| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017382377.1, is a part of gene, LOC108210917. |
| The genetic_marker, MK005818 K3262, is located in gene, LOC108210917. |
| 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_017382377.1 | XM_017382377.1 | mRNA | DCARv2_Chr3:45056850..45061986 |
ATACTAAACCAATCACAGAAGAAACAGATAACTTCCACAACTCCTCTGCT
ACACTCTACAGATCAAATCATTTAATTCATCCTCTATTTTTCTCATCAGT
GTGTCAATATATAATATTAATCTATATTAAATATTAATATTAATTTATAT
ATATTGTCATTAGCAATGTTCAAGAACCAATAAAGAGCTTCATTTGAATG
GTGGTTTGTGAAATTGACGTGCAATGGGAGCTCAGAAGAGCATCCATGCC
GGCAAAGGTTCAATTTATGATTCTTGAAATACCCATTTCTTGTTTGTGTG
AATTTGTGAATGTTTGTGTGTGTTTATATGTTTTTATTTGTGGGTTCTTG
ATTTTTCAGCTAAGGTAGACTTGAATGTTGATTTTACACATAAGCTATGT
GCTGCTTTGATGCTTCAGCCCTTCAGGTTTTGACCCATTTGTGTAATTTT
AAGGCCAATTTGACAAGATTCGAAACATCGACCTCCTGTAAGAGGAGGGT
ACATGAATTTTTGATTATTGAGTCACTGAATTTTTTTTTCTTGAATAGGG
ATACTGGTAGTCCACTCTCACTTGTTATTGGGAGGTGGGTATTTTTTGAT
ACATTTTAAGTTTGACATTAGATTATAGATGTGAAGTGTACATTTTTGAT
TAATTTTGATTGTTTGGTTTGCAGTCTTTGCATTAAACACCCTAATTTAT
TCGGAAAAAGTGAGAAGCTTGATTTATTGTGGGACAAAGGGTTATATGAT
TCCAATGTGTCCATTGCTTACAGAAAGCCGAGGCCTGAGTGGCTTACGCA
ACAAACATTGTTCCTTCAGGTGAATGTTGTTTATGTTTTTGTTTTCTCTA
GTTTGAAAGAAGTAGTGTGATGGTTGCAATGCATTGGGGTTGAGATCACT
TTTGTTGTTTGTTGGAATTTTGAGTTTCTTTATTTGAATTATAATGCGGT
ATGTGAGAAGAGATCTTATATTGTTTGAATGCCACCTTACAGTTGTAACA
TTCTTCGTATTAATTTGGTATAATATTTTTTATCTGTGGGCAATATATAG
CCAACAGAAATTTTCAGTTCTACTTTAGGTATTCAAAATATAGTTTTACA
TGCCATAAGTTTTTCTACTAAAATTTCCTCAGCTGTGCAAGTACGAATAA
TGTGCCCTAAAGTTATATAAATTTCAATTGGATATGGAATAAAGAACCAT
GTATCTCAATGTTCCCTGCTTCCCAGCACTCTGTTTCACCTGAGGTCGCT
ATCCATGGTTTGCCCTTCGACAATTTCTCCCGTTCAGGGAGTGGAGGTGT
GAATCTCTGTCGAGTATCTGCTGGACTAGATCTTAGTGAGCCTGCAGGCA
CCAACTGGAGCAGCAAAACAAGTGTAAAGTTTGAGGTGGGTGCCTTTAGT
GAGTGGCCAGGGCTTTTTCTTCATGTACTTCAAGTCCCAAAATTAGTTAT
TACCTTGTAATTTCTTTAATGGATGAATTCTGAATATAAACCAATGCAGC
ATGTCCGTCCAATGAATGACAATGGTCATTCGATCACCAGAGATGTTCAT
GGATTTCCAGTGACTTGCAGGTAGCTCAATAGTTTTCTACAAGTATATTC
GACTGGTTGCAGACTGATGTTTTTTTGTTTTTTTTTTTGCGTAAGTTGCA
GACTGATGTTAATCTTATTTGTGAAATCCTTGCATGCAGTGGTGCACATC
ATGACAGTATGGTAGTACTTAAGCAAGAGTCTCGTTTTGCACGAGCAAAT
GATGGGAGTTTCACCAAAGTATATTTCTAGTCTTGCATCATCCTAATTGA
AAATGATATGAATGCTTACAAGTTTGTACTTTTAAGTACACATCCAATAT
TGAACATTATCTTATCTTATTTTCAGCTTAATTTACAAATAGAACAAGGG
ATTCCTCTTCTATCTAAGTGGCTAATCTTTAACCGGTTCAAGTTCGTTGC
ATCGAGGGGGCTTAAGCTTGGGCCTACTTTTCTATTAACCAGGTGAGAAT
TACTCAGTTTCCTGGGTTCTTGGCAAGAAAATGTAACAAATACCTTTTAA
TGGTGAATGTAGGGAATTAGTATTAGTTACATGCTAAGTCCACGAGCACA
CAATATTAGTAAGAAAAGTATATTGAAGAATTACAGCTAATCTGCCTAAT
TATACGTTGATAGATGCTTAGGAGAAGCTTGCTATAATTACGTAGCCTGG
AAGGAGTTTGTAAGGAGTTTCGAATGGCTTACATTAGCAATAAGAAGATT
TATAATTTAACAATGAAAATAGTTAGTGATAGGAGAGTCACTCAAAACAT
GCAAAAGTATTCTCAACAGTATATCCATCTCACAAAATATTGATGTTTCT
TTTAGAAGATTAAGAAATAATGTCTTTGTGAATATAGCTAATTTGAACTT
TTCTACACAGTACTGTTTCTAAGACATTCATGCTATTTTTGAGAGAGTAA
TGTATAATTATTTTTTTAGTAGACATTTATAATGAAGTCTCTTATGGGTT
TTTTTTACCTTCTGTATTATATCCTTAAGTTGCTTCTTTTCCTCTGATAG
CCTTACAGGTGGTTCTATTGTGGGTGATATAGCTCCTTATCAAGCATTTG
CTATTGGAGGACTTGGTAGTGTGCGAGGATACGGGGAGGGTGCAGTTGGG
ACCGGTAGATCCTGTTTAGTTGCAAACAGTGAATTAATATTACCTTTGGT
ATGTAATAATTTCGCTGTAATAGATAATAACATCCTGATATGACCTCACT
CCAGTTTTTGTTATGTAGTCCTGCATAAAGCAACTCCAAATAGTTTACTT
CAATTATTTGAAGGTTAAAACTCTTACTGTTTCTACCTTTGTGTCCTCAA
CTTCTCCTAAAAGAAGAAATTTGAACATATTAAACAGCCGTATAGCCCTT
AAGTGCTTCTGTTAAACTATCTAAACTATTACAGTGTTTATTGTTTATGT
GAAAATTTCTTACACATTTGATAATAGAGTTAGGCTTGTACACACATAAA
TGCAGAATGCCTTGGTCTCACTAAAGGATTCATGGTCCTTATATTACTAT
TTACTGAAGAGCACATGTGCATCATCAACCTCAATCTGTCTCTTCTTTGT
ACCCCATACCTCAGTAGAAAAATGGAAAAGAGAAATTATTCGGTTTAACA
GCGAGTAACTTACTGGTCAGGCAAATTTTAAGGAGTAATAACAGTGTTGG
GCAGGTGATATTGCATATAATCATAAAAGCAAAGTTTCAAGCAAGATACT
TAAATTATACTTGTTGATCCTTACACCTAATACTGTGTTAACTGGTTTAA
TCCATGCAGAATCAAATGTGTGAAGGTGCGATTTTTATGGACTGTGGATC
TGACTTGGGTTCTGGGTGTTATGTTCCAGGTTAGTTCTGTACATCATATG
TCTTGTTGTATTTTTGTATTGTGTGTGTTTAGGGAGATGCAATTTGTCAA
AGCCTGCATGACTTTTGAAGATATATTAACTCAATATAGTAAAAATTTAT
GAAGTTGAGCTGTAGAAAGATAAGAGAATTGTGTTTATTCACATCTAAAT
CATATGATATAAATTTGTTTTCAATGCTTGCTATTTTACAACCGGTATTT
ATCATGTATGTTTTTGTTTTGGTTTCTAATTAGAAACAGCTTGTGTTGCT
CACTCTCGCCAAGCTAATCATAACACTGACCAATTACTGTTTTTTGCACA
AATTCCTAATCCTTTTTTTCTGATGAAGATAACTTTAAACAATTAGGCTG
CCATCCATTTTTAATTTTACAGCTAAAATCCTTTTGACGGGACTAGTCGA
CTACCATTAGTGGCTTTTATTATAGTGTTTATTAGATTCATGATTGGAAC
AGCATATTGGGGGGTTGCTCTGGTATTATTACTGCATTTGTGTTATTAAG
TGTAACAAAGCCATATGGGTATTCCACACTATATTCATACTTTTCTTCAA
TGGTAAAGCAGTATTTGTAGAGACAGAAAACTAAATTTAACAGTAGACAA
TTCCTAATTTTAGATATTACTGATAGGATCTGGTGGTTGAATCTACCTTT
GATTGCATATAACAACTATATCTCATTGTTCTTTAATTTTTTTTGCCAGT
AACACATCCAAGTTTTATGCTAACTTGAGTATAAAATTTTATAAATTATC
GAATTGATTACAATTTTTTTTAAGCTTCTACGTAAACCAATGAGGTCGTG
GGGCCTAAAATAGCATGGGAAGTTCGACTTTGTCAGGCTGTTAGGTGTAG
CAAATTGACTCACTTCTTTAAGTTATAAGGCGCTAATGGGGCATCTGAGG
TATTGGTATGTCTGGAAGAGTATTAGCTGAGCAAGTTACTTTTAGTAATC
TGTTCTTTTGCATGATTGCTTCACTTTTGATTTTTGCAAGTTCTGTATTA
TCTTGTTGATTAAGTAATTAGCAGGCATTAGAGTACCAGCAATGCTCTTG
CTATTGAGTTTTCCTGTAGCCCTAACCCCGTCAACCTATTTTATTGCTAA
GAGTTCAGAGAAGCAAACAAATATATCACTTTGAAATTCGAAGAGTTGTG
ATGAGGAAAATCTGGTCTGATTATATTTCTAATCTTTGACATTCAGTTTG
TATGTTATTCCTTTCTTGCCCTTTCATGCACTTCCTGTTTCCTATTTTTG
TGTTTTGTTTTCCCATTAGCTTCTTTAGTTCATAACCTTACATGCCATAA
TTTGCAGGTGATCCTGCTCTGAGACACGGTAAACCAGGGAGCGGAGTTGG
GGGTGGATGTGGCCTTAGGTTCAAGTTTCCGTTAGGTCACCTCCAGGTGG
ACTATGCTATAAACGCATTCCAACAAAAAACTGTTTACTTCGGTTTCAGC
AACGTTGCCTCATGATATTCACAAATTATGGTGCCGAAGATTGCAACATC
CCAATGTCAGATTGCCGCAGCTATAATATATCCTCTCATTATTGACACCT
CAACTGAAGAGAAGTTTGCATGTATAGAAATCGTTTCTCCATTGTGCTAT
TCCCCTGTAGTCAGTAACCATAACTAAACATGATCAAGTCCCTCGATTAA
GGACTGAAGATGTAGCTTCTTTCTGTTTTCTTGGACACAAGTGAATATAT
GAATCATTGATTATTTATACACATCATCTATTGTTA