| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017402170.1, is a part of gene, LOC108227144. |
| The genetic_marker, MK000940 DCDRTSG, is located in gene, LOC108227144. |
| The mRNA, XM_017402251.1, is a part of gene, LOC108227144. |
| 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_017402170.1 | XM_017402170.1 | mRNA | DCARv2_Chr1:41024380..41030038 |
| XM_017402251.1 | XM_017402251.1 | mRNA | DCARv2_Chr1:41024380..41030038 |
CAAGAGGAGACACAATTCACTGCACTCGCCTTGGCGGCACTCCGCGTCAG
GCGTGCGAATGTGCGATTATCTCTCTCGAAAATCTCTCTCTCTCTCTCTC
GGAAATCAATCTCTCTCTCATAGTTTCAAAAACCGCTGCTTGAGCCACTA
GTTTTCCTCACCCGCACACCTTTTCTGCCGTCAATTTCACTACATTTCGA
AATACATACATTTTGAATGTATAAAGCCCTAATTTCATCCACATTTCCTC
TTCTAAACTCACTTTCACAAACTTTGGCTCTCCGATCGGTAACTTCCTTG
TGCATATGAATGTTTGTTTGCTTTTCACAATTTACTTGTAATTGATGGTG
TGATTATTAATAAGAATGAGATTATTGTAATGTTTTCGCCTGCATTAGTT
AAAGCATCACCATTACTTGCGATGTTATGTTATAGATGCAAAGCATGAGC
TCATAGATGTTGATATATGCAATATTTGTTTCGCAACTTGTTTACTCAAA
TTACTGAACTTATAACATTCTACTCGTGGATTTACAAAAATTTGTGATAT
TCTTAGTGTAAGGTTCTGATTCAACTTTGGTTAGATTCTTTCAATTAAGT
TGTATTTGTTCTTTCGGAGAGTTTTCAGACTATTATTTCGTATTATTGTC
TATAACTATAGATAGTTGGAGTTTTGCTTCTTTTGATGGTTGAAATTTGT
TGTTGCTTTCTGTTCTTTTGATGTTTTCACCGCATTATTCCGAATTTCAT
AAGTATAAGGGACATAATAAGTTGCTGAAACTCGTGGCTTTTCATGTGTG
GGATTGTTCAGTGTTCTGTAATAGTGACTTATAAACAAGTATAAGATGCA
TGTGTGAAAGTTATATACTTATGTTTCACACTGTAGCTATGATCTTTCTT
GAGATAACTTGCGTCAACTTGGGAACTTTCTAGTTTTTGAAGAGAATAAT
AAGCCTGCCTGCCAGCAGAATTCTGCTATAATGTTGATTGTGTTTTTGCG
CGTTTTCTACTTCCCTTATCCACAGATTTTTGGAAATTTTGTCTATTCAT
TTATAAATTTTGGAATATAACATATTGTTCTCCATCTGTCCATCACTAAG
AAATGTTATTATCTTATTTTGATTTTTACGCCTTATCCATATCTTATTTT
CCAGTTTATAGACTTTGGATTTTGTATTTATGACAGGGGAATACTTAGTG
AGATTGCTGGTTTTTAATTCCCAACTAAATTTGAAAAAAGGTCATTTTAC
ATATCTTTATCTAGTTTATAGACTTCTCATTTTGTATTTTTGAGAAGGGA
GAGAAAGGGTGCAAAATTGTCGGTTTTTGATTTACTAAATTGAAACAAAG
TCTTCGTGACGTGTCATGAAACGTGTTCGATGTGATAATCATTATTTTTC
TTCTTAAATTCATCCTCTCCTATCTGGACATTAATGAGGAAGTTGACTTT
ATGCTTAGTATAAGAATCCATCCATCTTATACTTTGCCCTGCTGTTCATG
TTTTAGTAGTGTGTTTTACAATAGTGAATTACATTATTAATACTTTTTGG
TCAATTACCCTATTGGAGAGTTTGTGTTATCTATCATCCTCTTGTGAGTG
TTGTCGGTATTCACTTTCTCTGCTTACGTACTTGAGTCCGTAGAGACAGA
GAGTAGCTTTCCGATTTTCACCCCGAAACACAAATAAATTGTTATTGTTG
ACCTAAAAGCCTTTCTTGATGTTTGAATCCCAAATTTAATTAGTTAAATT
CAACTGTAATTTTTAAAGGTCACTTGAAATCTTGCACAGGCTTATATTTG
ACTTCTTATCTTCTGTGTTCTCAAAATCTATGTGTAATTAGTTTGATGTG
CACAATTTTTAATGTATAGCATTTCAGTTTTTATGTTCTCTGCGTCCTTG
TACTCTAAAAGATGTTCAGTTACGCTTTTGGTGAAGATTTGTGCACATTT
TGTTAATTAAGTGGTCAAGGTCTATTAATTATCTTATCAAGTCATTCTCT
AGTGTTTCAATCCTTTTAGTCACGTTGAATGTGCAAACTGGCAATACAGA
CTTCTTTCTGTATCTATCTTTATTGGGAAATATTAAGTTTCTTCATCCAT
CTACGTTTCCTTGTAATAGTAATTGTTCTTCCCTGTTTTGGTCTGATCTT
CTGGTTAAATTATATCTCTATTTATGAATGCAGTTATAGATTGATTAATC
TTTCTTGAATTTACAATTAATAATTTAAGTCATCAATCCATCTATTTTGC
TTTTCAGGCTTCTTTGTACTTGCTTACCAATTGCAACTTATCATCATCAA
ACTTCTCTCATTGCCATCGGTTTACTACATATATGGCTAGCGAAGCTCTC
GCAAATCCTACTAATGGAAGTGGCATTACACGCCCTGATCCACAAAGAAC
TTATCAGGTTGTGGTTGCTGCAACCCAAAATATGGGTATCGGTAAGGATG
GTAAATTGCCCTGGAGGTTACCTTCTGACATGAAATTTTTCAAGGATGTC
ACCATGACTACATCAGATCCTTTGAAAAGGAATGCAGTCATAATGGGTAG
GAAAACTTGGGAAAGTATTCCCATTCAACATCGCCCTCTGCCCGGACGTC
TTAATGTTGTTTTGACTCGTTCTGGGAGTTTTGATATTGCAACTGTCGAA
AATGTCGTAATATGTGGTAGCATGATTTCTGCTTTGGAATTATTAGCAGG
ATCTCCTTATTGTGTTTCAGTTGAGAAGGTTTTTGTCATTGGGGGTGGCC
AGATATATAGGTGAGCAACTGAGCAACATTTGGTTGTTAAATCCTTTACC
AAGGAGATCCTCTCCCACGTTTTAACAATCTGTTTTACTAATGCAGGGAA
GCTCTCAATGCTCCTGGATGTGATGCAGTCCACATCACTGAAATTGAAGA
ACACATAGAATGTGATACCTTCATTCCTCTTCTCGATGAATCAGTTTTTC
AGCCATGGTACTCATCATTCCCATTGGTGGAGAACAAAATTCGTTATTGT
TTCACGACTTATGTTCGTGTGAGGAATTCTGTTGCGGAGCTCACAAGTCA
GACCAACGGTCTGTCATCTGATAGTAAATCAGATTCTGGTAATTTTGAAA
TTCAGAATTTCTCTTTTCTTCCCAAGACAGTTTTTGAGAAACACGAGGAG
TATTTGTATCTGGGATTGGTTGAGAATATCATTTCTAATGGTGTGACAAA
GAATGATAGGACACGTACTGGTACTGTCTCTATATTTGGTTGCCAGGTAA
CGTCACTACAGATAAACATCTTTTATCTGTTTCTTATGCAGCAATGCTTT
ATGAAAATCATATTATAGGTTATGGCTGATGTGTAATGTGGTGCTCCTTT
AACTTGTTTACAGATGCGGTTTAATTTGCGCAAATCTTTTCCACTCCTCA
CAACTAAGGCATGTCTTGCTTTTTTTTTCTCTTTTACTTGTATTAGTTTT
TAGTGTTTAACTTGACATTCAGTTGTTTGTGATTTAACAGAAAGTGTTTT
GGAGGGGAGTTGTTGAGGAACTACTGTGGTTCATTAGTGGCTCAACTAAT
GCTAAGGTAATAACACCAGAATTTGGCACGATGCCAACCTTTTTTTTTTG
TTTAATCATATTATCTTCGCAATTTAATCATTCATATTCATAAGTTCACA
