| 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. |
CATAATTAGAAGACCTAAACAGAAAGAGATCGAACCACAGAGAGATACAC
CGAGAAAGAGAACGAGAGAGAGAAAGAGATTTTGTCGCTGGCGAGAATCA
TCGGAGTTGGCAAGTGACGGCAATTGCAATTTCGCCTCTTTTCGATACCG
TTTCGACTCGGTCGAGTTGGTCAGGTTTGTGGATTGTCGCGGAGTTGTCT
TGTTTTGTTGGTTAGTGTGGTTTGTTATTGATAAAGAAGGTATTGTCTGA
CGTTGGATGTGAGAGGAATGGCGTTTTATAGGAATTACTCGAGGGAGCCG
GTTTCGGATGGTGTACTGGATGAGAAAGGGCCGGGACCGGATGTGGAAAA
AGGTGACAGTATTGTCGGAAATGAAGATGGGAATTTAAGTGATAGGGATT
TTGATATTAATTTAAATGCTCAGTATAGGAGTGATGGTGAAGCAGATGAT
GTCGGCAAGTTCCAGGAGGATGTAGGTGCCGGTGGTGCATTACTGGATTT
GCAGCCATCTACGGGAAAAATGGCTTCTTCTGGGAGATGGGGTTCAACTT
TTTGGAAGGACTGCCAACCTATGCGCCATGGGTCTGAATCAGGACAGGAA
TCAAAAAGTAGTTCTGAATATAAAAATGGGGAAGGGTCTGAAGACGAATC
ATTAGGGGTCAGAGAGGATAAGTCGGAGTCAGAAGATCCGGAAACTGTTC
GAAGACATCAGGCTGATGTACCCGTAGATGAGATGCTGTCTGACGATTAT
TACGAGCAGGACGGTGATGAACCCTCTAATGATTTAATGCATCATAGACT
AGGAAATAGTTCAGCTGCCTTCATTTCAAATATAAAGCCTAGGCCTGTTG
CTGCTAACATACATCAGTCGAGAAAGGCAAAAGCTTTAAATGATGATGTA
TACGGCGATGATGATGCTGATTATGAAGATGGAGACGATCCCGATGACGC
AGATTTTGATCCAGACTTCACGAGTGAGCGCCTGGTAATGAAGAACCAGG
ATGATGACTGGGAAGGTGAAAATATGGATGAAGATTTTAATGATGTTGAT
GACCTTGATATTTTGGATGAAGATGATGATTTTCCAAGAAAATCCAAAGG
CAGGCAACGTGGAAAAGGTGGGCTTGTTTCAAAACATGCGAGGGTAGGTA
AGTCGATTACATCATCTAGTCAGCGAAAAAGAGGTGGACTAGCATTGGAA
GATGATGAATCATCTGCAAATGATTCTGACAATGAGAGTGATGAGGGTTT
TAGCAGCAAAGTGAGGAGAGGAGCTAGTTTAAGGAAGAAAAATGTTGCCC
GTGCCACATCTTATATTTCTAGCCGAGGGAGGGAAATTCGAACTTCAAGA
CGGTCTGTTCGGAAAGTCACATATGCCGAAAGTGAGGATAGTGAAGAAAA
TGATGAATCTAAGAAAGGGAAAAGTCAAAAGGAGGAGATTGAAGAGGAAG
ATGGCAACTCAATTGAAAGGGTACTGTGGCATCAACCAAGAGGCATGGCC
GAGGAAGCATTAGCAAACAACAAATCAACAGAGCCCGTGTTGTTAAGCCA
CTTATATGACTATGAACCAGACTGGAATGAAATGGAATTTTATATTAAAT
GGAAAGGCCAATCACATTTGCACTGCGAATGGAAGTCATTTTTTGAACTA
CAAAATCTTAGTGGGTTTAAGAAGGTCATTAATTACACAAAAAAAGTTAT
GGAAGATGTGAAGTACCGGAAGTCTGTCTCACGGGAGGAGATTGAGGTCC
ATGACGTGAGCAAGGAGATGGACCTGGATCTCATCAAACAAAACAGTCAG
GTGGAAAGGGTAATTGCAGAAAGGGTCAGCAAGGACAGTTTGGATGATGT
GGTGCCAGAGTACTTGGTGAAGTGGCAAGGACTGTCTTATGCTGAAGCAA
CTTGGGAGAAATACTTGGATATATCATTTGCTCAAGAAGCTATCGATGAG
TTCAAGGCCCGTGAGGCAGCAGTAGCAATACAAGGAAAAATGGTAGACGT
TCAACGAAGGAAAAGCAAAGAAAGTTTGAGGAAGCTTGATGAACAGCCTG
AATGGTTGAAGGGTGGTAAACTTAGAGATTATCAGCTTGAGGGATTGAAC
TTTCTTGTTAACAGTTGGAGAAATGATACGAATGTCATATTAGCTGATGA
AATGGGTCTGGGCAAAACTGTTCAGTCAGTTTCTATGCTTGGTTTTTTGC
AGAATGCTCAACAAATTCATGGCCCATTTCTTGTTGTTGTCCCATTGTCG
ACACTATCAAATTGGGCAAAAGAATTTAGAAAATGGCTGCCCCAAATGAA
TGTCATCATATATGTTGGAGCCCGTGCAAGCCGAGAGGTTTGTCAACAAT
ATGAATTCTACTCTGATAAGAAGAATGGCAGGGGCATAAAGTTTGATGCC
CTGTTGACTACATATGAAGTACTACTAAAAGACAAGGAAGTGCTTTCAAG
GCTTAAGTGGAACTATCTCATGGTTGACGAAGCACATAGGTTAAAGAACA
GTGAAGCTGCATTATATATAACACTTGCGGAATTCAGCACGAAGAACAAG
TTGCTTATAACTGGTACTCCATTGCAAAACAGCGTCGAGGAACTTTGGGC
TCTGCTTCACTTTCTTGATTCTAACAAGTTCAAGAGCAAGGATGAGTTTG
TACAAAATTACAAAAATCTAAGTTCGTTCAATGAAAATGAGCTCGCTAAT
CTTCACATGGAGCTGAGGCCTCACATTCTCCGGAGGGTTATCAAGGATGT
GGAGAAGTCCTTGCCGCCAAAGATTGAACGAGTTTTAAGGGTTGAGATGT
CTCCTCTGCAGAAACAGTACTACAAGTGGATTCTAGAACGCAATTTCCAA
GATTTAAACAAAGGAGTTCGTGGGAATCAGGTTTCTCTTCTAAATATCGT
GGTTGAGTTAAAAAAATGTTGCAACCATCCATTCCTCTTCGAAAGTGCAG
ATCATGGTTATGGAGGGGAAACTAATATTACTGGAAGTAGTAAACTGGAA
AGAGTTATTCTGAGCAGCGGGAAGTTGGTTATACTCGATAAACTTCTTGA
CAGACTAAATGAAACAAATCATCGTGTATTGATATTTTCACAGATGGTTA
GGATGCTTGATATTTTGGCGGAATACCTGTCGATTAAAGGGTTCAAGTTC
CAAAGGCTTGATGGAAGTACAAAAGCTGAAGTGCGCCATCAAGCTATGGA
GCATTTTAATGCACCTGGTAGTGATGACTTCTGTTTTCTTCTTTCAACAC
GTGCTGGTGGCTTAGGTATCAATCTTGCAACAGCAGATACAGTTATCATA
TTTGATTCTGATTGGAATCCCCAAAATGATTTGCAGGCCATGAGTAGAGC
ACACAGGATTGGGCAGCAAGATGTTGTGAACATTTATCGGTTTGTTACAA
GTAAAAGTGTTGAGGAGGATATTTTGGAACGTGCTAAGAAGAAAATGGTT
CTTGATCATTTGGTTATTCAAAAGCTGAATGCGGAGGGGAAGTTGGAAAA
GAAAGAAACAAAGAAAGGGAGTTCCTTTGACAAAAATGAGCTATCAGCGA
TCTTGAGGTTCGGTGCAGAAGAACTATTCAAGGAAGACAAAAACGAAGAA
GAAAGTAAAAAGAGGCTTCTAAGTATGGATATAGATGAAATTCTTGAGAG
AGCAGAGAAGGTAGAAGAAAAGGGTGCCAATGACGAGGAAGGAAATGAGT
TACTGAGTGCTTTTAAGGTTGCTAATTTCTGTACTGCTGAGGATGATGGG
AGTTTCTGGAGCCGGTGGATTAAACCTGAGTCTGTTAACCAGGCAGAAGA
AGCTTTAGCTCCTAGAGCTGCAAGAAATAGCAAGAGTTATGCAGAGGCTA
ACCTACCTGAAAAACTTGATAAAAGGAAAAAGAAAGGTGTTGAGACTCAG
GAAAGATTTTCTAAGCGCAGGAAAGCAGATGCTACTTATTTTTCTGTACC
GGCAATTGATGGAGCTGCTGCTCAAGTAAGAGGGTGGTCTCATGGTAACC
TGCCAAAGAGAGATGCTACACGTTTTTTCCGTGCTGTCAAGAAATTTGGC
AATGATAGCCAAATTGACTTAATAGCAGCAGAGGTTGGTGGGTCTGTTGA
AGCGGCTCCAACTGATGCACAAATTGAGCTTTTTGATGCTTTGATTGATG
GCTGTCGAGAAGCAGTCGACGGAATGAATCTGGACCCGAAGGGGCCTGTG
CTAGACTTTTTTGGTGTTCCTGTTAAGGCTGATGAACTATTAACCCGTGT
TGAAGAACTTCAACTCTTAGCAAAGCGCGTTAGTCGTTATGAAAAACCAA
TCTCACAGTTCCAGGCATTGATGTACCTCAAACCTGCTACTTGGTCTAAG
GGTTGTGGGTGGAACCAGAAGGATGATGCAAGATTGCTTCTTGGAATCCA
TTATCATGGGTTTGGCAATTGGGAAAAGATAAGGTTGGATGAAAAGCTTG
GTCTTACAAAGAAAATTGCACCAGTAGAACTCCAGCATCATGAGACTTTC
TTGCCTCGAGCTCCCCAGTTAAAGGAGAGGGCCTCCCAACTGCTAGAAAT
GGAATTTACTGCTGTTAGTGGGAGCAACTCAAACGCCAAAGCTAGCCGCA
AAGCTACCAAGAAGCAAAAAGAAAATTCTTTAGGCATTTCATTGTCACGC
AGCAAGGGCAAGCAAGGCAAGCAGGGATCGCCAAAATATAATCCTCAGGT
AATTAAGGTGAAGACTGCAAGAACACAGAAGGTCGAACCGTTGGTAAAAG
AGGAAGGTGAAATGTCAGATACTGAAGAAGTCTATGAACAGTTCAAGGAA
GTAAAATGGATGGAATGGTGTGAGGATGTCATGGCTGATGAAACAAAGAC
GCTGACACGTCTTCAAAGGTTACAAACTACCAGCGCAGAGCTCCCTAAGG
AAAAGGTGCTCTCCAGAATAAGAAATTATTTGCAGATCCTTGGACGAAGG
GTTGACCAAATTGTTTTAGAGCACGAGGAGGAACTATATAAGCAAGAAAG
GATGAAAACACGATTATGGAAGTATATATCAACTTTTTCGAATTTGTCTG
GAGAGGGACTGTATCAGATTTATTCCAAACTAAAGCAGGAGCAGGTAGGA
CTAGCACCTTCACATGTTAACGGTTCTTCACGTGGTTACAGACATGAAGC
CTCCAACCAGATTTCTGGAGTAGTTCAAAGGGGTGTTGATACAGGAAAAT
TTGAAGCGTGGAAACGAATGAAAAGAGCTGAGGCTGATATGAACTCTCTA
GTTCAACCCCTGCATGAAAGATCTTCAAGTAATGCTACATCTGGGATTCT
AGGATCAGGACCATCTAACAGCCGATACTCTGGTAATGAGAAGTCTTATA
ATATGCGTCAAACTGGTCAACCTCCGCGACAAGGCTTTCCGTCGGGTGTA
AAGTAGCCTTGATACCTTATTGAAGGAAATCTGTCTCGGAAAGTGGAATG
CAAAAAATTTCCCCTTCCATTCAATTCAGCTGCTTTGGCCATTAAATTTT
TTCTGGGTTCTTTTCCCTTGCTGGGAATAAACAATTGCAGATCTTGTGGA
GAATGTTTTAAAATCATCTCAAGCCTGCATCAGAAAGTGGGCCCCAAGCT
TTTGAGAGTGGAAAAAATGTCAACAAAAATACATATAATCTTGGGACCAA
AGTATATTATTGAACTTTATTTAAACAGCTCCCCAATTTCTTGAAAGTAC
ATAGTGAATAGGCAAAGAATCAGCTGCTCACCAGTTGGTATGAGGAAGAC
AACGAATGTAACATCCTTTGGATAGTGTAAATTACCCAGTTTTGCTTCTT
AAATGTCTGAACACAGAGATTACTAAAGTTGATCGCATATTTTTATGAAA
AGAATGATAGAATATTGAATGTCTTA
MAFYRNYSREPVSDGVLDEKGPGPDVEKGDSIVGNEDGNLSDRDFDINLN
AQYRSDGEADDVGKFQEDVGAGGALLDLQPSTGKMASSGRWGSTFWKDCQ
PMRHGSESGQESKSSSEYKNGEGSEDESLGVREDKSESEDPETVRRHQAD
VPVDEMLSDDYYEQDGDEPSNDLMHHRLGNSSAAFISNIKPRPVAANIHQ
SRKAKALNDDVYGDDDADYEDGDDPDDADFDPDFTSERLVMKNQDDDWEG
ENMDEDFNDVDDLDILDEDDDFPRKSKGRQRGKGGLVSKHARVGKSITSS
SQRKRGGLALEDDESSANDSDNESDEGFSSKVRRGASLRKKNVARATSYI
SSRGREIRTSRRSVRKVTYAESEDSEENDESKKGKSQKEEIEEEDGNSIE
RVLWHQPRGMAEEALANNKSTEPVLLSHLYDYEPDWNEMEFYIKWKGQSH
LHCEWKSFFELQNLSGFKKVINYTKKVMEDVKYRKSVSREEIEVHDVSKE
MDLDLIKQNSQVERVIAERVSKDSLDDVVPEYLVKWQGLSYAEATWEKYL
DISFAQEAIDEFKAREAAVAIQGKMVDVQRRKSKESLRKLDEQPEWLKGG
KLRDYQLEGLNFLVNSWRNDTNVILADEMGLGKTVQSVSMLGFLQNAQQI
HGPFLVVVPLSTLSNWAKEFRKWLPQMNVIIYVGARASREVCQQYEFYSD
KKNGRGIKFDALLTTYEVLLKDKEVLSRLKWNYLMVDEAHRLKNSEAALY
ITLAEFSTKNKLLITGTPLQNSVEELWALLHFLDSNKFKSKDEFVQNYKN
LSSFNENELANLHMELRPHILRRVIKDVEKSLPPKIERVLRVEMSPLQKQ
YYKWILERNFQDLNKGVRGNQVSLLNIVVELKKCCNHPFLFESADHGYGG
ETNITGSSKLERVILSSGKLVILDKLLDRLNETNHRVLIFSQMVRMLDIL
AEYLSIKGFKFQRLDGSTKAEVRHQAMEHFNAPGSDDFCFLLSTRAGGLG
INLATADTVIIFDSDWNPQNDLQAMSRAHRIGQQDVVNIYRFVTSKSVEE
DILERAKKKMVLDHLVIQKLNAEGKLEKKETKKGSSFDKNELSAILRFGA
EELFKEDKNEEESKKRLLSMDIDEILERAEKVEEKGANDEEGNELLSAFK
VANFCTAEDDGSFWSRWIKPESVNQAEEALAPRAARNSKSYAEANLPEKL
DKRKKKGVETQERFSKRRKADATYFSVPAIDGAAAQVRGWSHGNLPKRDA
TRFFRAVKKFGNDSQIDLIAAEVGGSVEAAPTDAQIELFDALIDGCREAV
DGMNLDPKGPVLDFFGVPVKADELLTRVEELQLLAKRVSRYEKPISQFQA
LMYLKPATWSKGCGWNQKDDARLLLGIHYHGFGNWEKIRLDEKLGLTKKI
APVELQHHETFLPRAPQLKERASQLLEMEFTAVSGSNSNAKASRKATKKQ
KENSLGISLSRSKGKQGKQGSPKYNPQVIKVKTARTQKVEPLVKEEGEMS
DTEEVYEQFKEVKWMEWCEDVMADETKTLTRLQRLQTTSAELPKEKVLSR
IRNYLQILGRRVDQIVLEHEEELYKQERMKTRLWKYISTFSNLSGEGLYQ
IYSKLKQEQVGLAPSHVNGSSRGYRHEASNQISGVVQRGVDTGKFEAWKR
MKRAEADMNSLVQPLHERSSSNATSGILGSGPSNSRYSGNEKSYNMRQTG
QPPRQGFPSGVK
| Relationships |
|---|
| The mRNA, XM_017401773.1, is a part of gene, LOC108226771. |
| The polypeptide, XM_017401773.1, derives from mRNA, XM_017401773.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |