| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017386368.1, is a part of gene, LOC108214388. |
| The genetic_marker, MK017688 3_39456541, is located in gene, LOC108214388. |
| The genetic_marker, MK009530 3_39461579, is located in gene, LOC108214388. |
| 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_017386368.1 | XM_017386368.1 | mRNA | DCARv2_Chr3:39455884..39462238 |
CTTGGAAGGTTTTTATACCTTTGATAATTTAACAATCTTTCCTCTTCTTG
TTCGGCTATCATTTCTCTTTCTTAGGGTTTTTTTTCAGATCGTCAATCAC
CCCTCTTTTCTAATCTCCCTAAAAATTAGGGCTTTTTTCATAACCCACCA
ATCTCAACCCTCAGAAATTCAATTCACCATGTGAAATCATCTCAAACACC
CCCAATTTGTTGATTTTCGAACAATTGAATCATGAATTTACAACCCAATT
TACCGAATGAAATGATGATGGGGCAAGTGCCCCAGATGGCTAATTCATCG
TTTAATGCGCAGGCACAGAATGTACAGAGTGGTGGTGATCATCGAAACCA
CCCGGATACGGAGAAAGTTCGGAGATTTGTGCAGAAGAAGATTTATGATT
ATTTGATTCTGAGAGGGCAACAGCAATCGAGTGATCTTTCGGCCAAAAGA
ATGATTGATTTGACAAGGTTGTTGGAGAAGGCTTTGTTTAATGCGGCTGC
GACTTTGGATGAGTATATGAATCAGGATTCTTTGGAGACTCGGTTGCTTT
TTTATTTGAAGCAGTTGCGGAATACGCAGAATCAGAGGTTGTTGCAACAG
CAGCAGATGAATTCTGGGTTGGCGAATCAGAATCAGCAGGTGATGCAGCA
ACAGCAAGTTAATTCGGGCTTCGGGAATATGAATCAGAATCAGCAGTTTG
TGCAGCATGGGAATTCCTCCGGGAATTTGAGTACTATGATCCCGACTCCC
GGTATGGATAATCAAAATTTGATTTTTAATGTGTGTATGTGTTTGTATGT
TTGTGAATATTTGTTGTGAATTATGATGATAATGGATTTTTTTAATTAGT
TCAATTTGGTCCCAATGACAGTATAAATATTTAATTTCAAGAATTTAAGA
ATGAGGCTTTCTGTTATAAATTAGGTAATAATGAAACAAAGGGTAGTTGG
CGTATGAATTTGATTACTATGATCCCCACTTCCGGTATGGATGACTCGAG
CTTTAATTTTTGATGTGTGTATGTGTTGTATGTTTGTAAATATATGTAGT
GCATTTTGATTATAATGGATTTTTAATTAGTTCATATCGTAAAAATTTTT
ACTTTCAAGAATTTAAGAATGTGGTTTTTCGTTATAAATTAGTTAATAAT
GTAACAAGGAGTAGTTCGAGTATGAATTTGAGTTCTATGATCCCCACTCT
CAGTATGGATAACTCGAGCTTCAGTTTTAAATGTATATGTGGGGGAAATT
TGTTGTGAATTATGATGATATTGGATTTTTGAGTAGTTCATACTGTTCTG
AATGTTAGTAAAAATATTTGCTTTCAAGAATTCAACAATTTTTCATTACA
AGCTAGAAATTTTACTGTGTTTATATGAGTTTTGTGTGTTCATCTGTATT
TGTTATAATGATTTAGGATTTTAGAGTAGTTCATTTTTGCTTAGAAAGCT
AGTCAATTGCTTATCTTTATGTAAGTGCTGATAAAGGTATCCTTGAACTA
AGTATCAATTCAAGAAATTTAAAAAATGGGACTTTGCAGTTCAAACTTAC
ATATAATACAAGAGGGAGTTGGGTTATGGATTTAGCAAAAAAACTAAAAT
GTAATGTATTTATTTTTTAAATTTAAGTAAAATACTATTATTTACAGCTA
TTAGGTTCTGCAAAATGGATTTTTTTAGTTGAAGTCGAAATTTGCTCAAT
TAATGGAGACGTGTAGATTAGAATCCAACTGATTAGCAAGTCACAATCAA
TCTTTAGCTATATACAAGAGCCTATTCGTAGTTCAATAGAATTAAATATC
TTGTTAAATTGATAGTACATCTTTTGTTATCAATGATGTTTAATATTCTC
