| NCBI Gene |  |
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| Relationships |
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| The mRNA, XM_017394059.1, is a part of gene, LOC108220319. |
| The genetic_marker, MK011821 5_2795140, is located in gene, LOC108220319. |
| The genetic_marker, MK009592 5_2795198, is located in gene, LOC108220319. |
| The genetic_marker, MK009593 5_2795239, is located in gene, LOC108220319. |
| The mRNA, XM_017394060.1, is a part of gene, LOC108220319. |
| 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_017394059.1 | XM_017394059.1 | mRNA | DCARv2_Chr5:2794872..2801741 |
| XM_017394060.1 | XM_017394060.1 | mRNA | DCARv2_Chr5:2794872..2801741 |
CATTACTGTCTATCTCTCGCTCCATTTGCGAAATTCGGGCACCCAAGAGT
CAGGAGTTCATACAATTTTATTGCGTGAAAACCTGATGCACTGTTGTTGA
GCTGAGATGTGGAACTCGATGAACCCCCAAAACGAAACCCTAATAACACC
CCCAACTTATAATTTCGATATTAATTATGAAAATCAAATTCAAATTAACG
AACCGCAATCGCAGCAATGGGAGGAGACAGCTCGAGCTTGGCTGTGCACG
CTTCCCGAGGGCAAAATTATAAGCTCCGAAGAAATCGAAGCTTGGATTGA
ATCGAACCAGGCTTGTTTGCCTGATTATATTGTATCCATGCCTCGTTCTG
AGCTTCACCAACACCTTGCTGCTATTTATTCTACCATTACTCGCTCCCCT
CAGGTAACTGCAGTATTGTGTGTTGTTTTGTCTTTTGTTTATGTTTGCTC
ATATTGTGATTTTGTCAGTGTTGTTGTTAGAGTCAGAGAGAGAGAGAGAG
AGGGAGAGAGAAGACTCTGAGAGGGGGAGAGAGAGAGAGAGTGTTGAAGA
CTCTGAGAGGGAGACTGACGGAGAGAGAGGCGGAAAGAGAGAGAGATTGA
GGGAGAAGGGGGGGAGAGAGAAGACTCTGAGAGGGAGAGAGAGAGAGTGT
TGTAAGACTCTGAGAGGGAGACTGATGGAGAGGGAGAGGCGGAAAGAGAG
AGAGATTGAGGGAGAAGGGGGGGAGAGAGAAGACTCTGAGAGGGAGAGAG
AGAGAGTGTTGTAAGACTCTGAGAGGGAGACTGATGGAGAGGGAGAGGCG
GAAAGAGAGAGAGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTGGGGGG
GGGGGGGGGGGGGGGGAGGTAGGGAGGGAGGACTTTCAATATATAGTGCG
TAATAACTAATAAGTAAGAGCGTTGTTCTCAGACTCAGAGAGGGAGTGAG
GGTAGCTAGGTAATTCGTGTTTTAATATTAAGTGATGTTTACGTTTATCA
GTTTGTGTTAGTATGCCGGGATGTTAAATTTGAAATGTAATGCGGATACT
ATGTAGGTATGTCTACGAATGTTTACCTGAGGAAGATGGGCGTAGTTTCA
TTGATAGATAAAAGGGAGATGATGTGAGGAAGACAGGAGTAATATTATTA
ATAGATAAAAGAGGAGATGAGTGGCAACTGCTTGACTCTGAGGGTGATGT
AACAAAGAAGAGTCAGATGTTACTATAAGTAATTTATTTTTCCTGTACTC
GGGATTATTTTCTTAATTCATGGTTTTTTTGTGGATTTACGGATGGTTTT
GCATTTAAAAAGTTTGACATCAACCTGAATAAGAATGCATTACCTGGTAT
GTTTGTGTCAGCCATGTTTAGTGCAAGTTCGATATGTTTCACTTTATTTT
ATACAGATACAAGCATTTAGAATTGATGCTCTACCTTTTTATTTCTTTCT
TTATGGGAAGTCAGTTTTTGTAGACGGTGTTAAGAGTATGCATAACTTGC
AACTGTGTGCACTTTGTATTTGTTTAATTTTGATTGTGGTCATTTATAGA
ATCATTTATCCCGTGTCAGGAAAATGATGTTAACCAGGGTGACCATTCGC
AAGCTCGATTTCAGCGCACTGATCAATGGAAACCAGTCTATACTTGGTTA
GAGACTTTAGAAGATACTGAGGTAGTGAAGTCAAATGATATTGCAGACTG
GCTATCTGCAAACCCGGATGTCAGAGATGATTTATGCTCGAGACATTCCC
GCTATCATTTGATGCATTACATAAAAAAGTGTCATGTCAAACTTCTGAAG
AGAAAGGAGAGGAAGAAGGTAAATGTATTGTTACATATACAATAGCATCC
CCCAACTTCTATGCATATGTATGCTTTGACTTCAACTGGCATGTATATGG
AACTGATCTGTGTTCTACTTCGGACAGGGATTGGCTATCACCAAAAAAGC
AAACACCGGTATAATGTCAAAAAGTGAAGGAAAAAAATTGCCAGGGCCCC
TTCCATGTATGTTGCTTATTTAACTTAGTATGTGACTTGTATATTATTGA
GCTTGCTAGCAACCTTTCTTATATGCCTTTTTGCTATGTGTATAATTGTT
ATGGGTGTAATGCATGCATGTATGTATGTCATATATAGTACTCTCTATTA
TGCATGACCTTAAAGTAGTCATATTTTTGGTACCAAGAGATTTCTGTTGT
TATGAAAATTATAAATCATCTGCCATTTGGATGGAAAAACTAGCAAAGAC
TAATTGTCACAACATACGTACAGATCTGTTGTGTTGAGGTTTGCCCTTAA
TTACTAGTTAGCTTTACTAAAATGAATAAGCTTTTGTGTTGATTCCTCTA
AAGGGGCATATCAAAGAGAGGTAAATATTCTCATTAAAAGCAGCTTTGGT
TTAAACAAATTATGAAGTGACTGACTGGGGGTTGATGGCATATTTCTTAG
TAGTAATAACCTGGCGGTCTTTCCCCATGATAATATATATGTAGGATTAA
GAATTCCCTTTTCTTTTTCCTTGAAAACTGAAATAAAGCAATATTGTACT
TATCATATGTATGTGCTCGACAAGTTTTTATAATCGGAATTTGAGAACAT
GTGTAACGTTAAGGTCTTTTAAAATTCTGCTTGCTCCTTAAAGGGCCTAA
AACTTTTTAAGGTGAGATTAATCACATTATCAGCGTGGTGAAAATAGGTA
TTCAATATTAGAAAAAAAAAATCATTATAGAAGAGAAAAGGCCCTCTATC
TCACTTTTATGTGATAAAAAACCCGGATTATCACGATGTGAAAAAAGACC
CAAATTATCATTTATTAACTCTCTTTGAGAGAGCGTTTCAAGGCATAAGG
CAAATGCTATATCTCGCAGCGTTTTAATCTAAACAATTTTTACAAAACTA
ATGGTAAACACACGAGCTGTGCAATCATCCTAAACGCTGTACAATCACCC
TAAACCGAAACTCACCTTCACTTTAAACCCCCACACACTACGACTGCTAT
GACTGCGATGCTTCAACAACCAGCGATCGATGATAGAAACAGAACCAGCC
AAGTATTGTTACGTTGTAAAGGTTTATATCCCCGCGGATACATACATACT
TTAACACTTTGATGTATGTATATCTGTATGTTTTTGTTTTTAGCATTATT
CAATTCCTGTTTATTTATTCAATTGGTTGGTGATATGCAAACTACCCTTC
AAACGTTCAACGAACTTGCGTTTTGTTAAATTTTTAAAAATAAAACGTCT
TGAACGTGAGACGATATTGCGTTGGGCCTGACAGCTGAATCGCCGGATTA
TCCACGTTAATATGTTATATTGAGGGCCATTTTTCCTAAAACTGATATTT
AGGGCATTAATTGTCAAAATTATGATATAATGGGCCAACACCCATCATAG
AACCTGTGAGTACCTGCTAATAAGAGTTCAAGAGACAAGAAATTTGGATG
CTTGAAAGTTGTACATATGTAGCACAAATCCATTAATAAATCTACCAATT
AGTTGTTACTTGGTGAAAAACTGTAATTATGTTCATCCCCCTTGTTGCAG
TTCATTTATTTGGGATACACCAACACTTCAAAGCATATATTAATCAAAAA
TTCCTGATGAGGAGTGAAAGTGGAAATAAAATAGAGCTTTTTAAGTAATT
TATTTGTAGTTTATATATACTCAATATTAAAAAATAACCTATACAATAAT
TGTGTAGGCTATAGTTGTTTAGTTTACATACTTTGAGCCTAACTCCACTT
TCTTATGGGCCTTGGTCCATTAGGTTTATGTAATGGTTATATATATGAGA
TCAGTAGATTATTAGGAGCATTCTAGGCTATGGTAGTTGGATTATAAAGA
GACTTGTTTCCATTTATTATTTATGGTAGCACATTGTTTGCTCATTATTG
GGAAGTAGATATAGATAAGAATTAGTCATATATATATATATATATATATA
TATATATATATATATATATATATATATATATATATTATAGGGTAGTGATC
AAATACAAACCACTATATACAAAGTAAGAGAAACTAGTCACATCACCCAT
CCCCTAGATGCCATCACCCACCCTCTAGATGACATTATCCATCTGGAGAC
CACTCTCGAGCCCCCTCAATCCACCTTGGGCTCACTAGAGCCTCACCAAG
GCTCTGTAGAGGCCCTAGAGGGACTCTAGACAAGTTGAAGAGCTAATACT
TGGCCCCACCCCTGTCCCGCTAGGCGTACCCAGGCCTTGCCAAGGTTCAG
CTCAAGGTCCATCGTCGAGGCCCACAAACCTTTCCATCCTCTTAAAATTT
GTATTTTAGTTTCTATTTAGTAGTTTGTACTGTAGTAAGACTATATGTGT
GTGTATGTTATGAATTTACGGAGCTTTTAAGTTGTGAGATATCTATAGTA
CTCTTGTAATACTCCTTATGAAGATTATGTTTATTATGAATTAATTTAAA
TCGGATGAATCAGTTTTATCCCTGATCTTTAACCATTTTTGAACCTTGTC
GTACATCAAGTGATATCACTAAAATTTGCCTATTTTATTTCTACCCGATT
TGCTAGCCTCACCATTTTTTGAGGGTCTAGAGAATGGGCAGTTGGACACT
TTGCTGACCGATCTACAACACTTAAACATTTTGCCTAGCCTCAAGTATAA
ATATCTTTTTATACAGATCCCATAGTACTTGAGGTTTTAGATTTCTAATT
TGGACTATTCCATGATATCAAAGGCATGCAGCGTGCTTAAATCCACATGG
TCTTAAACTTGTAACTGTTAGAAGGCGGTTGATACAATGAAGAATTGAGA
ATGGATAAATTGCACATTATATGATGGAAAATGCATCAAGCGAACTAGCG
AAGTCATTTTAAGTTTTTTAGAGCAAGGGTCTTGAAGTGAATTTAGATGT
ATAATTTGCCTGGAGCCACATAATCAGGTATAAGTAAATAATGTGGAGAT
CGTACAAGATCTTAAAGTTATTCAAGAATCACCCACAGACTGACAGACAA
ACTAAAGTAACTAGTACAACTTTGAGTACATTGCTGCGAGGTTTGGTGAG
CACGCAAAGGACTTGAGATATCAGACCTGCTTATATGAATTTCGTGTAGT
GTGACACCTACTTTTACTACTGAGACTTCTTTATTTGAGGTGGTTTATGG
GGTGAAATTATATTTATTGAACTAGTACATCACCTGTCTACTGAACTAAT
GCATCATCTCTTCTATAGAGAAATTGTGAACTAGGTACCAAAATCTGGGC
AAGTGGCAGTTATCAAGACTAATGAAGAAACAAATTAAGAAGATTAATGG
GAAGTACAAATGGGCTAGAACAAAATTAGGCACCGAACAGATTTTAAAGT
GCGGCATCTTGTTTAGCCTAATTTAAAAAATAATGTTTTCCTATTTAGCA
CAGAAACAAGCTCTTTCCAAGGGTGTCCTTTTAAGAAAATAGAAAGTTCT
GGTGATTCTACTAACAAAATTGACCTCCCTCTTGATTAGTGACTAGTGGA
GTTAGTGCTACCTTTAGTGTGGTGATTTGTCTCCTTGTTTAAAATTTGAA
CATTGCAAATTTCAGGACATTCTTTTTTAAGGACTTATCTTCTTGTTTAA
GAAGAGAATGAACAGGACATCAATGTTTAAGAATCCATAGTTACATGCAG
AAATACGTTTATTATGCTTAGTAATTCGAATACAAAGGCATACGAAGGTA
TGTGGCCATAGTCATACGTTTTTTAAAATCTTTTATCAGGTCTTAGTGTC
AGGTTGAACTATTTATATACTGACTAGCAGTCTGTTGACATATTTATCAC
TAGTTATCATCCAATGTTCCTTTACCTTGGTATGTTTGGGTATGAAGCAC
CCTGAACATCAGCAATCTGTTCATAAGGTTAACTGCCCTTTTTACATAAG
AAATCCTCTCGGTATGTTTGGATGTGAAGCATAGTAGCACTCTGTTATAA
TGTTGACTTCTTTCTGACAAAGAAATCTAAATGTGAGAGTGTGAGATAAT
GTTGCTTAATATATTTATGTTGTCACTCGTTTTTGGAGTCGAGATTTGAG
AACATGCGTAAACTTAAGGTCTCTTGTGGACCATTTTCAACTCATTTCGT
GGGTGGAAATTATTGTTAGAATGTTAAGACTCATAATGCAGTTTCTTAAT
TTATTTATAAGCGCACCAAGGTTTTCTGTTTGTATCGGTAGGGATTAGTT
ATATCAATTTCAAATCTTTTTAGTTGGCAGCCTATCATGTCTCATTTTAT
ATCGATGAAAGTTGCAGGCAGTATGATGAATAATATACCACCTGATAGTG
ACCTGTACAAGGCAAAACGCAGCGAGGCTTCACAGAAATACGAGATGTAT
GTGAACATAAATATTACCTCTTTCTATCACATTTGGCACAATACTAATTC
TTGTTCGCTTACAAATTTCTTTAATGTGTTCTCAGTTTGTTAGATTTGGA
GAAGCAACTTTCGTCCCTTTTTCCTAAGCCACAACTTTTGAACAAGTGAA
TTTAGAAATTACGGTGGACATGTTGTGCAGACAGTACTTCCCCAATATTA
AACTGATGCCGAGCTTCTTCTGACTCTCAAGTCTCATATGGTTCATATGA
AGATGGAACATGTAAATTTAAATCTTTGTATATGCAATTCCAGTTCCTTG
TAGTTGTAGTATTAGAATAATTTATGCTAATTTTCTTAAAGTTCAACGCA
ACTTATCCCTCTTGGTTATAGTTGCATATATTTTCTTTCATCAAAGAAGT
TGCGGATTTCTTTCTTTCA