| NCBI Gene |  |
|---|
| Relationships |
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| The genetic_marker, MK009323 1_792000, is located in gene, LOC108200978. |
| The genetic_marker, MK009325 1_791890, is located in gene, LOC108200978. |
| The genetic_marker, MK009324 1_791946, is located in gene, LOC108200978. |
| The mRNA, XM_017369267.1, is a part of gene, LOC108200978. |
| The genetic_marker, MK011692 1_790723, is located in gene, LOC108200978. |
| The genetic_marker, MK011691 1_790737, is located in gene, LOC108200978. |
| The genetic_marker, MK011693 1_790759, is located in gene, LOC108200978. |
| The genetic_marker, MK009319 1_791796, is located in gene, LOC108200978. |
| The mRNA, XM_017369285.1, is a part of gene, LOC108200978. |
| The mRNA, XM_017369273.1, is a part of gene, LOC108200978. |
| 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_017369267.1 | XM_017369267.1 | mRNA | DCARv2_Chr1:789481..794583 |
| XM_017369285.1 | XM_017369285.1 | mRNA | DCARv2_Chr1:790160..794583 |
| XM_017369273.1 | XM_017369273.1 | mRNA | DCARv2_Chr1:790322..794583 |
| XM_017369279.1 | XM_017369279.1 | mRNA | DCARv2_Chr1:790692..794583 |
AATGCACACTACTCCATCAAAACTACCACATCCTTGAAGATCTCACTGAG
AATCACTCACCTTCCTCACAACTAATATGGTGTCCTTACCAAAAAGACAC
TAATGCCACCCTTTTGATAAAACCCCATTAAATTACTCTCCTCTATCTCT
TCAATCTTCTTGCTCTCTCTCTCTCTCTATTAACTCCTTGCAGCTCTCCC
CATACACCCATACTTCTCTCCATGCCCATAATATATTCTACATTTTCTTG
CTCATTTTGCTCATTCACTTAGCCTACACTCCTTAAAGATTTCAACTTTC
AAGACCTCCAAGCCAACCCAGGTACTCCCTTTCTCCTTCTCTTCTTTTCT
CATCAATGTACTTGCACTTTCTCTCGAACCCGGTCTTTACGGAAACAACC
TCCCAAAATTAGTCTCCGGTATGAAACACATGTGCACATGTACTAATTAC
TGTCTGTGACAAAAATTTAAAATTTTAAAATTGACCAAATCTCTGCTACT
TCTCATTTATTTCATAATCTGCTTATCTGAGACATGTACTTATCTGACAG
ATCTGCTCTTATTGGTTCCATAATTTTTCTTCTATATTTTGAAAATTTTA
CATAGTATTTGAATTTTGTTTTATCTACTGTATAAAGAGTACCTTAAAGT
TATGTTCTTTTTGTTCAGATTAAAGGACTCCAGCTTTCTTTTTGTTATTT
TGTATCTTCACCTTTCTCTTTTTACCACATTACTTTCTAGGACTCTGTAG
TCTGTACTGCTTTGATGCATGTCTATGTAGTTGAGATTAAGTAAAGTTTA
GTACTTGTAATCATGTGTCTTTACCGGTAATTAAGGATTTTTCTTCAACC
TTCATGCATGTTAATTTAAGTTAATATTTTTTTTTAGTTTTATCAACTCA
TATTTTAAAGTCTTTAGATCTTTACACGAGGTAGTTTAGCACATGGTTCC
