGATAATATTGTAAGATA
TACATCTATGTGGTCATGTGGTGTTACTCTGGTTCTTGTAAGTTGTAAGT
TGCAACCTTGTTGTTATTTTCA