| NCBI Gene |  |
|---|
| Relationships |
|---|
| The genetic_marker, MK011783 4_22243979, is located in gene, LOC108219543. |
| The mRNA, XM_017393038.1, is a part of gene, LOC108219543. |
| The genetic_marker, MK009577 4_22243943, is located in gene, LOC108219543. |
| The genetic_marker, MK008732 85036.63365, is located in gene, LOC108219543. |
| The mRNA, XM_017393039.1, is a part of gene, LOC108219543. |
| The mRNA, XM_017393040.1, is a part of gene, LOC108219543. |
| The mRNA, XM_017393041.1, is a part of gene, LOC108219543. |
| 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_017393038.1 | XM_017393038.1 | mRNA | DCARv2_Chr4:22240726..22246281 |
| XM_017393039.1 | XM_017393039.1 | mRNA | DCARv2_Chr4:22241155..22246281 |
| XM_017393040.1 | XM_017393040.1 | mRNA | DCARv2_Chr4:22241292..22246281 |
| XM_017393041.1 | XM_017393041.1 | mRNA | DCARv2_Chr4:22241429..22246281 |
TCTGAAAAGTGTGAAGTGCAACATATACAACATACACACACAGACAACTA
GTCCTCCTAATAATAAAAGGCTCATAATAATTCTTTAGCTGCACAGTTCA
CAACCACTGCCCACATGCTCTTCCAGCTCCCCCACCACTTTTTTATATTT
CAAAATCAAACCGAACCCCCTTATTATCTGTACCCTCTTGTGGGTTCCTT
CTCCTGGTTTCACTGACATTCCACACTTCTTTAGCACCCCTTTTTTCACT
TTCTTGTTTAAAAATTCAATCTTTAATGTTCTTGACTAATCTTAAATCTG
AATACTCCAACCCCTTGTTTTGTTTATGCATTTTTCTTGGTTTCCTCGTT
TGATCTCTGGCCTTCTTCTGCTCTTCAGTCAAAGGTATATTTATTTTGTT
TTTGTTTCTTTCCAACTGTTTTCTGTTCTTGGTTTTTATATTCTTTTGTG
TGTGTTTATTTATGGTATTTTTGTTTACTGTTTGGTTGTGATGTTGATTG
GGAGCTGAGATGTTGGTCTATTAAAATGGGTATTGTTAGTTCTTCCAACT
TTATAGCTATAAATGAGTAGTTTTTTTGTATTCTGTGTCTGTGTGTATTT
GGTTCTTTAGTATTTCGAAATGTTGGCAATGTAGATGATGGTGATTGAGA
GCTCAGATGCTGGTTTCTTGAAATGGGTATTATTAGTTAATGATTTTTTT
TAATGTGTGGGCTTTTTGATGATTAAGCTGATTCCAATGGAATGGGTGAT
TAGATTTTACATTTGATTGGTTTGCTTTTGGGATTTATGAGGGTTTGTCT
TACTTTATTGATTTTTCAGATGAACTGATTTCCTTTATATAGGATTAGGT
GGTAGTACAAAATTGTTTGTAATCTGAAGAAATTTTATTAATCTATTGGT
ATCAGAAGCTGTGAAATTTTATCGTGTTGTTGGGTAGAGAACTTAATAGA
ATAGGAGTATATGTTAGGGTGGATTTGAAGCAAAGCTGGAAAAATGATAA
AACAAGTCAGTTTGTTAAATGCGTTTAAGTGCCCAAGTTGCAGGTTCTAA
GTTTTTCTAGTATTTTATAAGTGATTATATGCAGGTCTCTATGCTTTGCC
TTCTGAATTTATCTTGTAGTGTTGATAAAACCGAAACATTGTTTGCAGAT
TGACATTGTGATGCACAATTGAATCTTTTAGCTAAACAATCAGATGGAAA
AGAGAAACTGGTTATGGAAGAAGAAATCTTCTGAGAAAAGTCCAGGAGAT
