| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017371522.1, is a part of gene, LOC108202913. |
| The genetic_marker, MK006645 K4089, is located in gene, LOC108202913. |
| 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_017371522.1 | XM_017371522.1 | mRNA | DCARv2_Chr9:562920..568532 |
TTAGTATTAGTCAGAAAGGATCGGGTTGGGTCGGGTCAATACAGCTTCTT
CTTCAATTGGGTTCCTCTATCTTCTCACTCCTCAATCTCTCTCTCTCCAG
AGCTGCAAAATGGTAACATCAGCAATCTCAGCTTCTCTAAGCTTCTCTGT
ATCTTCAAGCCACAACCCATCATCTCTTTCTCAATGGTACACATATACAT
ACATGTTTTTAATATATATAGCTCTGAAATTTTCGCTCATATACTAAATA
ACTTAATTATTGTATTGTGTTTATATTTATATTTGAGTTGTTTCTTGATG
ATAGGAGCCTTAAAAAACCAATAATTTCTGCCCTGTCAACCCCTTATGGT
GATTCTTCAAGAACTGGTAAAGTTTACTTTTTTATTTTATTTTTAACTTA
AAGTTTGTTACTTTGACTTCAAATGTTGTTAATTTTTGCTAATGCACTGC
TTATTATGTTTTTAACATACCCTCTTGCTGATATTTGGGCACACTTTGTT
TAAGTTGTGTTGGATTGTTATTTCGAGTGTTGGAATGGAAAGTTGGTTTA
GGTTAATTAAGTGGGTGTGCTTGTTTGTTGTTACCAGGATTATCGAGTAG
GTCGCATGGATTAAGGTTGAAGGTCGATGAAAAAGAATCCCTTGCTGTTG
CTAGTCCAAGGTTTGCTGCGTCTGATAGTATATAAACTAGTTTGCTTTGT
ATATTTTTATGTCCTTGTCTCATTGTGGTAGTTACTGATGTTGTGCTCGA
TGTCCATATATCTTGTTTTTATGTGTAATACGCCTGGATTGTGATTGTCT
TCATGTTTTTGGTCATAGTATGTAGGAGAGAATTGAGCAGGAACTAGGGA
GTATGATTGGAACTTGTCAAGTTATGCGGAATTAGTTCTTGCTGTTTGAA
AAATTGCTATAAGTTAAAGTGTTTGGTTTCGGAATTTTTAAACTCATCAA
TTGTGATCGTTTTGGAAGAATACTAGGGCCAACTCTAGGGATTACTGATC
ATGATGTAATATCCACAAGGTCACTTTACCTTACTGCTAACATGATAATA
GATAATACAGGATCTCATGTATACAAAACAAATTGTTACCACTTTGTCAG
AGCTTGTCAACCGGAATCATGAGCTCACTTGATCATTCAGATCTTGAGAT
AGCTTATGCTTCTGAGGCTATTGCTAATATTTTTAGTATAAGAAATTTTA
ATCTCAAGTTTGAATTGCCTTCGTGTATATTTCAATTCGTAAGAATTATC
AGTTGCTTCCACTTATTTGTTATTCTCAAACCTCAACAGCTATGGTCCTA
TAGAAGCCAAAAAGGGGAATCCACCCGTAATGCCAGCTGTACTGACTCCT
GGAGGACCATTGGACCTTTCTACTGTATTATTCAGAAATCGTATAATTTT
TATAGGACAGCCAATCAACGCACAGGTGGCTCAAAGAGTAATATCACAGC
TTGTAACTTTGGCTACAATTGATGAAAATGCAGACATCTTGGTTCGTATA
CAATCTATAATGTCTTTATTACACTGGAAAATATCTTAAGCCCTCAAACC
TATATTATTAACTATTTAACTGTGTTTTATTAGATGTACCTGAACTGCCC
TGGTGGGAGCACCTACTCTGTCTTGGCAATTTATGACTGCATGTCTTGGG
TAAGAATGAAATTTACCCTCAATTAATTTGGTAATTCAGTATAAGAAAAT
AATCTTGCTGCTTCGTTCTCTTCTATTTTGTCTATACAAATATTTTTTAC
CTTTACACAATAAAGTTCAGATTGCTACTCCTCTCTCTCCTCCCATGTTC
CACTCCTATCAAACACATGAATTTAGACTTTAAATTTCACAAGATGAGTT
GACACATGCTTATTTTGTATAAATTTGAATGCATTTCTTTAGCCTGGTAC
TGGTTGCGTGTATAAATTTGGATGCATTTTCTTTCTTTAGCCTGGTACTG
ATTGCATGTATAGTAAATAGTAATCTTGGTTCTGATAATTTAAAACTCCT
CCAACTAATTATTAGCATGATTTTTTCCCAAGGACATCTATTTAAGTTAG
TTACAGTCTAAATATATGTGCATTTCAGTTAAGTTGGCAATATGAAAATG
CCAAGCTGCTAGCAAGAAGTTCTTTTTTATATACATTCATATTTATATTT
GTCACATTCATTTGCTGAAACTGTTTAATTTTCAGATAAAACCCAAGGTT
GGTACTGTATGCTTTGGAGTGGCAGCAAGCCAAGGAGCACTTCTGCTTGC
TGGTGGAGAGAAGGGGATGCGGTACTCAATGCCAAATTCACGTATTATGA
TACATCAACCACAAAGTGGCTGTGGGGTACGAATTGGTTCTATTTGAAAT
ATTTATTTATTCTTTGAAAGATTTTTTGCCATGTTTGGTGCGAATGTCCT
TACCGCTCTTATTGGAAATTGGAATACATTGAACTTGTTCATTTTAAATT
TTTGATATTGTTCCCTGATATTATCTTCACTTAATTTTCTTTTTACTCCT
CTCTTCTTTTTGCCTATTGTTCCAGCGTTTCTTTTGCTGTAATGTTCTTT
CATTTCCCTCTATTTTTCAAAGTAATAACAATTATCTCTTATCATATTAT
GTTCATGGTCTTATTGCTATTATTTCGATACTAGATTATATAATGTAATT
GTACAGAGAATAATGATATTTAAAATTGATGTAGAGTTTTACCAGTTCAA
ACTACTATATATGCAGTTAATCTGCCTCCAGTGGCATAAAACTGGATATA
TTTAGTCTGATCAGATTGGACATAGTGTACTCTTGTTAAGCTAAATTTAA
CTTTTCATCTCTCACGTGCATTTAGTGTAATAATTGAGCGTATCTTGTTA
AATTTTGATATGCGTCTCCTGGGCAAGCTACCAAAGATTAGATATTCATA
TCCTCTGGTTTATTCTCGAATAGAAGAAGATTCAACAGCCGTGGTGGGAT
TCTAATGTTAGTGCGATGGGAACCTTGTGAGACAGTGTGATATAGTATCA
TGGCCGCCTTTAATTACTTGTACTTTGAGACAACTAGCTTGAATCTTCTG
GTCTTTTCCAAACTTCATGTGTCTGCTTGTTTACTAGGTTACTTCCACAC
TTTGTATTCCGGTTACATATGTTATCTTACGTGCATTGACATGATGACAA
ACTATTAAACTTTTATATTGTGATTTTGGTGTAGGGACATGTGGAGGATG
TGAGGCGTCAAGTGAATGAAGCAGTTCAAACTCGCTATGTAAGTCTTTTT
TCCGTAGTTTTCGAAGCTTAGTTTCTTATTATAGTTCGTTTCAAATCAAG
GCATAGATTTTCTTGTTGAGAAGATGTTCCAACTAAACCTTATTTACTTG
GATACTTGAGGTGCTGAGATATCTTAATACTTAACCTTTTGGTGCCCTTG
ACTAGACAGGTACTAATATTAAGTGAACATACAGGGGTTGAAAGTTTTTA
TCTGCGAGTTAAAGCTCTTGTAATCATCATTACTTCATTTGTATGCTTCA
CTATTCAGATATTCTTTTGGGTATATATTTGGTGGATATGTAGCCACTTT
GTAGCATTACATGTGTACTTGTTTAGAACATGGTGAAGAACCATGACCTG
AATGGTTCTCTATTTTTCTCACAAGATATTGTGTAGAATAAATCTCTATT
CTCTACGTAGTAACATGTGACGTGATTCTCTCACTTAAGTATGTAAATAC
ATGGTACATGTTACAAATGTAAATAGGTAATACCTACTGACCATTATATT
CATTGCTTATGTACAATAGACTTTTGGATATTAGACTAATTTTTTGTCAC
TAGTCTATCTGATCTTGAGTCGGTTCAGTTAGAACTGCTGGATTTATTTA
TCCATAAAAATGTTAAACTTCCCACTGGGTTATATGAAGACAATATTATA
AACACTGCATTATCAACATATTTTGCTTTGGGCTCACTCAATACCCCTTA
ATCAAGTCTAAAGGAAGACACTAGATGATATCATTTTACAATCTTGATTT
TTCATTTCTTTCTCAAGCGTCTTATTTGCTCATATATTGTTGCAGAAAGT
AGACAACATGTTTGCTGCCTTTACTGGCCAACCACTCGAGAAAGTGCAGC
AGTATACTGAAAGAGATCGCTTTCTCTCAGTTTCTGAGGTAATGCTATCG
CAATTTAGTGTCTCCACTTTTTATTATCACCAGAAGGAGAAAAAGACACT
TACATCTTATAATAATATCAGAGATCATACAATTCCCACCATGTTGTAGA
CAGGATTAAAGTACAAACCAGAAATCTTTGCTAAAAAGTAGCAATTCACT
GTTGAGGGCACGAAACTGAGTGGAGGATCAGGAATTTGCAGCGGGTTACT
TTTATCGCTTATGCTTCAAGAGTATAATATACAATCGGTTTGTCTAGTGT
GTGCCCATGGGCACATGTTAAGCGCAGAAATTTTTGCATTTAGATCATTT
TGATTGGTGTGGTTGGTGTATTTGCAGGGGGGTCCACCATTATTAAGAAG
TAGGAGCCAATCAAAATGATCTAAAACACAAAATTTCCGCGCTTAGCATG
TGCCCATGGGCACACCATAGAAAAACCGATATAAAATTTATCCATAATTG
CAAATTTAAACAATTGCAAATTATAAGAATCTATAAATATCCTTAAAATA
TTTTACATATTGTGTTTGTAGAAAATTACAGAAATAAAAACTTTTAAATA
TATATGTAAACTATACTATATTATTAAAGCTGAACATGCAAAAGTTTGGT
CGTTGGTTTGTAGTGTCGTACAGTGCATTATAACCTTTAGATCACTTAAA
TCAAATTGATTAGAACTATTAGATTAAATTTTCTATATTTCACTGTGGTA
CTACTAAAAGAGTAATCTTCGAATCCCGTTAAAACATATTGAATAATTTA
TTAATTCAAACACACATGAGAAAATTATTAACTATTAAAAATCACCCATG
CATCGCACGGGGCGTATGTATGTACTGCCTCCTGCATTATTGTTATATAA
TATCCTATTGCATTATTGCTAGATAATATCCTCACACATTATATTCCGGG
TTGCTGATTATTAGTTTTGAATTATGCTGATTCTATTACTGTTACGCAGG
CTATGGAATTTGGTTTAATTGACGGAGTGCTAGAGACGGAATATTGAATA
TAATCGTATTACAGGAAGCAGAATATATCTGCTACTCGTGCCTGCCAAAT
TGTTGTTAAGATGATTTTGCAGTTAGTATACTGTAGTTACATGTGGCATC
CCGAACCAGTGGCTTCAAGATTAAAATGAACAGCCAGTTCTTCCAGGTTA
AAAAGGCAATTGTGCATATTCAATCACCAGGCTGCAGGTGTAATGTTGCA
AATGTCTTGAGAGACTTAATACATGTTTAACCCAAGACCAGATGTTTAGA
CATCACATATTTAGTTCAATGCACATGTAAAAAGCACCATTTCATTAGTC
CGGTTTCATTATCTGTACTCCGTAATTTTAACTATTTACTGTCCTTTACT
GTGTCTCGAATTCACCTCCAAAGGCATATATAACTGTAGTAAAGTATTAG
ATTACCATGCTATTCTGTAAATATATACATAAATATGAGCCTACTTTCCA
TTTAGCAATATA