AGAAAAGTATTGACCTGTTTGTATATCTGAATCTTACTCAAATTTAATAG
AGTTCTTTATTTTAATTACTCAGTTCCAAAGTGAAGATCTTCCCTAGTTT
TGTTAGCTAAAGTTAAGTAAACATTGTTTTGGACTTCTCCATATTGTTGG
CCATTATTCTCTATTGAATTTTTCAGAAGAATTATTTGTCAAAATTTTAA
GCTAAATCTGCAAACCTTGAAATTTCAGTGAAGGGCTAATACAAGCAATT
TGAGGTGAAAACTGCTGCATCCAGTTTGTTTTGGCCTTTGTCGATTTATT
CTTGCCTGATTTACGCGATCTAATAGAGATATTTAGCATGTAATTAGTGC
TTATCTTTTCGTAGATGCTACATTTTTATTGCAGCAATTTTATGATGAGC
ATTCTTATCTGTTAGTATTAGAGGTTCTGAGAACTAGGCTTGCACTGGAC
TTCAGCTTCTGTATATACTTCTGCTTGCTTTTTTATTTGTTTTAAAGGTC
ATTGAAATGTTTTAGGCTGTCACTTGTTGGGATGTTGGAATTCCTGGTAT
TGTCTATACTCGATCTGTTCTGCTGACATGTTAGAAGATTACTATTTCTG
TATATCTTTCTTAGATGATCCTTCTGGATGAGTTTTTTAGATATGAATTA
GCAACTCTTTTTGGAACAGAACATAATTTATTAACTTAAGTTTATTGTTA
GGGAGAGAATTTGCATGAAGCATATTGTTTTCTTGGATTCTTGAAGTATA
TTGATTTGATCACTTCTTTTCGGGCTTATTCATTTTGTTAGGCTCTTAAT
TGTCGTCTGTAATTTTCCAGATTCTTGTGATTTACATCCTTTTTCCAACA
ACTTTGCTATGAACAACCTTAAGCTTGGAGTTGATGTAGCTAGTGCCCAC
AACCTTCTGCCAAAAGATGGGCAAGGCTCATCCAATGCCTATGTGGAACT
CTACTTTGATGGCCAAAGGCACCGCACAACCATCAAAGAGAAAGACCTGA
GCCCAGTCTGGGATGAAAGCTTCTACTTTAACATCTCCGATCCATCCAAC
CTTCACAATCTAACTCTTGAAGCATACATTTACAATAATATCAAAATCGC
CCAATCAAATTCTTTTCTTGGAAAGGTTTCCATCAACGGGACATCCTTTG
TTCCCCACTCTGATGCTGTAGTCCTGCACTATCCTTTGGAAAAGCGTGGA
ATTTTCTCACGTGTGAGAGGAGAACTCGGTCTGAGGGTTTATATTACTGA
TGATGCATCCTTGAAGGCCTCTAAATCACAACATGCAGCTGAAGAGACTG
AAATGCATTCCCACGCAGCTGAAGCTCAAGTATCTAGGGCATTTTCTAAT
ATCAAATCTGAATCGAGGCACAGTTTCCATCATCTTCCAAATCCTAGTCA
TCACATGCAGCAGCAGCATTCCCCTTCTATGTCAGTTTATGAATCAACAA
AATATGGGGTTGATAATATGAAAGCTGAACCACAACCCCCAAAACTTGTC
CGCATGTATTCTGCTGCATCAGTGCAACCAGTTGACTATGCACTTAAAGA
GACGAGCCCATTTCTTGGAGGAGGACGAGTTGTAGGGGGGCGAATACTTC
ATACAGACAAGGCTGCTTGTACTTATGATCTTGTAGAAAAAATGCACTTT
CTTTTTGTACGTGTTGTTAAGGCTCGTGAACTTCCTGCCATGGATATTAC
TGGAAGTCTTGATCCTTTTGTTGAGGTGAGAATAGGTAATTACAGAGGAG
TCACAAAGCATATGGAGAAACAGCAGAACCCAATGTGGAATGTTGTTTTT
GCATTCTCAAGGGAGCGAATGCAGGCATCGGTCCTGGAAGTTGTAGTTAA
AGACAAAGATCTGCTGAAAGATGACTTTGTTGGCCTTGTAAGGTTTGACC
TGAATGAAGTTCCTATGCGTGTTCCACCTGATAGTCCACTGGCTCCTGAA
TGGTACCGACTCCAGGATAAGAAAGGAGAGAAAATTAAGAGTGAACTGAT
GCTTGCAGTGTGGATTGGTACCCAAGCAGATGAAGCTTTTCCTGATGCTT
