| 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. |
CGAAATAGGGGAATTGAAGGCAAGTCCATACTAGTTCTTCTTCTTCTTGT
TGATAATCGAATACTGCGCATCACTGAGCGGGTGTCAATGGACTCCTACA
CTCCATTACTGGAGAGAACTCGAGTTCCCCAACCCTCTATTCAATCCTAC
GCCGTTATATCCATTTTCGACAAGTTCCGATCCTCTCCGCCCCACCTGAT
TGACGCCGGAAGAGAAGCAATCGCTCAATGTCTTCTCTCCTCTTCCCCCG
CCGTCGTCGATCAGTCCGTACGCCAATTGTGTCGTCTCGTGATCCAGGAG
AAATTCAAATTGTCTGATGCTTTGATGGAGCTCCAATCAGCCTTAGAAGC
CTCCCAATCACGTTTTGTTGATGTGTTTGTCAAGGCTTTAGGCTTTCTCG
TTCGCTTAGGCTTCCGGAATCATCCTCATTCGTTTCGCTTTTCGTCTTCC
AATGCTCATCCTTTTGTCAAGATACTTTGTTGCAGGCCAGAGGTTCAATC
GGAACTTGTCAAACAAGTTGTTTTGTTTATGGTGTCCAACAAGAGTATTG
GAATGCTTAAAGTTTGTGATTTTTTAAGCTCCTTTTTCAACTTTATGACC
ATAAGAATGTCCGATTTTAATTCCTGTTGTCGAAGTCTGGTTTCGTCTGT
GGCATCTCTTTGCTGTTCATATCCTCTGGACGCTCTGCCTGTTATGAAGC
TGCTAGTTAAATGTCTCAGATTTTGTCCTAGCAAAAATGAAGAAGAAAAT
GTTTCTTACGTTTTGGAACACATGGTGAATATGTTTATTGTGGTTTTGCG
GCAGCTGGTTGAGATAGGATTGCTTGTTCATGAGACCCAGCTACAATGTG
TGGAACTTCTCGAAACCATCTTTTCACTGAATATATATCTTGACAAGGGT
TCCTGTAGGAGTGAAGCTGTGATTGAAATGTCAAGGCGTCTAGTAACTGT
CCAGAACGATCTTAGTTTGAGTTATATACCTGAATTTTCGTCTGTGGTAT
TATCATTATTTATTGCTCTTGTTCAGGAAGAGTTTGAGCACAAACAACTC
TCCATACTCCGAATGCTTTTGCTTCTCTTGAAATGGAAAGGTGAAAAGGG
TAATCTTGTTACTGAATGTGTGGTTGAAGAACTTCTTTTCATATTTCCTC
TCATGAACCTCATGTCCTCCCCTTCAATATCTGTTAAACAAGCAGCAACA
AATTTGCTTTCCATGTTGTATAAGTCCGCAACAAACTTGTTGGTTACACA
AGCCAAAGATCAAGGCATTAGAAGGAAAAAACCACCCATTAGCAGACCTG
AGCATATCTTTTACAGGCTTCTGCTGCATATATGGTATCAGGATCAATTT
TTGTCATATGCTTCATCCAACTTAGTTATGACGAATGGTGAAATTAATAT
GAAAGGAACATATCAGTTACCAAAGAGATGGACTGACATGATGGCAGAGT
ATGCACTTGGGGTCATTGAAAAACAGAAGTCTTCCGTACCCATCTCCCAG
TCTGAGAGCATCTTGCTCAAGGAGATGGCACCATATCTTAGTGCTATAAT
GAGTGTTCTTGTCCTGCATCGTGCCATGGGTGCTTCAGCTGTAGATCTAT
TGGCTGTTTCTGGCGACATGAACCCTAAACTTGGTGTACCACTGCTACTA
GTCATCTTATTCTATAATAACATAAACTGTGCTAAAGATCGAGACTTCCA
TCAGATACTGCTAAAGCTTTTGGGGATACTTCCATCGCTTGCTTCGCATC
CTGCAATGGTTCCACTTGTTGTTCAGACTATATTGCCGATGCTTCAGAAT
GACACGAAACCTGTGCTGTATGCTACTGCCACACGTGTACTTTGCAAGAC
ATGGGAGATCAATGATCGTGTATTTGGGAGTTTGCAGAGCGTATTACTCC
CGAATCGATTTATCCAGTATGCATCTCAAAGAGATATATGTATAAGCATG
GCAATTTCTATACGAGATGTTTGCAAGAGAGATCCTGATAGAGGCGTGGA
CCTTATTCTCTCTGTATCGGCTTGCATTGAGAGCCGTGATTCTTCAATTC
ACACTATTGGCCTTTTAAGTCTTGCCCATCTTTGTGAAGCTGATGTAATC
GATTTCTATACTGCTTGGGGTGTTATAAGAAAGCATTTGCTCAATTACTT
GGAAAATCCTATTATATGTCACGGCGTTTCTCTTCTTCTACGATGTGGTG
CAATGGATGCTGCTGTATTCCCAGAAGCAGCAAATGATATATTGCATATA
TTGTGGGAGATTGGAACCACCCTCCATCCTGCTAGTGAATTAATGTGGAC
AAAGGCTCGAGCAGCTGCCTTTGAATCATTGACTTATTATGAGGTATTAC
ATGTTCAGAACAGCACTCCAGAATTTAGAGAGAGAACCATGGAGTTGCTT
ACTGCTGAGACCGATACCGAAGTGCTTTGGGCTATGGAAAAATTTGTCAT
AAATATTATCAAATTTGAGCACCAGACAAGGCAAAGATTAGTGAAGGAGA
AACGGGTACCTCGAAATAAAATCGAGAAGTTGGTAAATATATCTCCACAG
CTAAATTTCAAGCAAGGAGATGATAGAAAAATTAGAGATTTACCTGGTGC
AGCTCTTTTTTCCCTTACCTTTACTCATGATGTGAACAAGCCCGGGGCTG
CAAAAGATCTGCATGCTAAATTTAGGACTGCATTATTGGACATAGCAGCA
TCACTCCATCTATCAAGAAATATTTCGGTTGCGGTTCTTTCCTTCCAGTC
ATGGAAAATTTTCATGCAACGCTGGATAAAGGAGCAGATCATGCTAAATG
ACGTGAAGGGATTATCCACATCATTAAATAATACTAATAAACCTGCTAAT
GATATCTTGAAGAGTATAATACAGATTGCAGAGGAGTCTATTCCCAGATT
GGCTGAAAATATTGCACTAGCTGTTGGTGCATTTTGTATGGTTCTTCCTG
CATCGGCTCATGCTGTCAAATCTACTGCCTTAAATTTCCTGCTGAAATGG
CTATATCAGTATGAACATGAATATCGCCAGTGGTCTGCTGCAATATCTAT
TGGAGCAATCTCAAGTAATTTGCATGCAACTGACTATAAACAAAAGTTTC
AAAATATCAATGCACTTCTTGAGGTTGCATCAATCTGCAAAAGCACATTG
GTAAAAGGGGCTTGTGGACTTGGATTGGGGTTATCTTCTCAAGATCTCAT
TACCAGGGTAAAAGTTGATGATGAATCTGACTCGCATAAAGAAACATACA
TGATGCAGGAAACATATCTGCTTGGACGGATTGTGAGGGCTTTATGCCAA
ATGTTAAGCAAAATTACTCGACTATCATCTGATGCACTAGAATTACAAAG
CATATGTGCATACTTTGGTCAAGCAACAGATGCTGGTGATTCAGAGAGCT
TTCTCATTATCCATGATAACTTGGAGGAAGATGTATGGGGTATTGCTGGA
GTTGTTCTTGGTTTAGGAAATACTGTTGCAGCAGTGTATCGGACCGGAAA
TCATGACGCTGTGTGTAAAATAAATGGCTTGATAAGTTCATGGATGCGAC
ATGTCAATCCTTTAATTATTAACTCAACTACCAGCGAGAAAATTGAATTA
GCATTGTTAGTAGGATCTTGTCTTGCTCTTCCTAATTTAGTAGATTTCTT
CCAGAGAGTGGATGATCTTGATGATTCTGAACTGGATAATCTGATAAGTA
GCTTTAAGGATCTTATTTCTGAACTTGTCTCAGTTAACAAATCAGGCGTA
CTTTATCAAAGTTTGTTGTTTGCATCCTGTACTGGAGTAGGAAACCTTTT
GGCATGCATCTTGAATGAAGGGGTGCATTTAGTTCGAGTTGAATATGTTA
CTGACTTGCTAATGTTGTTCAAAAAATGCTATACAGCCTCTTATCCCCCT
CTTGTCCATTTGGGTGGGATGCTTGGAATTGTAAACATATTAGGTGCTGG
TGCTGGTTTTCTGTTCCAACGTGATTGTTCAACCTTTCTGCACCCTGTTC
ATGATCTCAAGAATTCTTCTTATATTACGGGGTCTTTGCTTTCAAGTTCT
GCTATGGAGCCAAATCTGGTGTCATTAGTTCAGGACATCTTTCTTGTTTC
TCAAAATCCTGATGACCAACAACTACAATCATATGCCGCATGGGCCATTT
CTTTTCTTAGACATTATTTGTGGTACAGAAATGTTAGAAATGAAGATGAT
AACTCCCAGCGCGATGCAGTTGGTTCAAAATTTGTTTCTTCAAATCCTCC
AGACGACAGTTTAGTCATGAAGCTCTCTTTGTGGTTAATGAATCACAGCT
TCCCTGGGACAGGTACTGCTCATGTTAACACAGTTTTGACTGCTTTACGA
TGTCTTACTAGTGCTCCAAGATTACCACTATTAGATTGGGGAGCAATCAT
CAGACGGTGTATGAGACTCAATTCTGTAGATCATGTATTATTACCCTCGG
ATTCAGCTTCTTCAAGGAGAGTATTTGTACGGGAGGAGTGCCTGTTATTC
TCTTTAGCCCATGCAAAGGAATTTGATCCTCTTCTCAGCTTACTAGATGA
GTTGTCTGACTTGCCCAGGTTTAGGATGCTCGAGCTAAATATGCAGTCTT
TTCTGCTCTCTCGTCTTGCAGACATGAGTAAGGTTTTTTCAGGTTCTAGG
ATCGAAAAGCTATTTGATGATGTGGCAAACTTTGTAAAACTGTTAGTTCC
TTCACATCAGCTATATAATTCGGAACAGAAAAGTTTATTAAGGATTTCTT
GCTGGAAGGGTCTTTCTTTATGTTTAATGGGAGCTACAGCTGACGGAGAA
GATCATGTTTCTTATATGGAAAACTGCTTGAAGGTTCTGTTTTGTTCAAC
ATCTTCTAGTGCAGTAGTTGGTCAGGATCATTTATCAGAGGAGTGGTCTG
CTGCAATTAAGTGCTTGGCACAGGCTCGGCAGCCTTGGTTACTTGACTTT
TTTAAGGTCTCAGAGGTGGATTTCAGATCTGGAGACATGTACTTTCTTGA
AGTAAAGAAAAAAATTCAAGCAACATGCATGCTAGCGCGGACCGGTTCCA
TTCCATTGTCTCATATTGGAAGCCTGAAAGCATACATGCTAAACACCAGA
TCACAAGATATCTGGGAGGTGCTAGTAGAAGTTGCAGCCACCCTTCAAAA
TGCTGATGGAAGCATTAAAAGACAGTGGGTTCTTGATGCTGCTGAAATTA
GCTGTGTAACCAGACATCCGTTGACGGCGATGCAGTTCCTTGGCCTGCTA
TGTGGCAGCTTCAGCAAGTATATGCCTTTTCTGATTGTTGACCGGATGAC
TGTGTTATGTGACTTTCCAGTTGCTCTTGCTTCTCTTCTATCAGAAACTA
GCTGGGGCAATGTAGCAGAATCTGTAGTTTCACTTCTGTGGTCAACAACA
GAACGGTTACATGATTGGGTTACAAACACGGAAATAGTTCTCAGTGATTC
CCCAATTTCCCAGTCTATTGACCAAAGTGAGGATTCTATGGCTGATTTTC
TCTTGAAGTTGCTGCATCATACATGCGTTTCTCTGAAAGACTATCTGCCG
ATGGAGAAGCAGCTTAGTCTTGCTAACATGGTTATTCCTTAACCCTTCAA
CTCTCAGAGGACCAAATTTACGAAATTTAGATAGAAAATAGTTTACTAAT
TTCTGTAGCTATCATTAAATATGATCAGATGTTATTTTGTTGTAAAACTA
GAAGTATATAAAAGATGTGGCAAAAAAAAAAAAGAAGTATATAAAAGAGA
TTAGTGTGATACAGTACAAAAGAGGGAGATGTTATCAATCTGAGACTAGC
CATTATTCGGTTGAAA
MDSYTPLLERTRVPQPSIQSYAVISIFDKFRSSPPHLIDAGREAIAQCLL
SSSPAVVDQSVRQLCRLVIQEKFKLSDALMELQSALEASQSRFVDVFVKA
LGFLVRLGFRNHPHSFRFSSSNAHPFVKILCCRPEVQSELVKQVVLFMVS
NKSIGMLKVCDFLSSFFNFMTIRMSDFNSCCRSLVSSVASLCCSYPLDAL
PVMKLLVKCLRFCPSKNEEENVSYVLEHMVNMFIVVLRQLVEIGLLVHET
QLQCVELLETIFSLNIYLDKGSCRSEAVIEMSRRLVTVQNDLSLSYIPEF
SSVVLSLFIALVQEEFEHKQLSILRMLLLLLKWKGEKGNLVTECVVEELL
FIFPLMNLMSSPSISVKQAATNLLSMLYKSATNLLVTQAKDQGIRRKKPP
ISRPEHIFYRLLLHIWYQDQFLSYASSNLVMTNGEINMKGTYQLPKRWTD
MMAEYALGVIEKQKSSVPISQSESILLKEMAPYLSAIMSVLVLHRAMGAS
AVDLLAVSGDMNPKLGVPLLLVILFYNNINCAKDRDFHQILLKLLGILPS
LASHPAMVPLVVQTILPMLQNDTKPVLYATATRVLCKTWEINDRVFGSLQ
SVLLPNRFIQYASQRDICISMAISIRDVCKRDPDRGVDLILSVSACIESR
DSSIHTIGLLSLAHLCEADVIDFYTAWGVIRKHLLNYLENPIICHGVSLL
LRCGAMDAAVFPEAANDILHILWEIGTTLHPASELMWTKARAAAFESLTY
YEVLHVQNSTPEFRERTMELLTAETDTEVLWAMEKFVINIIKFEHQTRQR
LVKEKRVPRNKIEKLVNISPQLNFKQGDDRKIRDLPGAALFSLTFTHDVN
KPGAAKDLHAKFRTALLDIAASLHLSRNISVAVLSFQSWKIFMQRWIKEQ
IMLNDVKGLSTSLNNTNKPANDILKSIIQIAEESIPRLAENIALAVGAFC
MVLPASAHAVKSTALNFLLKWLYQYEHEYRQWSAAISIGAISSNLHATDY
KQKFQNINALLEVASICKSTLVKGACGLGLGLSSQDLITRVKVDDESDSH
KETYMMQETYLLGRIVRALCQMLSKITRLSSDALELQSICAYFGQATDAG
DSESFLIIHDNLEEDVWGIAGVVLGLGNTVAAVYRTGNHDAVCKINGLIS
SWMRHVNPLIINSTTSEKIELALLVGSCLALPNLVDFFQRVDDLDDSELD
NLISSFKDLISELVSVNKSGVLYQSLLFASCTGVGNLLACILNEGVHLVR
VEYVTDLLMLFKKCYTASYPPLVHLGGMLGIVNILGAGAGFLFQRDCSTF
LHPVHDLKNSSYITGSLLSSSAMEPNLVSLVQDIFLVSQNPDDQQLQSYA
AWAISFLRHYLWYRNVRNEDDNSQRDAVGSKFVSSNPPDDSLVMKLSLWL
MNHSFPGTGTAHVNTVLTALRCLTSAPRLPLLDWGAIIRRCMRLNSVDHV
LLPSDSASSRRVFVREECLLFSLAHAKEFDPLLSLLDELSDLPRFRMLEL
NMQSFLLSRLADMSKVFSGSRIEKLFDDVANFVKLLVPSHQLYNSEQKSL
LRISCWKGLSLCLMGATADGEDHVSYMENCLKVLFCSTSSSAVVGQDHLS
EEWSAAIKCLAQARQPWLLDFFKVSEVDFRSGDMYFLEVKKKIQATCMLA
RTGSIPLSHIGSLKAYMLNTRSQDIWEVLVEVAATLQNADGSIKRQWVLD
AAEISCVTRHPLTAMQFLGLLCGSFSKYMPFLIVDRMTVLCDFPVALASL
LSETSWGNVAESVVSLLWSTTERLHDWVTNTEIVLSDSPISQSIDQSEDS
MADFLLKLLHHTCVSLKDYLPMEKQLSLANMVIP
| Relationships |
|---|
| The mRNA, XM_017373679.1, is a part of gene, LOC108204308. |
| The polypeptide, XM_017373679.1, derives from mRNA, XM_017373679.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |