| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017386764.1, is a part of gene, LOC108214641. |
| The genetic_marker, MK002919 K0363, is located in gene, LOC108214641. |
| 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_017386764.1 | XM_017386764.1 | mRNA | DCARv2_Chr3:28194083..28198478 |
ACCGCAGACCAAAATCTCCGTTTTGCCCTTTCCCTCTTTCTCCCCGTTTA
TCATTCCTTGTTTCCCTTTCTCCTCTACTCTCACTTCACACTTTTTATAT
TTTTGTAACAAACTCATCTAATCTCTGTAATGGACGTGCCTTGAAGTTAC
CGCTCTGCTCACGTTTTTACTGCTTACATTTTTACTCTTCTCACCAGAGC
CGCAGTTGATTTTCAAGGTATGTGTTTGACCAAGCACACACTTACAGAGA
TCTCTGCGTTGTTTGACTTTGTGGTTATATTTCTGCTTAATTTGCTGTTC
TTACAGATTTTTTTGTTATAATTACAAGCTTTTGTGAAATTCATCAGCTA
GGTAAAAAATGTGGTTCTGGAAATTTTATCTGTATGTAAATTTTGTTTTT
GTTTTTGTTATTAATTGTTAATTAGGTTTTTGTTTTTGTGATTCTAGATC
TAAAACAGGTAGTTATGTTTTTGCAACATGGAGTAGTTAAAATTTGGCTA
AAATACTTGCATGCCCCCTTTTTTTACTCCAGTAATTTATTTTTTAATAT
TTTGTTAATCATATATATTTTTTTAATTTGAGCTTGTTTTTGTGCCTTTA
TCATGTGAGCCTGAGGAAATTATTTGTTGGTTTGATGTATTTTTGGACTT
GGGTTACATATTCGAAAATCGAGATGAAATTTAAGGTTTAGTTTGTTAAT
GTGAAAGCTTTTGACATTTTGTGCAAATAAGTTTTATCTGATTAATTTAC
CTGAAATAATTAGTAATTTTCAATGTCTGGTAGTTATGAATGCTTAACTT
TTGCTGTTGGAGGCTTGGAGCTGTTTATGGATTATTCTGATTGTATGGTT
TAATAATGTTCGGAGTCGGCAAAATTAGTTCTGGCAACTGATAATTTCTT
GTTTTTTGCTGGATTACTTGCCTTCTGTCCAAACAAGATTGTGTAGGATG
TGAATTGTTTCGGTTAGTTGATTATTTAGAAGCAGTATAATATACTAGCC
AATTGCCATAGGTTGACTAGCTGTCTAATATGTTGAAATGGATGCATTGC
AGTTTCTTGATTTCCTGATACCATTTTGTAGTGGTTTATAGTTTAAACTT
TTAGTACTTTATTCTGCAAGAAGTTTAGTCCCTCTTTTTTCAGTACAAAG
GATTCATTGGTGGCAACAACAATTCCCCTTTTCCGTATTAGCGGACTTAT
CTAAACATATTAATTGGAGTTATATGATTTTTGTTGTTTTACATTATTGA
TTTGGTCCACAAAATCAATTTGTCATTTTATATTGCAGGTTTAGAGGCAA
ATTTAAGTTGTGGTATCTGATGTCTCCACCTTTATTGAGTGTTGAGGGGC
TAGGACAGGGAAATGTGACACGAATGGCTTCACAAGTTACTGTAGACTCT
CCTTCCCCTGCTAGCTTGGAATTCAAAGAACGCAATTACCTTGGATTGTC
AGATTGTTCCTCTGTAGACAGCTCACCAGCTTCGAGCGTATCTAAGGAGA
ACCGGAGCAATCTAAATCTCAAGGCTACAGAACTAAGACTAGGTCTTCCG
GGATCTCAATCCCCAGAACGAGAGCCAGAACTAAATCTGCTTGGCACATG
TAAACTCGACGAAAAAGCTTTATTTCCATTGGCCCCTTCAAAAGATGGTA
TCTGTGCATCTACACAGAAGACTGTTGTTTCTGGTAACAAGAGGGTTTTC
TCTGATACCATGGATGGTTTCTCAGAAATAAAAGGACCTTCATACACTGA
AGGAAATTGGATGTTTAACCCAAGCAGGACTGATTCTGAAACTGCACAAA
ACGGAGGACTTGGAAAGTTTTCAGGCAGTGCAAATATCAATGTAATGCTA
TCATCGGGTTCATCAGCTGTGACACATGCTGCGATAGTTAAAGAAATTCC
TCAGAAAGCATTAGAAGTTGGGCATCATTTGAAAGCTGCAACTACTAATA
AAGTGAATGGTTCCAACAACAATACTAGTGCACCTGCTGCAAAGTAAGAA
CTACTCTGGTTTCTGTATGTAAGGATTTGAAAAAAGAACAGTATTCATAG
AATGTAGAATACTTACTTTTCTTCTCCACAGGGCACAGGTAGTTGGATGG
CCTCCCATAAGATCATTCAGGAAAAATACACTAGCAACTAGCTCAAAGAA
CAATGAAGAAGTGGATGGAAAGCCTGGTCCTGGTGCTTTGTTTGTGAAGG
TCAGCATGGATGGTGCTCCTTATCTAAGGAAGGTAGATCTTAGAATGTAT
ACTACATACCAAGAACTCTCGTCTGCTCTTGAGAAGATGTTCAGCTGTTT
TACTATTGGTGAGCCTACACTATAGTGCTACTACAGTTATATCTTATTTA
TAATGCTTTAAGCTTTGCTACTATTATAATGAGCATCCCAAGTCATTAAT
CAACAAAATTCCAGGTCAGTGTGGATCCCAGAGTACTTGTGGGAAGGAAA
TGTTAAGTGAGAGTAAGTTGAGAGATCTTTTGCACGGATCAGAATACGTG
GTCACGTACGAAGACAAGGATGGGGACTGGATGCTTGTTGGAGATGTTCC
ATGGGAGTAAGCATTGTTCCATTTCACGTTCTTTTCTTGCATGGTTATAT
ATGTGATATTCATAAAGAGTCGGTCATTCTTTTGCATAAGGCAAGGGAAG
GTACACGACTCTTTTGCCACTCTGATATCACACTTATAGGGCAGATATCT
TTTGTCTTGTTATGAGACCCTGTGGCTTTAGCTTGCATATAACCCTGTGC
CACCTTGAATCTAGATTACTGTGTCTTTACCCAGCATATACCCCTTCCAG
CCTGTAATAAGAGATTGATTGTTTGATGAACTTGGATATATGAGTTCTTA
ATTTTACAGATTTATAAAAATAGAAATATTCGTCTTGACACCTACATTCA
CTGAATATTGTCTATTGATAGAAAGTGCAAAGTTTGGTAGATTATGGCCA
TATGCATGTTATGGTAATCTACTAATCTATGAATTTGATCCTTCTTCCTG
TGGCCAAGGTTACCCAAAAGCACTTGTCACAAGTATATTTCTATCCTTGA
CATAGGCATGGTTAATGTATAGAATGTCATTGTTGCTACCTTGTGCAAGA
GAAACAGAACAAATCTGTTGGCATATCTGGAACTGTGGAACTTTCTTCTC
TGTTTTCCATGTACCACATGTTAGACCTATACTGTAATTTTGCTGATTTT
TTTTGAAAACATCATCTCTAAAATAATGTTAACCCTTTACTGAATAAGAG
CATTTAAATTTTCACTTGTGAGTAGCATTTAAGTTTTTGAAACACTGGGC
CTGTTTAGATGATCAACAATGATACATGGTCTTAAATTTTGTATTCTGAA
TGCTTTTTCCCCCCAGCTACCTCTCCCCCTCTCAATATTGAGTTCTAGAG
TAATACCATTTTATTTAGTAAAGTTTACTTGTGTTGTTCCCTAAAAATAT
ATGGTTTATTTGAGCTGGTTGACCTGCATCCCGGTGTATGTTCAGTATCT
CTATCCCTATCCTTGGTATCAGGCTCCAACGGAAGTCATTTGATTTATAT
TTTAGTTTTATATGGCCTATCTGTATGTTAATAAACTACTGATATTGCGA
TGCTTGTCTTAGGATGTTTATTGATTCATGCAAGAGGCTGAAGATTATGA
AGGGCTCTGATGCTATTGGATTAGGTTTGTACTACTATTTGGTTATTTCA
ATTCACCATTTCTAATAGATCCAATTCTCCTAAAACGTCAAGATGTTGGG
AGAAGGGCTTACCAGGATCATATTATATTATAATGAGCTCTCATTTATTT
AGAGTTTGGGTAATTTTTCTAAAAATAAATGAATGTTATAAATCTTGGGG
GTTGCCCTGCATTGGTATACAGAGTTACTTGATAACTAATGTTCAACTTT
CTGGCTATACCCCCTAGTCCCTAGTAGCATTTCCCAGTCCAGAAATGAAT
GTGGTAAACATTAGAATACGTGCAGCCTAGTTTGTGACCTCTATTAACTG
TTGTTTCCTTCCACAGCTCCCAGGGCAATGGAGAAATCCAAAAACAAAAA
CTAGCATATTTGGGCTTCATGACTAATTTTCAGCTGCTTAGTTTGAAGGG
TGATGAGTGGGCATAATATCAGCAGAAATGGCAAAATTACTCACGCCTAG
GCTGGTGGCTGAAATGTGGATTATGGCCTAGTTTCCTTGTTTGTTTGTTT
GATTGCCTCAGCAAATTTCTTGTGTATTCTGTGTTTGTAGTAGGTCTAAA
ATTATTATTGTAGGGACTTTCCTATGGTAAGAAGTCGACTTTGTGAAATC
TATATTTCCTTATAGCAATTTAAGATTCGAAGTGCATTGTATTTTCTATA
TTTGTGGTAAAACCTCTTCCGGTGCTTCTGAGCAGTGTGCCTTTA