GGCACTCTGATGCAGCAACGCCTATTGACAGCTCCGGAGCTGCCTCAACA
CTAATTCGGTCAAAGGTCTATCATGCACCGCGATTATGGTATGTTCGTGT
GAATGTTGTTGAGGCCCAAGACTTGGTTCCAACAGAGAGAACTCGCTTCC
CTGACGTATATGTAAAGGCACATATAGGGAGCCAGGTTTTCAAAACAAAG
ACAGTTCAAGCAAGGTCTCTGAATCCTCTTTGGAATGAGGATCTCATATT
TGTTGCCGCAGAACCATTTGAAGATCATTTGGTCCTTACTGTTGAGGATC
GTGTGGGTCCTGGAAAAGATGAGATTCTGGGGAGGGTAATCATCCCCTTA
AGCATGGTGGAGAAGCGTGCTGATGATCGTCTCATCCATTCTCGTTGGTT
TAATTTGGAGAAACCTGTCGCTATAGACGTGGATCAGCTAAAAAGAGAGA
AGTTCTCTAGCAGGCTCCATCTTCGAGTCTGTCTAGATGGTGGTTACCAT
GTTCTTGATGAATCTACACATTACAGCAGTGATCTTCGTCCGACAGCAAA
ACAACTTTGGAAGCCATCTATTGGGGTTCTGGAACTTGGTATTCTCAATG
CAGTTGGACTCCACCCTATGAAAACAAGAGATGGCAGGGGCACATCAGAC
ACATATTGTGTAGCCAAGTATGGTCATAAATGGGTTAGGACGCGCACAAT
TGTTGATAATTTGTGTCCAAAATACAATGAGCAGTACACTTGGGAGGTGT
TTGATACTGCTACAGTTCTAACTATAGGTGTTTTTGACAATAGCCAGCTA
GGGGAAAAAGGGGGCAAGGACCTGCAAATTGGAAAGGTACGAATTCGCCT
TTCTACACTTGAAGCTGGCCGCGTTTACACACACTCTTATCCTCTACTTG
TTCTTCACCCTACTGGTGTCAAGAAGATGGGGGAGGTGCATTTGGCAATA
AGGTTTTCATGCACTTCTTTTGTAAACATGATGTACATATACTCTAAACC
TCTGTTGCCGAAAATGCACTATGCTAGGCCATTTAGCGTAATGCAGCTTG
ACATGCTGCGTCACCAGGCTGTGAACATAGTTGCAGCGCGCCTGGGACGT
GCAGAGCCCCCTCTTAGGAAGGAGGTCGTGGAGTATATGTCTGATGTGGA
CTCACATTTGTGGAGCATGCGCCGCAGCAAGGCCAATTTCTTCCGTCTCA
TGTCAATTTTTTCGGGATTATTTGCTGTTGGAAAATGGTTTGGGGATATA
TGCATGTGGAAAAACCCCATCACAACAGTGCTTGTCCATGTCCTATATGT
TATGCTTGTTTGCTTCCCAGAACTAATTTTGCCTACTTGTTTCCTTTACA
TGTTTCTGATTGGAATCTGGAACTTTCGATACCGGGCAAGATACCCTCCT
CACATGAACACAAAGATCTCACAGGCAGAGGCAGTGCACCCTGATGAACT
TGATGAAGAATTCGACACATTCCCCACAAGTCGTAACCCTGAGATTGTCA
GAATGAGGTATGATCGCCTGAGGAGTGTAGCTGGTAGAATTCAAACAGTG
GTAGGTGATATTGCTACACAGGGTGAGCGTGTTCAATCATTGTTAAGCTG
GAGGGACCCTCGCGCTACCTCCATCTATGTCACATTCTGCGTAGTAGCTG
CTATAGTGCTGTATGTGACACCATTCCAGGTGATTGCTGCATTGGCAGGG
GTATACATGATGAGGCATCCCAGATTCCGCTATCGTCTGCCTTCTGTGCC
TGTCAATTTCTTCCGTCGACTTCCTGCAAGGACTGATAGTATGCTCTAAC
TTAACAAGAAATTGTTGCAGGCTCCAAGCATGCCAGTTATTGCAACTCAA
GTCACGGTAATTAGTCTGTTACCCTGTTCGATTATCAAATGTTCCATGTA
TTCTTTCTCCATTGTGCTGAAGATTTTGTCTAATAATATATATCCAGTGT
TCTTTTTCTAGACAGTAGCCGGAATCTTTGCTGTTTAGCAGCAGAAGAAC
ATTTAATTACTAGAATGTAAAACTTGTTGAACAGACGACCTCTTGGTCAG
ATAGTATCTCCCTCGTTCCGCTTACTAGAAGTAATTGCGACAATAAAACA
CA