TTCACCTCGTCATTTCAATATCCAGTATCTATTTAAAATCATGTGCCTTT
CTCCTCATCATTTAAAAATATTGTAATATCCTTGAGCATTAGTTGTCTAT
GCGTTTCCGAATACGTGTGGAATCATCAAATTGACATATTAGTTATTGTC
GGATGAGTGCTAACTTAAAATTTGGTTTTTTTTTTTTAATTTGATGTACA
GATTCTAAAAGAGAAGGGCGTTAATATTTGGGAAGGCAATGGATCAAGGG
AGTATCTTGACAGGTTTTAGGCATTACATGGTTCAAATACAAGGGCTATT
TCTTATGAGGTTCTTTTTATGATGTGCTTTCTTCTTTGCTTCCCAGTATT
GGTTTGACGGATAGAGAAGAAGGTGACTTGGGGCCTATATATGGTTTTCA
GTGGAGACACTTTGGTGCAAGGTTTAACCTTCTTTCCTATAGGCTGGTTA
AGTATATTTGATATTGAAGTTTAGCCTGTGTGTTAACTTTTATAACTTGT
CATATTCAGGTATACTGATATGCATGCTGACTACTCAGGCCAGGGATTTG
ATCAGTTGCTAGATGTTATTTCAAAGATAAAAAATAATCCTGATGATAGG
AGGATCATTCTATCAGCTTGGAATCCATCTGATCTCAGGCTAATGGCACT
TCCACCCTGTCACATGTTTGCACAGGTTACTATTACAACTAGTTAATATA
TGTATGGTTCTTTGTAAGTTTTTATCAATCTCTTTTCTGTTCAGTTCTAT
GTAGCCAATGGCGAGTTATCTTGTCAAATGTATCAGCGCTCTGCTGATAT
GGGTCTCGGTGTTCCATTCAACATTGCATCATATGCACTTTTGACATGCA
TGATTGCTCATGTTTGTGGTATGTACTTCTGTCACAGCTAATCGGTATTT
CTTTATCTACGTTATTTACTGCTACAACGGTTTAATGCTTGTTGCAAATT
AAACACAATTGATGCTCATAATGCTAAAGAGCTAGCTTTTGCTGTAGCCC
ACTGTTAAAAAGTAAACCTGTGGACCTATCTGCTGGTTCTAATCATAGTT
GATTTTTTACCTGTGGATAGTGTCTTGGTAACTTGTCTTTGATTGATCTG
TATCTTGTGCAGACCTGGTTCCTGGAGATTTTGTTCATTCTATTGGTGAT
GCTCATGTCTACTGCAACCATGTCAGACCTCTTCGAGACCAGCTTCAGAA
GTTGCCTAAGCCATTTCCGGTACGTTTCAGTATGAAGACAGGGACTGTAA
CTTGCCTGGTTGTTGTGTTTTTTACATTATTAATGTGTAGGTTTTGAAGA
TCAATTCTGAGAAAAGGGACATTGACTCATTTGAGGCTGCTGATTTCAAA
CTCATTGGTTATGATCCGCACCAGAAAATCGAAATGAAAATGGCAGTATA
AGCTGTTGTTCTCAGGCAAGTATTGGCAGTCTTCAAACCTCAAGCATGCT
AGTTATCAAATTTTAAAATCTCAATTTTGTAAGTTCAATATGGAGCATAT
CATTTGAGCATGTGGTTCCATTTGATTAATGACTTGTGAGTCTTGATTAA
TTCTTGAAGTCATTACCTTTGTATATCGAGATCATGTTTTAGCGTCAAGC
CTTGTGCATGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTATAGTATATGTTTCACAAGAATATCTTTTTCAGTAGTACTGAATGTGT
TTACCCGTTGATGCAGGAACAGGAACGGATACTAGGAATTTTGGCAGTGA
TCTGTATCCGCTGGGAAGAAAAAACATTAGAATATTGTTACATGAATATA
CCTTAGACACATGTAGGTACTGGGAATCCTTTAGTTCTACAGACAGTGGT
TCTAAGGTGATTTAGGATATGTTATCTGACTTTCTGGTTTGGCTGTCCAT
TGGAACTTTCAGTTTATGTTTGTGTTTACTTCCCCTGCCTTGAAAATGTT
TAAATTTGTGGAAGGTCTTGTGTTGGATGTTTCAATGGTTAAGTTTTGTG
TTTGTTTA