| 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. |
AGAAAGTAAATTAATAATCTCCACTCCCCACTCTCTCACCTTCCTCCATC
TACTCCCAATTCACTTACCTTTCCTTCTTTCACAGCAAACCCAATTCACA
ATTTAGGGTTTTTCCCCATTCCCCTAATTTTCAATATATACATACACGAA
TCCTATCTCTATAATCTATAATCACTCTCTTCACTTTACACACACTCACA
CACTAAATTAGGGTTTTGTTCTCCGATATGCAATTCGTAGCTCCTGATTT
AGGGTTCACTATGTAATCACACTATATATACACTGATTATTATATATATA
TGGGGAATTTATATGTTTTATCGGTTGTTCTTGTTTTGTTTGTTTGGATT
ACAAACCCTAGGTTTTTTATCGGTTATGTGATTTCGAGAGATGAAGAGTT
TTCGATCTCGAATTTCGATGATTTGAGTTTGTTTCACCAGGATTACTCAC
CGCCTTCGCCACCGCCTCCGCCTCCACATCCACCGTCGGTGACTTGTGAG
GATGATTTAGGTGGAGTAGGGTCGTTGGATACTACTTGTAAGATTGTTGC
GAGTGTTAACATTTCGAAAAATGTGTATATAGCAGGGAAAGGCAATTTTT
ATATCCTTTCGAATGTTAGTGTTACTTGTTTGTCTCCTGGATGTGAGGTT
TCGATTAATATAACGGGGAATTTTAGTTTAGGGGAGGATGCTCAGGTTGT
AGTTGGTTATTTTGACCTTACGGCTGATAATGCGACTTTTGGTAACGGTT
CTGTGGTGAATACGACTGCATTGGCAGGGGATCCGCCGGCTCAAACGAGT
GGGACACCACAGGGTATTGAAGGTGCGGGTGGAGGACATGGAGGGAGAGG
TGCTTGTTGTTTGAATGATAAGGAGAAGTTACCAGAGGATGTTTGGGGTG
GGGATGCGTATTCGTGGAACTCTTTGAGGATGCCGGATAGTTTTGGGAGT
AAAGGGGGGACAACAAGTAAGGAGGAGGATTATGGTGGCGGTGGAGGTGG
AATTATTAAGTTGATAGTTAACAACTATCTTGAGGTGAATGGTAGTTTGG
TGGCTGATGGTGGGAATGGAGGTCCTAGGGGTGGAGGAGGATCTGGAGGC
AGCATTTTCATCACTGCTCATAAAATGATTGGTACTGGCACAATAACTGC
TTGTGGAGGTGATGGGTTTGGTGGCGGGGGTGGTGGAAGGGTCTCTGTTG
ACGTGTTTAGCAGGCATGAGGATCCTAAAATTAAAGTTCATGGTGGAAGC
AGTCTTGGTTGTCCTGAGAATGCAGGTGCTGCAGGGACTTTCTATGACAC
TGTTCCACGGAGCCTTTTTGTTAACAATCATAACAAATCAACAGATACTG
ACACACTTCTTTTGGAATTTCCATACCAGCCCCTGATGACAAATGTTTAT
ATTGAAAACCAAGCTAAGGCTGCTGTCCCTTTGCTCTGGAGTCGTGTCCA
GGTCCAAGGACAAATCAAACTTGTAACTGGTGGAGCGTTGAGCTTTGGGC
TAGCACATTATTCTTTATCAGAATTTGAACTGTTAGCAGAAGAGTTGTTA
ATGAGTGATTCTGTAATCAAGGTTTATGGTGCACTTCGGATGTCTGTCAA
AATATTTCTGATGTGGAATTCAGAACTGCTAATAGATGGCGGTGGAGATG
CTAATGTTGAGACATCCTCGCTTGATTCTAGTAATCTCATAGTTCTCAAG
GAATCTTCTCTTATCCATTCAAATGCCAATCTGGGTGTTCATGGACAAGG
TTTATTGAACTTGTCTGGACCAGGAGACACTATTGAAGCACAACATCTGG
TTCTGTCTTTGTTTTACAATATCAATGTTGGCCCTGGATCTACTTTGCGT
GGTCCACTAGTAAATGCCACCAAAGATGCTGTGGTACCAAAGCTGAATTG
CAACAGTCAAGAGTGTCCAGTTGAATTGCTTCATCCACCTGAAGATTGTA
ACGTGAACTCTTCGCTGTCCTTTACGCTTCAGATATGTCGAGTTGAAGAT
ATCCTTGTTGAAGGCCTTGTAGAAGGGTCAGTTGTTCATTTTCACCGTGC
AAGAACTATTGACATTCAGCCTTCTGGAATCATCACCACCTCTGGGATGG
GTTGCATTGGTGGTGTTGGTAGAGGTAAATTAGTTGGTGGTGTTGGCAGC
GGAGCTGGGCATGGCGGGAGAGGTGGTAATGGCTGTTACAATGATAGCTG
CATTGGGGGTGGTATTTCATATGGAGAGGCTGATCTTCCTTGTGAACTGG
GAAGTGGAAGCGGAAATGATAGTGTAATTGGTTACACAGCTGGCGGCGGT
ATTCTAGTGATTGGTTCGTGGGAACAGCCGTTAACAAGCTTATCAGTTAA
AGGCTCAGTGAAAGCTGATGGAGGAAGTTTTGGGGACAAGAGTCATAGTA
GATACTTTGTTGGGTCAGATAATGTGAATGAAGGTATTGGCGGTGCATCT
GGTGGAACAATTCTTCTGTTCTTGCGGGCACTTGCTCTTGGTGACTTGGG
TATTCTTTCAAGTGTTGGGGGTCATGGTAGTCCAGATGGAAGTGGCGGAG
GGGGTGGTGGTAGAATCCATTTTCATTGGTCAGACATTCCGACAGGAGAT
GTGTACCAGCCTGTAGCTAGCGTGGAAGGAAGTATCCATGCTAGCGGAGG
CGTGGGTGGGAAGCAAGGTGGTGCAGGGGAAAATGGAACAATAACTGGAA
AAGCTTGCCCAAAAGGGCTTTATGGGACATTTTGCACGGAATGTCCTGCT
GGTACATATAAAAACGTAACGGGATCCGATATGTCCCTTTGCTATGAGTG
CCCGTCTTCTGGTCTTCCCAGGCGTGCATTTTATGTTGCTGTCCGAGGCG
GTATCGCTGAATTACCCTGCCCTTACAAGTGCATTTCCGACAGATATCAC
ATGCCACACTGTTACACAGCACTAGAAGAGTTAATATACACATTCGGTGG
CCCATGGTTATTTTGTCTCATTCTTTTAGGGATTCTCGTACTTTTAGCTC
TGGTGCTTAGCGTTGCTCGAATGAAATTTGTGGGCACTGATGAATTGCCT
GGTCCTGCCCCCACACATCATGGGTCTCAGATTGATCACTCATTCCCTTT
CCTGGAATCACTGAATGAGGTCTTGGAGACTAATAGAGTTGAAGAATCAC
AAGGTCATGTGCATAGAATGTACTTCATGGGATCTAATACTTTCAGCGAA
CCTTGGTATCTACCTCACACTCCCCCGGAGCAGATTAAAGAAATAGTATA
CGAAGATGCCTTCAATAGATTTGTGGATGAGATAAATGCAATATCAACTT
ATCCGTGGTGGGAGGGATCAGTGTACAGTATTGTTCGCATACTGGCATAT
CCTCTAGCATGGTCCTGGCTACAATGGCGGCGTAGAATTAAGTTGCAAAG
ACTTCGTGAATTTGTGCGATCAGAGTATGATCATGCATGTTTACGTTCAT
GTCGCTCACGTGCACTCTATGAAGGGCTGAAGGTAGCTGCAACCCCTGAT
CTAATGTTAGGGTACGTAGACTTTTTTCTTGGCGGTGATGAGAAGAGGAC
GGATCTTCCTCCTCGTCTTAGTCAAAGATTTCCTTTGTCTTTGATGTTCG
GAGGTGATGGAAGTTACATGGCACCTTTTTCGCTTCACAGTGACAACATC
ATCACAAGCCTCATGAGCCAGTCTATTCCACCTACCACTTGGTACCGATT
TGTTGCTGGCTTAAATGCACAATTACGTTTGGTACGTCGGGGTCGCCTCA
AAACAATGTTTCGAGCCGTTCGCAGATGGCTTGATACTTATGCCAATCCT
GCATTACGAATCTCTGGTCTTAGGGTTGATCTTGGTTGGTTTCAAGCTAC
TGGAGGTGGTTATTGTCAATATGGACTTCTTGTCTATGCTGCGGATGATG
CTAATCATCTATCCTTTGGAGGTGTGGACCATGCAAAACCTAGTCAGCAG
CACTCACGTGTGGAAGATATAATTCATAGAGAGAATTATTATGGCCATCT
GAAAGAAGAGACAACCTTAATCCAATCACCCGTAGTTGATGAAACTAATA
TGAGACGAAGAATGATACATGGTGGAAATGTAGATGCTAATGACATAGAA
GTGCTGGAGGAGAAGCGGGATTTATTTTTTCCTCTCTCTTTCATCATTCA
CAACACTAAACCCGTAGGCCATCAGGATCTTGTTGGGTTGATCATTTCAA
TGCTGCTACTAGGAGATTTTAGTTTAGTTTTGCTTACTTTGCTCCAGTTG
TATTCCATTTCATTGGCCGACGACTTTCTAGTTTTGTTTATTTTACCCCT
TGGGATCATACTACCATTTCCTGCTGGAATCAATGCTCTATTTAGTCATG
GACCCAGACGCTCAGCGGGGCTTGCACGTGTCTATGCTTTGTGGAATATC
ACTTCTTTGGTTAATGTGGCGGTTGCATTTATATGTGGATATTATCACTA
CAGCACGCAGTCAAGTAAAAAAGTACCTTATATTCAGCCGTGGAACATGG
ATGAAAGTGAATGGTGGGTGTTTCCAGTTGCACTAGTTCTATGTAAATGT
ATTCAGTCCTGGCTTATAAATTGGCATGTAGCAAATTTGGAGATTCAGGA
TCGATCATTGTATAGTACTGACTTTGAGGTGTTCTGGCAGTCATGATATT
TAACCAATCAAAAATTTTAGTACAGTAGGAGTTACCTATGACGGCAGGTT
AGAAATGAAAGGAAATGGAAGTACAGAGAAGATGAGGGAATATTTTGGAC
CCCTCATTTCAGTGATATAGTTATAGTTTTCTGCACCGTGTAAATATTGC
CTTGGCAAATCATAGAGGGTTGTAATCTTCGGTGATTTTCATAATGTTAT
CATGTTATGGTCCACTTTATTATATATATAGTTTTGGAAAAGCTTAATGA
ATGCAAATGAGCAGGAGGATTAAAATGTCATA
MGNLYVLSVVLVLFVWITNPRFFIGYVISRDEEFSISNFDDLSLFHQDYS
PPSPPPPPPHPPSVTCEDDLGGVGSLDTTCKIVASVNISKNVYIAGKGNF
YILSNVSVTCLSPGCEVSINITGNFSLGEDAQVVVGYFDLTADNATFGNG
SVVNTTALAGDPPAQTSGTPQGIEGAGGGHGGRGACCLNDKEKLPEDVWG
GDAYSWNSLRMPDSFGSKGGTTSKEEDYGGGGGGIIKLIVNNYLEVNGSL
VADGGNGGPRGGGGSGGSIFITAHKMIGTGTITACGGDGFGGGGGGRVSV
DVFSRHEDPKIKVHGGSSLGCPENAGAAGTFYDTVPRSLFVNNHNKSTDT
DTLLLEFPYQPLMTNVYIENQAKAAVPLLWSRVQVQGQIKLVTGGALSFG
LAHYSLSEFELLAEELLMSDSVIKVYGALRMSVKIFLMWNSELLIDGGGD
ANVETSSLDSSNLIVLKESSLIHSNANLGVHGQGLLNLSGPGDTIEAQHL
VLSLFYNINVGPGSTLRGPLVNATKDAVVPKLNCNSQECPVELLHPPEDC
NVNSSLSFTLQICRVEDILVEGLVEGSVVHFHRARTIDIQPSGIITTSGM
GCIGGVGRGKLVGGVGSGAGHGGRGGNGCYNDSCIGGGISYGEADLPCEL
GSGSGNDSVIGYTAGGGILVIGSWEQPLTSLSVKGSVKADGGSFGDKSHS
RYFVGSDNVNEGIGGASGGTILLFLRALALGDLGILSSVGGHGSPDGSGG
GGGGRIHFHWSDIPTGDVYQPVASVEGSIHASGGVGGKQGGAGENGTITG
KACPKGLYGTFCTECPAGTYKNVTGSDMSLCYECPSSGLPRRAFYVAVRG
GIAELPCPYKCISDRYHMPHCYTALEELIYTFGGPWLFCLILLGILVLLA
LVLSVARMKFVGTDELPGPAPTHHGSQIDHSFPFLESLNEVLETNRVEES
QGHVHRMYFMGSNTFSEPWYLPHTPPEQIKEIVYEDAFNRFVDEINAIST
YPWWEGSVYSIVRILAYPLAWSWLQWRRRIKLQRLREFVRSEYDHACLRS
CRSRALYEGLKVAATPDLMLGYVDFFLGGDEKRTDLPPRLSQRFPLSLMF
GGDGSYMAPFSLHSDNIITSLMSQSIPPTTWYRFVAGLNAQLRLVRRGRL
KTMFRAVRRWLDTYANPALRISGLRVDLGWFQATGGGYCQYGLLVYAADD
ANHLSFGGVDHAKPSQQHSRVEDIIHRENYYGHLKEETTLIQSPVVDETN
MRRRMIHGGNVDANDIEVLEEKRDLFFPLSFIIHNTKPVGHQDLVGLIIS
MLLLGDFSLVLLTLLQLYSISLADDFLVLFILPLGIILPFPAGINALFSH
GPRRSAGLARVYALWNITSLVNVAVAFICGYYHYSTQSSKKVPYIQPWNM
DESEWWVFPVALVLCKCIQSWLINWHVANLEIQDRSLYSTDFEVFWQS
| Relationships |
|---|
| The mRNA, XM_017371965.1, is a part of gene, LOC108203182. |
| The polypeptide, XM_017371965.1, derives from mRNA, XM_017371965.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |