| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017364557.1, is a part of gene, LOC108197069. |
| The genetic_marker, MK003799 K1243, is adjacent to gene, LOC108197069. |
| 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_017364557.1 | XM_017364557.1 | mRNA | DCARv2_Chr8:23607787..23613252 |
AAAAAATCTAGCATCTTGCCCTTTTTTTCCTCCCACCATCTACTCCCTCA
CTCCATCCCCCTCAAAAGCAAGCTAAGTACATGGGACATGGGTGCTAATT
AACAAATTGAGAAAGTCATATAAAAATATATTCTGAGTTGTACTACCAGT
ATTCAAGGGTTATGAAAGGAACAAATAAAGTCCATTTATAAAAGAGGTCT
ACACTCCAGACCATTCTCTATAAATGAGATCCTTTCCTCTCTGAAAGCTT
TGAATTATCAACCATTCATCACTATTCTTTCCTCATCTCAATTCCAAAGA
AGATATAATGGTGGGTACCCTTATCTCCTCCTCCCTTTCTCTTAGTGCAT
ATATCACCTTTCTTCAAACAAGAATCATATGTGTTTTTGTGAGTGTACAT
ATGTTTATATTCTTGTAGTTATGTAATAGTTTGGTCTTGGTGTATAATTG
TAGGAAGTGGAGCACCAGCTAGCCAGATGGGATGGTTATGTTGACTGGAG
AAACAAACCTGCACTCAGAGGGAGACATGGTGGCATGCTGGCTGCCTCCT
TTGTGCTTGGTAACAATTTATCTTCATACTATTTCATTTTGTTATAGAAA
ACTAGAAAAGCTCATCTGTGAATTTGAGGTGCATTGACAAGTGTGCATGG
ACACTAGGGCTTGGTGAAAACTTTAGTTCATGTGATCAACTTGAATAAAG
AGTTCCTTTTTGTACCTATAAATTGAATTATAAATTGAATTAATTAAAGT
AATTAATCTGGTTTGCTTTATTGACCCCTTTTGATAGTGGTTGAGATATT
GGAGAACTTGGCATTTCTGGCCAATGCAAGCAATCTGGTCATGTATCTGT
CGGAGCATATGCACTTTTCTCCGAAGGATTCAGCAAATTCGGTCACTAAT
TTCATGGGGACAGCCTTCCTTCTTGCCCTTCTTGGTGGCTTCTTGTCTGA
TGCTTTTCTCAACACTTATTTCATTTATCTCAGCAGTGCTTTCCTTGAAT
TCCTAGTAAGTTAACTTAATTTTTTAAGTCTTTTATTCATTATATATCAA
TTTGCTTTCACCACAACAAATCATCATCTTGACTGGCCTAGCTGTTTGTA
TAACATGAGGAACCTTAATTTGTTGAAACTTCAAAGGAATTAAATAGGGT
TTTGTTTTTTGTAATTAATGAAAATGGGTAAGCACAAAGTCCAATAAAAG
AAGTTGAAATATGGGTCTCCATAGTAATGACATCACATGCAGTTTTTGAT
GCTTCACTTAAACTAATTTTATGGGGAAAAGTGAGTGTCTCACAATTTGC
TTGCAGACGAGCGTTACTGCTTGTGTTCTCCCACTAAACTACAGTAGTAA
GTTACAAGTTACAAGCATGAGACACATGAATACATGATCGTCGGTCAAGA
AAAATGTTACTTGAACTAAAATTGCATCTTGTACGTTAAGTACACTAAAC
AGTGCCCTAATTTTAGCAACATTCGAGGTTGCATGTTCCCTGCAGAATCT
ATGAGCGTATGGTGTTTCAGGTGGGGTGTTTTTACTGTTCCCCAAGTCCC
CAACTCACTTTATACGTTGCTACTCTTTAGTTTCAGTAGTCTCCGGATTA
CTATTTACGTTAACATTCATCCACTCGTTCCATCCCAATTTTTATTTTAC
AAGTGTGAAGGGTTTTGTTTGATTTTCTATAAATTTTGAAAGATTGTTAA
TAAATAATCCATTAAAACACAGAAGTTTAACTAAACTGGGAAAAAATTAT
TCAAAAAGCTCATTAAAATTTTAGAGCAAGCCCGATAGGTTATCAATCTC
ATTACCTATTAATAATATAAAATAATAAGTCCCAGCGAATTTTAGTAATT
TAGGGAATTTATTTTAGTGTCAACACCAATAACAATACTTTTTTTGTTCT
CTATTATTACTTTAATAATAAATCTGAAGGAAATAAGAGGAAAAAGAAGG
AAAAAGATAAAGAAAAAAGAGGAAAATGAATTTTTTATTCATAATTATTA
AATAGGTCAGATTAGTGGTATCTAAAAATAGATTATTAATGATTAAAATA
TTTGAAAATATGATAGAGTCCAAGTAATTACAGATCATGTTGAAATACTT
TTTTTTATACATTACCTAAATATAAGTTGAGGAACTCGTACAGATAACCT
GCTCTTGGATGAATGGATCACTCATCTTCTCCTCTACATATCTGAAAATC
GGACTTCTCTTTTTGTTCATATATACGTGAGTCCGCAAAATATGTTGGGT
ATCGAAAATGTGGTGTCTGTTGTGTGATGATTGCTCAACAATTTGGAGTT
TGACATAAATGCGTGTGTGAATCTGTACATGTGTTTGTCAGGGTGTGTCG
GTCCTCTGTCAATTTGTCAACCATGCATGCATCACCTTCCTCTTCCTCTT
CTCCTCCGCTAAATTACAATCCTTAATATATTAAATATATTAATATTAAT
ATGATATGAAGAAAAACAAAATTTAAGTCCTATGGAAATCATGTGATACA
CGCAACACTACGATAAGTATATGTACGTGAGAGTGATGGATGTTCAACAA
ACTGGACAGGTGTCCGGTTGGCGTGCCCTTAAAAATCACTATTTTTTTTG
TTCGTCGAGTGATAAACAACAGTAGCTATCCTGAAAATATTGAATATATT
TATCTATTACTCTTCATTACATCAGATTCTTTACGGTTTACTAGTATTTA
TTTTTGGTAAGGGAGTGATTATGTAACTTTGGATGAAGACAAAGAGCTTT
TAATATAAATGTAATGAAATGATTGTGTAATCTAAAGGATTTGTACAAAT
AATTATGAAATTAACATTAATTTATATATAATAGTACTCATGTAACTGTC
CTATTATTTTTCCCGTATTTCTCAAATTGTTTTAATAGTAAAAGTCAATG
ACTTGGTTTGTGGACAGTGCTTTCCACTTGAACTAGACCACATTCACATG
TCTCAATTATCGTTCTGGTCAAACCGTCCAGAATGGCCACTCACTATTTA
CTTATTTTTGTAATAATACAATAATTTGATGTCGCTGGAGTTGAATATTA
ATATTAACATCACGCCGATATAAAAAACACACAAAATTGCATATATCGTT
ACGGTGCCCATACTTGCGAGCTGTTTTGTTTCAACCTACTAGCCCCAGTT
TTCATCTTGCCTTGACATCTTGTCATGTTACTTCAAAGCCTGATTTTGAA
TATAAGTTGCTTATTTTTGTGAAAATAAGTCCATTTCGATATGTTCCAAG
TTTTATAAGTTACTTCCAGATATGGAATAGTCATAGGAAGTAGTTGTTAC
TTTCTCCTGTTTCTTTTCCCTAGTGTGGAGAGCATTATTTGGAAATGGTG
GGCTTGGCCTACCAGGAAAGCTTGACATGAATGAAATGTGAGTTTGAAGT
ATACTTTCTGCAACTATCTCTTCCCACTAGCAAGTGTCACAAGAAAAGAG
AGATCTTAGTGGAGGATGAGTTAGACTTATCACATCTTCTTCTACAGTTT
CTTAATTTCTCCTTTATTCCCTTGCCATCTCCCACCTGATCAAAAGTTAT
GGTACCCCACAACCCTCATTATCCAATCATCTGCTAATAATCAAAAGGAT
ATATAATTGGCTGTCACTTCACAGCGAGTCGAACTCGAGTCTCCCACGAG
ACTAAACTATGATATCATGTTAAGTGATCAATTCTCTTAAAATCTCAAAG
TGTTAGGAGACTTACCAGATCATATTTATTGTATTCTAGCAATAGCAAGT
AAACAGTTGACTATGTTACCGTAAATTTAATTTACCATGTAATATAAAGA
TGGAAACTAAGTTTGGTTTGGAACAGGGTTGGCTGATACTAACCGTGCAA
GCTCAATCAGCTTCTCTAAGGCCAGCAGAATGTGAAGCAAATGTTCCATG
CCGCAGAGTTGGTGGCGCTAAGGCGGCAATGCTGTTTGCAGGCCTCTACC
TAGCAGCACTCGGGATCGGAGGCATCAAAGGATCTCTGGCAACACATGGT
GCTGAACAATTTGATGAGGACACTCCACAAGGAAGAAAGCAAAGATCAAC
TTTCTTCAACTACTTTGTATTTTCTCTGGCAACTGGAGCTCTTATTGCAG
TCACATTGGTCGTATGGATTGAGGATAATAGAGGTTGGGTATGGGGTTTT
GGGATTTCGACATTCACAATTTTCTTGTCGATTCCTCTCTTCCTTGCCGG
TTCAAAGTTTTACAGGAACAAGATACCTTGTGGAAGCCCGCTGACAACCA
TACTTAAGGTATGCTTCATCACATCAAGAAAGATCGTATATAATGTCATT
GACTGAATGGTTTCTTCTGTTTTTACAGGTGCTCGCCGCTTCTGCTTTGA
ATACTTGCGTTGCTGTGGCCAGAAGTCCAAACAATGCCATAGCAAGCATG
TCCGCGAGCCCTGCCTTTGGAACATCGATGAAGATGGAAAATCAACAGAT
GACGAAGAAGAGTAGTAAGTCACTGGATCTTCTTGAAACTCCATCTGACA
GTCTTAAATTTCTCAACAGAGCAGTGACAAGAATGCCAGCCCACAAATTA
CTAGAATGTACAGTGAATGAAGTAGAAGATGTGAAAATTGTGCTCAAAAT
CCTCCCTGTTTTTGGCTGCACTATCATGCTCAACTGCTGCCTAGCTCAGC
TTTCCACATTCTCAGTCCAACAGGCAGCCTCCATGGACACAAAACTCGGA
TCGTTTAAAGTACCTCCTGCATCTCTCCCTGTGTTCCCTGTCATCTTCAT
AATGATTCTTGCACCAGTATATGACCATTTAATCATCCCATTTGCGCGTA
AAGTAACTAAAACAGAGACGGGGATCTCTCATCTACAACGCATTGGAATA
GGGCTAGTCCTTTCCATTGTCGCCATGGGAATAGCAGCTCTTGTGGAGAT
TAAACGGAAAAGAGTTGCGACTGATACTGGCCTAGACACTACCCAGCCAT
TGCCAATAACATTCTTCTGGATTGCTTTTCAGTACCTGTGTCTTGGCTCA
GCTGATCTTTTCAGCCTAGCTGGTTTGTTGGAATTCTTCTTCACAGAAGC
TCCGAGTAGCATGAGATCGTTGGCCACTTCTTTGTCTTGGGCATCACTCG
CAATGGGTTACTTTCTAAGCACAGTAATCGTTTCCATAGTGAATAGTGCG
ACAGGCAGCGCGAAGAACAAGCCATGGCTCTCTGGTCCTAATCTGAATCA
CTATCATCTGGAGAGATTTTACTGGCTAATGTGTGCACTCAGCATACTGA
ATTTTCTGCACTATCTTTTCTGGGCAAACCGCTACAAGTATAAAGCCCTT
AACAAGGGTTAGGGCCAGGTACTGTAGATGATTTACAGAAAGAAACTTCC
CAAGTGCATACATTTGACAAAGGGACAGTTTTAACATGGGCAATCTCTTA
ACTACTGGGGCTGTAAATATGCTGGAGATTATTTGATGGAAGTATTTTTC
TTGATTTATGGCCAA