| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017397414.1, is a part of gene, LOC108223255. |
| The genetic_marker, MK004027 K1471, is located in gene, LOC108223255. |
| The mRNA, XM_017397412.1, is a part of gene, LOC108223255. |
| The mRNA, XM_017397413.1, is a part of gene, LOC108223255. |
| 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_017397413.1 | XM_017397413.1 | mRNA | DCARv2_Chr5:7628252..7635211 |
| XM_017397412.1 | XM_017397412.1 | mRNA | DCARv2_Chr5:7628252..7635210 |
| XM_017397414.1 | XM_017397414.1 | mRNA | DCARv2_Chr5:7628252..7634908 |
ATTATTCATTCTTGATAAATCATTAGTTAGTTCAGCCACATGACCTCCTT
ATCTCGGTCTCAATTGCCTGTGAGAAATTATAAAATAGCCAAGTATTCAA
CTGCTTTTCTCATTTTTCATTGACCAAATTGAAAAACCCCGGCCAAAAAT
CTCCAATCTCATCCAATTTACTAACAAAATTCTCATGAATTGATGTTAAC
CTTAAGCTCTCAATGGCGATTCTTGAGTTTATCACTCTTTTTCTGTGTGT
AATCGCGTGTATATATGCCGGATATGCCGACTTATCGGCCAACTCCGGCA
GATCGGAGATCTCCGTCGCCGAACAAAATCTCGACGGTGCAAATGGGTTT
CAAAAATTCCACACCACCTCTCTACTGCCGGCTAAAAAGTGAGGCTACTA
ATTTTACTGCTTTGATTTTATGATTTGTGGATGTGATTGTCATAATTGAT
TCTTATGGTTGATTTCCATTTGATTGTTGTAATTGAGAATATTAACTGAA
TTGGGAGTGAATGGTGATGTCGATTAGGTCGCAGTTAAAGTTTTCGTATC
TTAGTTGTTTCCCCTTAATTTAATTACAGTGTGCCGAAAGATCAATCTTT
TATCCCGTTTAATTTTATCACAATGTGCTGAAAGATCAATTCTTTATCAG
TTAAATCCTTTTTTGCCTCATGTATGTATTATGGATGTGAAACATTTTTA
CGATACTTTGAGTAGGTCTGAAATAGCTGACCTTTTATTTGAGGTAAAGA
GTGTTATGCATTTTCCACGGAGTTTAAGTAAGTTGGGAATTGGTGATCTT
TGATTTGAGGTTGTGTGTGTGTTTGTGTGTGTGTGTTGTTTAACTACTTA
ATGTAATATCTATGTACTTTAGGTTTTGTTACACATTTGTAGATGCCTGA
GGTAATTATAAGCCAGAAGGTGATTTTGATCTCATCATGAGCATTGTATC
TGATTGAATTGTTGATTCAAGTACACAAGGAAGTTTAGTTCTTTATGTAG
CCTCCTAGAGACTTACAGTGATTGGTGATAGAATTAGGATTCTCCTCAGC
TCCAGGGGGTAGCTTCCAGTTACATATTTTCCAGAATATTTAAACAAATA
TATACATATAAAAGTTAAAACTTTGACCCCTCTACTTGATTAAAATTTGA
TCATATTTATTTATTATTTTTTTTAATTTTCAATCTCTCTTATCACTTAC
TAGTTTTGATCCTATTTATTCATAATGATTGATTATACGTTCTCGGTTAT
TTGTGGGAATTGACTCAGTAAACATGATAGAGCATTGGTGGTTGCTCCAG
ATGGTACAATATCCCTCATGGATGTGAGCTCAAAAAAGATCATTTGGTCG
TTTGCATCAGGACCATCTATCTATTCTCTGTACCAGGCTCTTCCTGATCA
CGAAGGTGACAATGGTAGCTTCTTTATTGATCTCGGACAAGATGATTGGG
AACTCTACATGCATGTTAATGACTCTACAGCTGTGGTACTGCACTGCAAT
ATATTTGCATGTACAAATGAGCTAGTTTTTGACTTGCATAAAGTTAATGT
GTATACTGTACAGTAAAACCTTGATGTATTAATAATCGATAAGCTACCAC
GAGTAATTGATATTTCTAATTATCTTTTTAGTCTCAGTAGAGATAGTGTA
TATTTATCCTTGATAGATTAATAAAATTTACCGGTCCCAATGCTCTTAAT
TTATAGAGGCCTTACTGTATAGTGAAATTTCTTTTGTTATAATCCTTTTG
CATTTAATATGAAAAGAATACAAAATTAAAGCTTAAGTGGAAATAGTCAC
TTTTGTTTATCTATGTGGACTCATAAAGTATGCTATGCGAACTTTGGTGA
ATTCTTCCTAAATGGATACGTCTGTAAGTGTTTGACAACATTTTGAATAT
TCATGTTCTTGGTCCAAACAAAGTGTCACAGATTTTAGGTGTCAAGTGTC
CGGCATTTGCACCCAACGTAAACTAAATAGGCGGGGTCACATAGAGTATA
AATTTGTCTATGCATGAACTTGAACACAGCATATATGTGGATGCATGCTC
AAGAAGAATCCAGGGGCTACAAGTCCTACTAAATATTGAGTAATGTAATT
CAATACTTGGCATATCCAGAATATTAGTTTATAGTTTATTGTTAAATTTT
ATTTTGGCGATTTGATATGGGTTCAGTACTTGCCATCTGCTTTTTTGATT
GATATATCAATTATGAAGTTTTAGTTACTTATGTTATTGATATATAGATT
GAATATATCTTCCTTGAGATAAATTTCTATTTAACCAGACATGTCTGATT
TTAATTTATATAACTGGAATGATTAAGTAGATATCGTTATACTCCCTCCG
CCGCTCTCATTTCTTTACAGGTTTTTTACATTGCTTGCACACAGTTTAAG
GTGCATATAAAATATAGTTTCATAACTTAATTTTTAAAATTTTCCTTTTT
TGTGTAAATATTTGAACATTAAATTTTATTCAGAAGAAAAAGAAGTCTAA
AATAATCTATGAAACTACATTTTATATGTGTTAAACTGTGTGCCAAGCCC
TCGTCCCCCAAGATAAACAACCTAGGGGGACAGAGGGAGTATTAAACTAG
TTTAATATCTAATAATATATATTAGTAATATTTCTTTAACCCCTAAATAA
GAATTATTTAGTAATCATTATCCTATCTTTTAAAGATATATTATTCATGG
TAATTAGAATACAGAGCTTCTCAGAATATATACATTTACTATATAATTCC
TTTTTATCACATGTCAAGTTCTGGACAAAGAATGTGGCTTTTGTTCATAA
TACATGGTACATTTTTTTTTTGAATAAGTAATGAATGGGACATTTTTACT
ATACCATAAATTGTTTTTCCTTTTACTTGTCATCTGCAGAAACTTGGTTT
CAGTGCAGAAGAATTAGTCAGGCGTGCACCATATGTATCATCTGATACAG
TCTTGTTAGGGATGAAGAACACCACTGTATTCCTTGTTGATGCTAAATCT
GGTTCAGTTATTCATACATTTGGATCAGCTGGCTCTCCCAATCCTGTGGA
TCTGATTGGTACTAAGAAACCTATTGTGGCGAGGAAGGACGGATTGCATG
AACCTAGTGGTCCTGATCCCCTGTATATTACTAGGACCGACTATACGCTG
AAGTACTCTTCTCAAAAGACTGGTAAAGTATTATGGTACTTAACTTTTGC
TGATATTGAAGCTTCTTTCCAGTGCCAGAGGATTGAGAAACTGTTTAGTG
GAGGCTCTTCTGGAGATGAGTTTTGTCAGACAAAGCCCCTTGTCTATCGA
ATCCGTAATCTTCCTACTTTAGAGTCTATTATGGTCTCTGATAGGCTAGG
GATGTTTCCATCTCGAGGTAGAAACCCTTCTCTGCCAGTTCCTGGTACAA
ACCACCAGGAGTCTAGGGGTAAAACATTTCCTGCTTTGCTCCATTCAGAG
AGTGACAACCTTCTTGATTTTAGTCAACATGAGCAAAGGAGTTTACCAGG
GGGTCGTCTGGATGTTGAAGGAAAGTTAGTGCCTGCTTTACCTCATTCTG
ATACTGAAGGGCGTATCTTTGCTCTTCCTGAAGGAGAGCATGTTAATGCT
GCCAGAAAATCATCTCCAGAAGGCCAACCCCTATATAGTGTGAGCTTCAT
TGTGCAACTTTTTGTCTTCATACTCTCCATTGTGGCTGTTTTTTTCCGTA
CTCGTAGCAGGAAACAAAGCATGTCAAAACTTCAGGCTCAGGGCATTACG
GCACAAACTGCTACATATAAGAAGAAAAAGACTAGAAAGCCAAGTGTAAT
GAAGAACAATGTTAGTACTAAAAGAAGTCAAAATGAAAAGTCAGGTGATG
GCAGCAGTGAAGTTTTGGACTTTGATAAAGTTGAAAAAAAATTTGAGCTG
GCATTTGATTGTGCTGATAATGACATAGATGGACGCAAGGTTGGTAAAAT
TCTCATCTCCAACAAACAAATAGCTAAAGGAAGCAACGGAACAGTTGTAC
TGGAGGGCAATCATGATGGTCGGTCAGTAGCTGTTAAGCGCCTCGTACGG
ACCCATCATGACGTGGCCTTGAAAGAAATTCAGAACCTAATTGCATCTGA
TCAGCATCCTAACATCATTCGCTGGTATGGAGTGGAGTTTGACCAAGATT
TTGTCTACCTTTCTCTGGAGCGTTGTACCTGCAGCTTATATGAGTTGATA
ACAACATATTCTGATAGTTGTCAAAGCCAATCAAGTGGAAAGGGAAAAGA
TCGCCAGACTTCAGCTGATGCAACTGCTAGTTTACTTTGGGCAGTAGATG
ATATCCACTACTTAAAATTGTGGAAGGCCAATGGGTACCCTTCCCCTCAT
TTGTTAAAGCTCATGAGGTAAGTGAAGAGCACTATTATTTGTTTTTAGCA
TGTGATATTGCACTTGTGAGATATCATCTCAGATGCAGGAATTATAGCGA
AGCTACTGACACTCCATATACTTATATGTATATAATTTTCCCAGTGACGC
ATGTATAGATGTCTATATATTAAGTTTTGTTTTCTTCTACAACTTGCAGT
GACTAAGCTTGCGATCAGCCGAGGACATTGTTCTGCACTTTAAACAATAT
GCAGAACAGTGTATACAGAAAGTTTAGAACAGTTTTCATTTATTCTCACA
TGTTTTGACGTTACTACATAGAGCGCACCCCATGTTCCAGAGAAAACTTA
ATGGTCTTTCAGTTATATCTTACGTAGCATGTTCTTATAAATGCATCCAA
ATGAAATGCTTGTTAAACGTGTTCTAGAATTACCTATGTCTAATATATTG
ATAGTGATTGTGAATATTAATTGTATACTCCCTTTTCAATGAAAGTTAGC
AGTTCATGGACTCCCAAGAACTGGTCACCAAATTTCACCAATGATAAAAC
TGGTATTATGTTTTAATTAAATGAAAGAGATCAAGTATGATTGACAACTA
AGTTGAGAGAATATAATGAAATAGAACCATTGTGGTTCCCTACAAAATTA
AATGAGATTATGCTTAAAGTGGAGCTGAGTTTTTTTTAAAACCATTGCAG
GGATATAGTTAATGGACTTGCACATTTGCACGAACTTGGAATCATACACA
GGGATTTAAAGCCTCAGAATGTGTTGATCCGCAAGGAGAGAACCTTGTGT
GCCAAGGTCTCGGATATGGGTATAAGCAAGCGCCTTTCTGGTGGAATGAC
TTCATTATCTAAGCAGACAACTGGTGAACGTCTTTCTGTCCTTTTAAATA
TTTCTCGTTTTGTTTCTATTTCTGGAAGCAACGTATTAAGTTTGCTCCAC
TTTTATAATATTTCTGTTTTTAAATTATATCGTACTCTAAATTCAGACAT
TAAGATGACAATAAAACACATATAATCAATTGTTTATATCTACAGTATTT
TAAGTATGAGTGCTATCATGTTTCAACGACATCTCTAGAATTCAGCTAGT
AGAAGGATATGCTTGGAATCTTGGATAGATTAGTGTCTGTGAAAGTTGTC
TTCTAAGTCTTGGCTGAGTTCCAAGTTAAGCTAGCATAACTTTAAAACCC
TCATGTTACAATTTAAAATTTATATAAGATATTTACAAGGAGTTGAGGCC
ACTCTACTCATACCCTTATGTTGTCTTACTGATTAATTAAAAATACATAT
ATGCATACTACATTCTTACAATATTGTTTGATGCAGGTTATGGGAGTTCT
GGATGGCAAGCTCCTGAACAACTGCGTGATGAACGGCAGTCTCGTGCTGT
GGATTTATTTAGTTTAGGTTGCATTCTCTTTTTTTGTATCACTGGTGGAA
ACCACCCATTTGGAGATAGCCTTGAGCGCGATTTGAATATTGTAAATGAT
AAGAAAGACCTTTTCTTGATAGAAAATATTCCAGAAGCTATGGATCTTGT
AACTGGCCTCCTAGATCCTAACCCAACTTTGAGGTATTACTTAATCTTCC
TTCAAGTTAACTTATTCTCCTGTAGAAATATATAAGCTGCATGCACAATG
TTTCTCCAGTCCATTCAACTGCACTATGCAGACATTCCGTTTTGCGGACA
AAGCCAAAAACAGTAGTGTACCTACTTAAGTAAGATTAATTGTCTACATT
ATAAGTGTTGACTGGTCCAACGGTTGCAGACATATTGCATAATCTTTTGT
TTTCTTCAGGCTATAGGCATTGTATGTACTAGAACATCAGTACACCTACT
TTTTCAGTGATAACTGACGCATATAAGATTAATATACATAATATGTGTAT
TGCCTAATGATCTCTACATTATGGTGTTTTCCAGGCCAAAGGCTGTCGAC
GTATTACATCATCCTCTATTTTGGAATTCTGAGATGCGGCTCTCATTCCT
TCGGGATGCTAGTGATCGGGTAGAATTAGAGGACAGGGAGACTCAGTCTG
AAATATTGAAGGCATTGGAAGGTATTGGATCATTGGCGTTAAATGGCAAA
TGGGACGAGAAACTAGAGAATGCCTTTCTTAATGACATTGGCCGTTACAG
GCGGTACAAGTATGATAGTGTGCGGGACTTGTTACGGGTGATACGTAATA
AGCTGAATCATTATAGAGAACTCTCTGAAGAAATACGGGGGATTCTTGGG
GTGGTTCCTGGAGGATTTGATAGCTATTTCTCAAGTAGGTTTCCAAAACT
CCTGATTGAGGTCTATAAAGTCATACACAAGTACTGTTCGGAGGAAGAAT
CTTTCAGCAAGTACTTCACAAGTATTTATGTATAAAAAAAGGTAAAGAAC
TGACTAATTTTAGCTCCAACTGTACAAGGTTTTTATGTAAATCAGGGAAA
TATAAAATTAGGGCATGAAATATATTACATGACTGTGTAAACTTTCCGAC
TTATTGAACATGTATCTATATCTTGTATTTGGTTGGGACGAACGAAATGT
ACAAAATTAGAAGGGATGAATAAAATTGGAAGGAATGTAATGAAATTTAA
ATTATAACA