ACAGACAGTTCAGGATCGATTTCTTCACATTCTGAGCGATACTCAGGCGA
ACAGGTATTGAATTATATTTCAGTGTCCAGGACTTATTAAGATAGCTTTT
ACATACATGAGTGTTTTTTTATATTATGTGTATGTGTATATAGAGGGGTA
TATGTTACATTTTGGTTCTTTGCAATTCATTTGCTGATTCTGCAAACTTA
TTTTGTAAGTGCTGAAACAGGCATTTGCTGTTATATAATATGAAAGTGGA
TATTGATCAGTCAATGTTGTAAATGAACAAACTCCATCAAGTATGTTTTA
AGACCCCATTGGAAGGTCACTATGATTCACCTAGGAGGCAGATGCATAAA
CAAATAATCAAAATTATGCCGATCTTGTATCTGACCAAAAGATATAAGAT
TTAACATATTCTTGCCACCGATACCTCTGCCACTATTTTGTTTTCAGCAT
AAGCAGTTTTGTGTCCTTGATGGTTGCTGTGCTAGCGTAATATGATTTAC
TTGTAATAGAACCTTAAAGAGTTATTAAGTTACCCAGGAGTATTCATCAT
CGAATGCTCTTGTTTTAGTTCTATTATTAATAATGTGTCACAGGCTGGCT
TCCTCATGCCTGCATTTCTACCTTCATTGTGGTTGAGCCACAATGTACAA
GCCTTCGTAATTGATCTGTTGCTTCTATCTCAAAGAAGTTTATAAAAGCT
TATGGAACCAGTGATTCTCTATTAGGATGCATCTCCAGGTGAGGTAGCCA
TTTTGAGATGGCAGTTTATGCATTCTAAACAAGGTAAACTGGCCACATAT
CCTTTTGAGGCGGACATCTGATTTTTCAATGTGAATTACAATTGGGTAAA
ACTGTAATACTCTGTAAGACCTAGATACATGATCTGATGATCGTTAGTGA
GATGTTAAAAACATACTCCGTATGAAATTGTCTATTTGAAGTGACATAGA
TACTTTTTTGATGTACAACAAATAAGGGGTGCGTGAATGATGACCGCAAA
TGCAATTATAGTTTCTATAATCTAGTTCTTTAAAAGTATGTTGCTGTGGG
TGTTCTATGCCTAGTGACATTCTAGGGATTTTTGAGTTATTTAGGACTGA
TAGGCAGAAGAGCTATGGAAAGAAGAGTGTATAGTACTTTAAAGACTGAG
AATCTGAATAATTCTATTATTTAAAAACAATCAATATAATGCAGTGTAAA
CCTGTAAAAACAAAATTATGTTGCAGGCACTTCTTGTTAAATCCCCAATA
ATGTCAATCCACTTAAAGATTGCGAATTCTGAGTTCTAATGCAATTGGAT
GCAGAACATGACCTTTTATGATATTGGTCCTGTCTATGAAATGAGCACAT
ATCAGCTGGCTAAACTGCTCTAAAAAGTTCTCTGTTTTTTGCCTTTATGC
TTTACCCTGACACTTGATCTGTCCTCTCTTATTCTCTTTTGTACTGCAGG
AGACACTAAAGGAATACTCAAATCTTTTTTCTCAATCACCAGAAGTCACC
TCAAAAGTTACAGTTTCAAATGGAGAAGTTAATGATGGTATTAAGATTCT
AACAGAGAAACTATCGGCTGCCCTTGTAAATGTTGGTGCCAAAGAAGACT
TGGTTAAGCAGCATGCTAAAGTCGCTGAAGAAGCTATTGCAGGTCAGTTT
GTTTTTTATGATACTATAAATAGCTATTTGTACTTTTTAGCACGGTGCTG
TGCCCACCATTTTTTTGTTTAAGGCTATTCAATCAGTTAATTAAGATTGC
TACTTGTAACAAAAATTGTGGACTTAAAATTTTATAGTGAAACTGATAAC
TTCATGGTAAAGCTATGCTTGAACAAACAATTCAACCAGTATTTTTGACA
CTTTATTAAGTTGATTCCTATTTACATTTATGTCTAATATACATACATTT
AGGCTGGGAGAAGGCAGAAAATGAAGTGTCGATCCTGAAACAGCAACTTG
AGGCAGCAGTTCAGCAGAATTTGGGTCTGGAAGTTAGAGTGAACCATCTT
GATGGTGCTCTCAAAGAATGTGTCAGGCAGCTAAGACAAGCAAAAGAAGA
ACAAGAGCAGAGAATCCATGAAGCTTTAACAGAAAAATCTAATGAATGGG
AAACCACAAGATATGAGCTTGAAAGCGAGCTTCTAGAGCTCCAAAACCAG
GTCCAGGAAGTTAAAGATAATGGTCCTATTTGTATTGATCCTGGTGTTCA
GCACAAGCTGGAGTCGATAGAGAAGGAAAATGCATTCCTCAAATCTGAAC
TTGAATCTCTGTCGGAGGAGTTGGAAATTAGAACCATTGAGAGGGACCTG
AGCACACAAGCAGCGGAAATGGCTAGCAAGCAGCAGTTAGAGAGCATAAA
GAAGGTTGCAAAGCTTGAGGCTGAGTGCCGGAGGCTGCAAGCTGGAGTAC
GGAAGTCATTAATGGTTAACGAGCAGAAGTCCCCAGCTGCGTCTTCCCTT
TCTGTTGAATCTCTGGCAGATAGTCAATCGGATAATGGTGAACGGATTAA
AACTCTGGATGCTGATGTGTACAGGACAAGTGGAATAGATACCAATGCTG
GTGATAAAGGCTGCTCTGACTCATGGGCATCAGCCTTAATTGCGGAGCTT
GATCACTTTAAGGCTGAAAAGACTTCAAATAAAAATCTAACATCCTGTTC
TCCTGACATTGACATTATGGATGATTTTTTGGAAATGGAGAGACTTGCTG
CACTTCCCGAGCCTGAGAGTAAAACCTGTGAGGTTGAATCAGAATCTGTT
TCCTGTCAAACAAATGATACGGAAAGCTCGTTGAGGGATGAAGTAAAAAC
CACATACCAACGTGTTGCTGAATTGGAAAATAACTTGCTGCAGATTGAAG
CTGAGAAAGAATCTATTGCTTGTCGAGCAAATGAAACTGAGAACATGTTG
AGGGCTGAACTAGATACCATGACTCAACGTGTTGCTGTATTGGAAGATAA
GCTGGAGAAGATAGAAGCCGAGAAATCTGAACTGGTGAAATCCTTGATTG
CAAGTACTGAATCTGTTGATCTTTCTAAAGCACAGCTAAAAGAAACTGAG
ACCAGGCTAGAACAGTTGCAGAAGGAGCTTAATGCGATGAATGAGTCAAA
AGAGTTGCTTGAATATCAACTCGTTGGTATGGAAGTGGAGATACGTACTA
TGTCTAAGGAGGTTGATACCTTGCACTTAGACGTTAAAAAAGAGCAAAAT
ATATCAGCGGAAATGGTACTCAAGTGTCGAGATTTGGAGGACGAGCTAAC
TAGAAGAACCCAGGAAGTAGAGCTTCATCAGGCAAAAAGTTCGGATAGTG
ACGTGAAACTAAATCAGGTCAGCACTTGATGACTTGCAATCATAGTTCAC
ATTGCATATATGAAATCTTGCTTACAAATTCAAAGTTTCCCTAAAACATG
CTATACATACATAATTATTATAGATAATAAATTCGGTAGTGCTGAGAGGG
CTTATATTACAAATACTTGATAAGCACTTGATAGAACTCATAAAACCTCC
AAGACTCTGAATGTGATGTCAGTTGATAAATTTTTATGGGTGGACATGAA
TAATGTTCAATAAAATTTTTTTGCAGGAGGACCTCGTTGTAGCGGCTGAC
AAACTTGCAGAGTGCCAAAAAACAATAGCATCTCTTGGGAGACAGCTAAA
GTCTTTAGCAACATTAGAAGACTTCTTGACTGACACACCAAATGTACCTC
GACTACGTAGAGGGGAATCTTCGGTGCCTCCAGCAGTTGGAGCAGAGCCA
TGGAAGCTGCACTCCAACGAATCATTTCTGCCAAAGCGTGACCCAAGTTC
AGAACTATCTGCAGAAACTCCGACTCCTCTAGTGAATGGTTATAATAAAG
AATCACCAGTGTCTGCCTCATCATCAAGTTCCTCGGATGCTTCACTAAAT
CATATTAGTTCTGGTAAGAGCAAAAGTGGTTTTGGAAAATTATTTTCACG
TAGTAAGAGCGGCGTACAACTTGGAAATCATCAAGGACTAAATTGAGAGA
ATAGAATGTAGAATTAAGGCATGTGATCGTAGCGATGTGGGGGCATTGTG
CACTGATTACGGTTTTTATGACACCTATTCAGGACTTGCTGATTAAATAC
TTCTTAGTCGGCTTAGTTTTAGTTTGTAAATTGGTGGGAATGAAGCCTCT
GTTATACAAGACTGTCTTAATTGTTTTCAAGAAATTTGATATTTTAGCTT
ATTGTTAGTGGCTTTGTTTGGCGTGTGAAAGTGACAGAGGTTTACTCTTG
TGCAGCAGTAAGCTTTCAATTTATATGAAGTCCTTAGCTTATTATTTTTA
CCAAA