TGACGTATATTTTTTTAATGGAAAATACAGGTGGCTTTTTGCCACTTACT
AGTAGCATGGGTAGTGCATCTTCTTTTTCTAATGGTTATCAACAGCCAAC
TTCAGTCTTTCCCACAACTTCGGGTAGCAACAACATGGTTTCATCAGTGG
GTGGTGGTGAGAGAATTCTTAGCCAGATGATGCCTACTCCGGGATTTGTT
AATTCCAATAATACTGAGGCTTACAGGAGTTTGGAGTCTAGTAATAGTGG
TGTGGTCCCAACTGTTGAATCTATGATGGTATCACAGCCCCTGCAACAAA
AGCAGCACATCAGTGGTCAAAACAGACGTATATTGCACAATGTTGGTAGT
CATATTGGTGGTGGGATCAGAAATGGGACCTTCAGTGGTGGTTTGGGAAT
GATGACTAACTATGCACAGCCTGTGAATGGTACAGGTAGTTTTGAAAACC
AACTGCCAATGTCACAAGTTCTGCATCATGATGGGTACGGGAGTGGTAGT
GCTGATTTTTCTGGCTCTGGTACGGGTAATGTGTATGCTTCTTTGAATGC
TCCTGGGCTTATGGCGAATAATCAGGGCAACCAATCAGAATTTCTCACTG
CTCAACAGGATGTGCATGTAAAGCCTTTGATTGAACAGTCCGTAAAGATT
AATTCTCAATCGACACAGTCATTAACTGAGAATGTTGTGCAGTCTCATCA
GCAACAACTTCTCCAGCAACCTAATCAGATTTCCCAACCAAGGCTGCAAA
ATCAGCCAAACCAGCTAGTCCAGCAAAATCAGCTTATCCAGCAAAACCAG
CACATCCAACAAAACCAGCACATCCAGCAAAATCAAAGTTTACCAAATGG
CGAATTACAAATGCGCAAAAACCAGCTGAGGTGGTTATTGTTCTTGGGTC
ATGCCAAATCTTGTCGTGCTGCTGAATCTTGTGCAGAAAAGCATTGCATA
ACTGTTCAGAAACTGTATAAGCATATTGAAACATGCACACTAACTCAATG
CCCATATCCTCGTTGCCATGGTACAAGGTCATTACTTAATCATTACAAGA
TATGCAGGAGGACAGACTGCCCTGTTTGTGTTCCGGCTAGAACTTTTGTG
AACAAGTGTAAAGAATCTAGGACTAATGATCCCTCTGTCAATGGATCTTT
TAGTACCTATGATAATAGGAATGCCTCAGGCAGGTTGATTAATCAGTCTG
TTATAGATACAGAAGATGTAAATCCTCCTACAAAACGCACAAAGATCGAG
CAGCCTCTGCAGTCTCCAGTGCCTGACCCTGAAACTTCTGCTCAGCCACT
TCCTGCTTTTCGTGATTCTTGTACTCTGCCGGATGTACAGTATTTGGAAC
ATAGACCTGATGAAACTTGTAGACCAGTGAAATCAAATGTTACAGGGGTG
AAGTTGGAAACTTATGCACAAGATGTTCCTCATGTTGAGCTGAAAAAAGA
TATGAATGAGAACTCTATGCGATTGTCTGATGGCGTTTCTTCTGTACCCA
GTGGTGCTAGTGGCATCCCTAAGGACGAAAGTTTTAATGCTGGTAAAGAA
GTTTACCAGACTAAGCCTGAGAGCGTTACATTGCCTGCTGAAAACGTGAG
TACAACCAAGTCTGGGAAGCCAGAAATTAAGGGAGTATCATTGACAGAAT
TGTTTACTCCAGATCAAGTTCGGGAGCATATCACAGGTCTCAAGCAGTGG
GTTGGCCAAAGTAAAGCGAAGGCAGAAAAAAATCAAGCCATGGAACACTC
AATGAGTGAGAACTCTTGCCAGTTATGTGCAGTTGAGAAGCTAAATTTTG
AACCTCCACCAATTTATTGCACACCTTGTGGTGCTCGCATCAAACGAAAT
GCGATGTATTACACCATAGGAGCAGGTGATTCACGCCAATACTTTTGCAT
TCCTTGCTATAATGAAACTCGTGGAGAGACTATTTCTGTTGATGGAACTC
CTTGTCTAAAGTCAAAACTTGAGAAGAAGAGAAATGATCTAGAGACGGAA
GAAGGGTGGGTTCAGTGCGACAAGTGTGAAGCTTGGCAACATCAAATATG
TGCATTATTTAACAGTCGGAGGAATGAAGGTGGACAAGCTGAGTTCACTT
GTCCAAACTGCTATATTGCTGAAGTTGAAAGAGGAGAACGTACGCCCTTA
CCACAGAGTGCAGTACTTGGAGCAAAAGATCTGCCGAGAACAATTCTAAG
TGATCACTTGGAGCAACGACTCTTTAAACAATTGAAGCAGGAGAGAATAG
ACAGGGCAAGAGTCCAGGGGAAAACTTATGATGAGGTTCCAGGAGCGGAT
TATCTTGTTATTAGGGTCGTGTCTTCGGTGGATAAGAAGTTGGAAGTGAA
GCCACGATTTCTTGATATTTTTCGTGAAGTGAATTACCCCAACGAGTATG
CATATAAGTCGAAGGTAGTGTTATTGTTTCAGAAAATAGAAGGCGTAGAG
GTATGCCTATTTGCTATGTACGTTCAGGAATTTGGAGCAGACTGTCAACA
GCCAAATCATCGCCGTGTTTATCTGTCCTACCTGGATTCTGTGAAGTATT
TCAGGCCAGAGATTAAAGCAGTAACGGGAGAGGCACTCCGTACATTTGTA
TACCATGAAATTCTGATTGGCTACCTTGAATATTGCAAGAAACGTGGCTT
TACGAGTTGCTACATATGGGCTTGTCCTCCACTAAAGGGTGAAGACTATA
TTTTATATTGCCATCCAGAAATTCAAAAGACCCCAAAATCTGATAAGCTC
CGGGAGTGGTATTTATCAATGTTGAAAAAAGCTTCAAAGGAGAAAGTTGT
GGTTGAGTTGACTAATTTATATGACCATTTCTTTGTATCTGGTGTTGGTG
AATGTAAGGCTAAGGTGACTGCAGCTCGACTCCCATATTTTGATGGTGAC
TATTGGCCTGGTGCTGCTGAAGATATTATCAATAAGCTTCAACAAGAAGA
GGATGGTGGGAAGCTGCATAAGAAAGGGACAACCAAAAAAACATTCACTA
AAAGAGCTTTAAGAGCATCTGGTCAAGTTGATCTGTCTGGAAATGCCTCA
AAGGATCTCATGCTAATGCATAAACTTGGTGAAACAATTAGTCCAATGAA
GGAAGACTTTATCATGGTCCACTTGCAGCATTCATGCAGTCATTGTTGTA
TTCTGATGACTTCAGGAAACTGTTGGTTTTGCAGCCAGTGCAAAAGTTTT
AAGTTGTGCGATAAGTGTCATGAAGAAGAACTAAAACTTGAAGAAAGAGA
CAGGCATCCCATCAATCAGAGGGGTATGCATATGCTCTATCCTGTTGAAG
TCACTGGCGTGCCTGCAGATACACAAGATACAGATGAGATTCTTGAAAGC
GAGTTCTTTGATACGCGGCAGGCGTTTCTTGGTCTTTGTCAAGGTAATCA
TTATCAGTACGATACCTTACGCCGCGCTAAACATTCTTCAATGATGGTCC
TTTACCATCTTCACAATCCGACGGCTCCTGCTTTTGTGACTACATGCTAT
GTATGTCATCTTGACATAGAAACTGGTCAAGGTTGGCGCTGTGAGATATG
CCCAGATTATGATGTATGCAATGCTTGTTATGAAAAGGATGGAGGAGTTG
ATCATCCTCACAAGTTGACTAATCATCCATCAATTGCGGATCGTGATGCA
CAGAACAAAGAAGCTAGGCAACAAAGAGTGATTCAGCTGAGGAAAATGCT
CGATCTGCTGGTACATGCATCTCAATGTCGTGTTCCGGAGTGCCAGTATC
CTAATTGTCGCAAGGTGAAAAGGCTTTTCCGCCATGGCATGTCCTGCAAA
ATTCGTTCGGGTGGAGGCTGCCTTCTATGTAGAAGGATGTGGAATCTTCT
TCAACTTCATGCTAGATCATGCAAAATATCTGAATGTCATGTGCCTCGGT
GCAGAGATTTAAGAGAACATTTCCGTAGGCATCAACAGCAGGCTGATAGT
CGTCGACGTGCTGCTGTTACAGAGATGATGAGGCAGCGGGCTGCTGAGGT
TGCTGGTGGTAATTCCTGATATCAAGCTGTGGAGATGTGTCAATCAACCA
AGATAGTAGTTTTGCTGTTTCTTGTCTTCGTTGCTGATACCTACAATCAG
GACAGTAAACAACACAAGCAGCTTTCCGTTGGTGCTTGGGGTGGCAAGGT
TGCTGCGAAGTTGGTTGACTATGAAGCGACTTGATCAATTTTTTCATTCT
TAGCAGGGGGAGTGAGTAATTTTTTGATTCTTAAAGTTAAAATCTTTCCT
TCCCTTCTAATAATTAGTAGTTTGTTTAAGCTGTACACAAGTCAGAAATA
CATGTAGCAGCAGGAGAAAGGAGTTAATATGAATTATGGATTTTGTTTTG
GCAAAATATGGCCAGTTATACTTTTGCAGTTGGCAATATGGCCAGTTATA
CTTTTGCAGTTCTTTACATATCATTGACTTCACTCACATTTGGTTTGTGT
TGTGAATCATTTCTATGAAATCTTTATGGGAATATTACTCCTTTGAACCC
CAAA