| 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
TCGGAGGGTTTATTCATCGTCTCTTTCTCGCAATTCGCTGACGATTCTGA
TACGCATATACATACATATATCTGTTTCTATATTACCAGTTGGCAAGTGA
CGGCAATTGCAATTTCGCCTCTTTTCGATACCGTTTCGACTCGGTCGAGT
TGGTCAGGTTTGTGGATTGTCGCGGAGTTGTCTTGTTTTGTTGGTTAGTG
TGGTTTGTTATTGATAAAGAAGGTATTGTCTGACGTTGGATGTGAGAGGA
ATGGCGTTTTATAGGAATTACTCGAGGGAGCCGGTTTCGGATGGTGTACT
GGATGAGAAAGGGCCGGGACCGGATGTGGAAAAAGGTGACAGTATTGTCG
GAAATGAAGATGGGAATTTAAGTGATAGGGATTTTGATATTAATTTAAAT
GCTCAGTATAGGAGTGATGGTGAAGCAGATGATGTCGGCAAGTTCCAGGA
GGATGTAGGTGCCGGTGGTGCATTACTGGATTTGCAGCCATCTACGGGAA
AAATGGCTTCTTCTGGGAGATGGGGTTCAACTTTTTGGAAGGACTGCCAA
CCTATGCGCCATGGGTCTGAATCAGGACAGGAATCAAAAAGTAGTTCTGA
ATATAAAAATGGGGAAGGGTCTGAAGACGAATCATTAGGGGTCAGAGAGG
ATAAGTCGGAGTCAGAAGATCCGGAAACTGTTCGAAGACATCAGGCTGAT
GTACCCGTAGATGAGATGCTGTCTGACGATTATTACGAGCAGGACGGTGA
TGAACCCTCTAATGATTTAATGCATCATAGACTAGGAAATAGTTCAGCTG
CCTTCATTTCAAATATAAAGCCTAGGCCTGTTGCTGCTAACATACATCAG
TCGAGAAAGGCAAAAGCTTTAAATGATGATGTATACGGCGATGATGATGC
TGATTATGAAGATGGAGACGATCCCGATGACGCAGATTTTGATCCAGACT
TCACGAGTGAGCGCCTGGTAATGAAGAACCAGGATGATGACTGGGAAGGT
GAAAATATGGATGAAGATTTTAATGATGTTGATGACCTTGATATTTTGGA
TGAAGATGATGATTTTCCAAGAAAATCCAAAGGCAGGCAACGTGGAAAAG
GTGGGCTTGTTTCAAAACATGCGAGGGTAGGTAAGTCGATTACATCATCT
AGTCAGCGAAAAAGAGGTGGACTAGCATTGGAAGATGATGAATCATCTGC
AAATGATTCTGACAATGAGAGTGATGAGGGTTTTAGCAGCAAAGTGAGGA
GAGGAGCTAGTTTAAGGAAGAAAAATGTTGCCCGTGCCACATCTTATATT
TCTAGCCGAGGGAGGGAAATTCGAACTTCAAGACGGTCTGTTCGGAAAGT
CACATATGCCGAAAGTGAGGATAGTGAAGAAAATGATGAATCTAAGAAAG
GGAAAAGTCAAAAGGAGGAGATTGAAGAGGAAGATGGCAACTCAATTGAA
AGGGTACTGTGGCATCAACCAAGAGGCATGGCCGAGGAAGCATTAGCAAA
CAACAAATCAACAGAGCCCGTGTTGTTAAGCCACTTATATGACTATGAAC
CAGACTGGAATGAAATGGAATTTTATATTAAATGGAAAGGCCAATCACAT
TTGCACTGCGAATGGAAGTCATTTTTTGAACTACAAAATCTTAGTGGGTT
TAAGAAGGTCATTAATTACACAAAAAAAGTTATGGAAGATGTGAAGTACC
GGAAGTCTGTCTCACGGGAGGAGATTGAGGTCCATGACGTGAGCAAGGAG
ATGGACCTGGATCTCATCAAACAAAACAGTCAGGTGGAAAGGGTAATTGC
AGAAAGGGTCAGCAAGGACAGTTTGGATGATGTGGTGCCAGAGTACTTGG
TGAAGTGGCAAGGACTGTCTTATGCTGAAGCAACTTGGGAGAAATACTTG
GATATATCATTTGCTCAAGAAGCTATCGATGAGTTCAAGGCCCGTGAGGC
AGCAGTAGCAATACAAGGAAAAATGGTAGACGTTCAACGAAGGAAAAGCA
AAGAAAGTTTGAGGAAGCTTGATGAACAGCCTGAATGGTTGAAGGGTGGT
AAACTTAGAGATTATCAGCTTGAGGGATTGAACTTTCTTGTTAACAGTTG
GAGAAATGATACGAATGTCATATTAGCTGATGAAATGGGTCTGGGCAAAA
CTGTTCAGTCAGTTTCTATGCTTGGTTTTTTGCAGAATGCTCAACAAATT
CATGGCCCATTTCTTGTTGTTGTCCCATTGTCGACACTATCAAATTGGGC
AAAAGAATTTAGAAAATGGCTGCCCCAAATGAATGTCATCATATATGTTG
GAGCCCGTGCAAGCCGAGAGGTTTGTCAACAATATGAATTCTACTCTGAT
AAGAAGAATGGCAGGGGCATAAAGTTTGATGCCCTGTTGACTACATATGA
AGTACTACTAAAAGACAAGGAAGTGCTTTCAAGGCTTAAGTGGAACTATC
TCATGGTTGACGAAGCACATAGGTTAAAGAACAGTGAAGCTGCATTATAT
ATAACACTTGCGGAATTCAGCACGAAGAACAAGTTGCTTATAACTGGTAC
TCCATTGCAAAACAGCGTCGAGGAACTTTGGGCTCTGCTTCACTTTCTTG
ATTCTAACAAGTTCAAGAGCAAGGATGAGTTTGTACAAAATTACAAAAAT
CTAAGTTCGTTCAATGAAAATGAGCTCGCTAATCTTCACATGGAGCTGAG
GCCTCACATTCTCCGGAGGGTTATCAAGGATGTGGAGAAGTCCTTGCCGC
CAAAGATTGAACGAGTTTTAAGGGTTGAGATGTCTCCTCTGCAGAAACAG
TACTACAAGTGGATTCTAGAACGCAATTTCCAAGATTTAAACAAAGGAGT
TCGTGGGAATCAGGTTTCTCTTCTAAATATCGTGGTTGAGTTAAAAAAAT
GTTGCAACCATCCATTCCTCTTCGAAAGTGCAGATCATGGTTATGGAGGG
GAAACTAATATTACTGGAAGTAGTAAACTGGAAAGAGTTATTCTGAGCAG
CGGGAAGTTGGTTATACTCGATAAACTTCTTGACAGACTAAATGAAACAA
ATCATCGTGTATTGATATTTTCACAGATGGTTAGGATGCTTGATATTTTG
GCGGAATACCTGTCGATTAAAGGGTTCAAGTTCCAAAGGCTTGATGGAAG
TACAAAAGCTGAAGTGCGCCATCAAGCTATGGAGCATTTTAATGCACCTG
GTAGTGATGACTTCTGTTTTCTTCTTTCAACACGTGCTGGTGGCTTAGGT
ATCAATCTTGCAACAGCAGATACAGTTATCATATTTGATTCTGATTGGAA
TCCCCAAAATGATTTGCAGGCCATGAGTAGAGCACACAGGATTGGGCAGC
AAGATGTTGTGAACATTTATCGGTTTGTTACAAGTAAAAGTGTTGAGGAG
GATATTTTGGAACGTGCTAAGAAGAAAATGGTTCTTGATCATTTGGTTAT
TCAAAAGCTGAATGCGGAGGGGAAGTTGGAAAAGAAAGAAACAAAGAAAG
GGAGTTCCTTTGACAAAAATGAGCTATCAGCGATCTTGAGGTTCGGTGCA
GAAGAACTATTCAAGGAAGACAAAAACGAAGAAGAAAGTAAAAAGAGGCT
TCTAAGTATGGATATAGATGAAATTCTTGAGAGAGCAGAGAAGGTAGAAG
AAAAGGGTGCCAATGACGAGGAAGGAAATGAGTTACTGAGTGCTTTTAAG
GTTGCTAATTTCTGTACTGCTGAGGATGATGGGAGTTTCTGGAGCCGGTG
GATTAAACCTGAGTCTGTTAACCAGGCAGAAGAAGCTTTAGCTCCTAGAG
CTGCAAGAAATAGCAAGAGTTATGCAGAGGCTAACCTACCTGAAAAACTT
GATAAAAGGAAAAAGAAAGGTGTTGAGACTCAGGAAAGATTTTCTAAGCG
CAGGAAAGCAGATGCTACTTATTTTTCTGTACCGGCAATTGATGGAGCTG
CTGCTCAAGTAAGAGGGTGGTCTCATGGTAACCTGCCAAAGAGAGATGCT
ACACGTTTTTTCCGTGCTGTCAAGAAATTTGGCAATGATAGCCAAATTGA
CTTAATAGCAGCAGAGGTTGGTGGGTCTGTTGAAGCGGCTCCAACTGATG
CACAAATTGAGCTTTTTGATGCTTTGATTGATGGCTGTCGAGAAGCAGTC
GACGGAATGAATCTGGACCCGAAGGGGCCTGTGCTAGACTTTTTTGGTGT
TCCTGTTAAGGCTGATGAACTATTAACCCGTGTTGAAGAACTTCAACTCT
TAGCAAAGCGCGTTAGTCGTTATGAAAAACCAATCTCACAGTTCCAGGCA
TTGATGTACCTCAAACCTGCTACTTGGTCTAAGGGTTGTGGGTGGAACCA
GAAGGATGATGCAAGATTGCTTCTTGGAATCCATTATCATGGGTTTGGCA
ATTGGGAAAAGATAAGGTTGGATGAAAAGCTTGGTCTTACAAAGAAAATT
GCACCAGTAGAACTCCAGCATCATGAGACTTTCTTGCCTCGAGCTCCCCA
GTTAAAGGAGAGGGCCTCCCAACTGCTAGAAATGGAATTTACTGCTGTTA
GTGGGAGCAACTCAAACGCCAAAGCTAGCCGCAAAGCTACCAAGAAGCAA
AAAGAAAATTCTTTAGGCATTTCATTGTCACGCAGCAAGGGCAAGCAAGG
CAAGCAGGGATCGCCAAAATATAATCCTCAGGTAATTAAGGTGAAGACTG
CAAGAACACAGAAGGTCGAACCGTTGGTAAAAGAGGAAGGTGAAATGTCA
GATACTGAAGAAGTCTATGAACAGTTCAAGGAAGTAAAATGGATGGAATG
GTGTGAGGATGTCATGGCTGATGAAACAAAGACGCTGACACGTCTTCAAA
GGTTACAAACTACCAGCGCAGAGCTCCCTAAGGAAAAGGTGCTCTCCAGA
ATAAGAAATTATTTGCAGATCCTTGGACGAAGGGTTGACCAAATTGTTTT
AGAGCACGAGGAGGAACTATATAAGCAAGAAAGGATGAAAACACGATTAT
GGAAGTATATATCAACTTTTTCGAATTTGTCTGGAGAGGGACTGTATCAG
ATTTATTCCAAACTAAAGCAGGAGCAGGTAGGACTAGCACCTTCACATGT
TAACGGTTCTTCACGTGGTTACAGACATGAAGCCTCCAACCAGATTTCTG
GAGTAGTTCAAAGGGGTGTTGATACAGGAAAATTTGAAGCGTGGAAACGA
ATGAAAAGAGCTGAGGCTGATATGAACTCTCTAGTTCAACCCCTGCATGA
AAGATCTTCAAGTAATGCTACATCTGGGATTCTAGGATCAGGACCATCTA
ACAGCCGATACTCTGGTAATGAGAAGTCTTATAATATGCGTCAAACTGGT
CAACCTCCGCGACAAGGCTTTCCGTCGGGTGTAAAGTAGCCTTGATACCT
TATTGAAGGAAATCTGTCTCGGAAAGTGGAATGCAAAAAATTTCCCCTTC
CATTCAATTCAGCTGCTTTGGCCATTAAATTTTTTCTGGGTTCTTTTCCC
TTGCTGGGAATAAACAATTGCAGATCTTGTGGAGAATGTTTTAAAATCAT
CTCAAGCCTGCATCAGAAAGTGGGCCCCAAGCTTTTGAGAGTGGAAAAAA
TGTCAACAAAAATACATATAATCTTGGGACCAAAGTATATTATTGAACTT
TATTTAAACAGCTCCCCAATTTCTTGAAAGTACATAGTGAATAGGCAAAG
AATCAGCTGCTCACCAGTTGGTATGAGGAAGACAACGAATGTAACATCCT
TTGGATAGTGTAAATTACCCAGTTTTGCTTCTTAAATGTCTGAACACAGA
GATTACTAAAGTTGATCGCATATTTTTATGAAAAGAATGATAGAATATTG
AATGTCTTA
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_017401765.1, is a part of gene, LOC108226771. |
| The polypeptide, XM_017401765.1, derives from mRNA, XM_017401765.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |