| 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
TCACGAGTGAGCGCCTGAACCAGGATGATGACTGGGAAGGTGAAAATATG
GATGAAGATTTTAATGATGTTGATGACCTTGATATTTTGGATGAAGATGA
TGATTTTCCAAGAAAATCCAAAGGCAGGCAACGTGGAAAAGGTGGGCTTG
TTTCAAAACATGCGAGGGTAGGTAAGTCGATTACATCATCTAGTCAGCGA
AAAAGAGGTGGACTAGCATTGGAAGATGATGAATCATCTGCAAATGATTC
TGACAATGAGAGTGATGAGGGTTTTAGCAGCAAAGTGAGGAGAGGAGCTA
GTTTAAGGAAGAAAAATGTTGCCCGTGCCACATCTTATATTTCTAGCCGA
GGGAGGGAAATTCGAACTTCAAGACGGTCTGTTCGGAAAGTCACATATGC
CGAAAGTGAGGATAGTGAAGAAAATGATGAATCTAAGAAAGGGAAAAGTC
AAAAGGAGGAGATTGAAGAGGAAGATGGCAACTCAATTGAAAGGGTACTG
TGGCATCAACCAAGAGGCATGGCCGAGGAAGCATTAGCAAACAACAAATC
AACAGAGCCCGTGTTGTTAAGCCACTTATATGACTATGAACCAGACTGGA
ATGAAATGGAATTTTATATTAAATGGAAAGGCCAATCACATTTGCACTGC
GAATGGAAGTCATTTTTTGAACTACAAAATCTTAGTGGGTTTAAGAAGGT
CATTAATTACACAAAAAAAGTTATGGAAGATGTGAAGTACCGGAAGTCTG
TCTCACGGGAGGAGATTGAGGTCCATGACGTGAGCAAGGAGATGGACCTG
GATCTCATCAAACAAAACAGTCAGGTGGAAAGGGTAATTGCAGAAAGGGT
CAGCAAGGACAGTTTGGATGATGTGGTGCCAGAGTACTTGGTGAAGTGGC
AAGGACTGTCTTATGCTGAAGCAACTTGGGAGAAATACTTGGATATATCA
TTTGCTCAAGAAGCTATCGATGAGTTCAAGGCCCGTGAGGCAGCAGTAGC
AATACAAGGAAAAATGGTAGACGTTCAACGAAGGAAAAGCAAAGAAAGTT
TGAGGAAGCTTGATGAACAGCCTGAATGGTTGAAGGGTGGTAAACTTAGA
GATTATCAGCTTGAGGGATTGAACTTTCTTGTTAACAGTTGGAGAAATGA
TACGAATGTCATATTAGCTGATGAAATGGGTCTGGGCAAAACTGTTCAGT
CAGTTTCTATGCTTGGTTTTTTGCAGAATGCTCAACAAATTCATGGCCCA
TTTCTTGTTGTTGTCCCATTGTCGACACTATCAAATTGGGCAAAAGAATT
TAGAAAATGGCTGCCCCAAATGAATGTCATCATATATGTTGGAGCCCGTG
CAAGCCGAGAGGTTTGTCAACAATATGAATTCTACTCTGATAAGAAGAAT
GGCAGGGGCATAAAGTTTGATGCCCTGTTGACTACATATGAAGTACTACT
AAAAGACAAGGAAGTGCTTTCAAGGCTTAAGTGGAACTATCTCATGGTTG
ACGAAGCACATAGGTTAAAGAACAGTGAAGCTGCATTATATATAACACTT
GCGGAATTCAGCACGAAGAACAAGTTGCTTATAACTGGTACTCCATTGCA
AAACAGCGTCGAGGAACTTTGGGCTCTGCTTCACTTTCTTGATTCTAACA
AGTTCAAGAGCAAGGATGAGTTTGTACAAAATTACAAAAATCTAAGTTCG
TTCAATGAAAATGAGCTCGCTAATCTTCACATGGAGCTGAGGCCTCACAT
TCTCCGGAGGGTTATCAAGGATGTGGAGAAGTCCTTGCCGCCAAAGATTG
AACGAGTTTTAAGGGTTGAGATGTCTCCTCTGCAGAAACAGTACTACAAG
TGGATTCTAGAACGCAATTTCCAAGATTTAAACAAAGGAGTTCGTGGGAA
TCAGGTTTCTCTTCTAAATATCGTGGTTGAGTTAAAAAAATGTTGCAACC
ATCCATTCCTCTTCGAAAGTGCAGATCATGGTTATGGAGGGGAAACTAAT
ATTACTGGAAGTAGTAAACTGGAAAGAGTTATTCTGAGCAGCGGGAAGTT
GGTTATACTCGATAAACTTCTTGACAGACTAAATGAAACAAATCATCGTG
TATTGATATTTTCACAGATGGTTAGGATGCTTGATATTTTGGCGGAATAC
CTGTCGATTAAAGGGTTCAAGTTCCAAAGGCTTGATGGAAGTACAAAAGC
TGAAGTGCGCCATCAAGCTATGGAGCATTTTAATGCACCTGGTAGTGATG
ACTTCTGTTTTCTTCTTTCAACACGTGCTGGTGGCTTAGGTATCAATCTT
GCAACAGCAGATACAGTTATCATATTTGATTCTGATTGGAATCCCCAAAA
TGATTTGCAGGCCATGAGTAGAGCACACAGGATTGGGCAGCAAGATGTTG
TGAACATTTATCGGTTTGTTACAAGTAAAAGTGTTGAGGAGGATATTTTG
GAACGTGCTAAGAAGAAAATGGTTCTTGATCATTTGGTTATTCAAAAGCT
GAATGCGGAGGGGAAGTTGGAAAAGAAAGAAACAAAGAAAGGGAGTTCCT
TTGACAAAAATGAGCTATCAGCGATCTTGAGGTTCGGTGCAGAAGAACTA
TTCAAGGAAGACAAAAACGAAGAAGAAAGTAAAAAGAGGCTTCTAAGTAT
GGATATAGATGAAATTCTTGAGAGAGCAGAGAAGGTAGAAGAAAAGGGTG
CCAATGACGAGGAAGGAAATGAGTTACTGAGTGCTTTTAAGGTTGCTAAT
TTCTGTACTGCTGAGGATGATGGGAGTTTCTGGAGCCGGTGGATTAAACC
TGAGTCTGTTAACCAGGCAGAAGAAGCTTTAGCTCCTAGAGCTGCAAGAA
ATAGCAAGAGTTATGCAGAGGCTAACCTACCTGAAAAACTTGATAAAAGG
AAAAAGAAAGGTGTTGAGACTCAGGAAAGATTTTCTAAGCGCAGGAAAGC
AGATGCTACTTATTTTTCTGTACCGGCAATTGATGGAGCTGCTGCTCAAG
TAAGAGGGTGGTCTCATGGTAACCTGCCAAAGAGAGATGCTACACGTTTT
TTCCGTGCTGTCAAGAAATTTGGCAATGATAGCCAAATTGACTTAATAGC
AGCAGAGGTTGGTGGGTCTGTTGAAGCGGCTCCAACTGATGCACAAATTG
AGCTTTTTGATGCTTTGATTGATGGCTGTCGAGAAGCAGTCGACGGAATG
AATCTGGACCCGAAGGGGCCTGTGCTAGACTTTTTTGGTGTTCCTGTTAA
GGCTGATGAACTATTAACCCGTGTTGAAGAACTTCAACTCTTAGCAAAGC
GCGTTAGTCGTTATGAAAAACCAATCTCACAGTTCCAGGCATTGATGTAC
CTCAAACCTGCTACTTGGTCTAAGGGTTGTGGGTGGAACCAGAAGGATGA
TGCAAGATTGCTTCTTGGAATCCATTATCATGGGTTTGGCAATTGGGAAA
AGATAAGGTTGGATGAAAAGCTTGGTCTTACAAAGAAAATTGCACCAGTA
GAACTCCAGCATCATGAGACTTTCTTGCCTCGAGCTCCCCAGTTAAAGGA
GAGGGCCTCCCAACTGCTAGAAATGGAATTTACTGCTGTTAGTGGGAGCA
ACTCAAACGCCAAAGCTAGCCGCAAAGCTACCAAGAAGCAAAAAGAAAAT
TCTTTAGGCATTTCATTGTCACGCAGCAAGGGCAAGCAAGGCAAGCAGGG
ATCGCCAAAATATAATCCTCAGGTAATTAAGGTGAAGACTGCAAGAACAC
AGAAGGTCGAACCGTTGGTAAAAGAGGAAGGTGAAATGTCAGATACTGAA
GAAGTCTATGAACAGTTCAAGGAAGTAAAATGGATGGAATGGTGTGAGGA
TGTCATGGCTGATGAAACAAAGACGCTGACACGTCTTCAAAGGTTACAAA
CTACCAGCGCAGAGCTCCCTAAGGAAAAGGTGCTCTCCAGAATAAGAAAT
TATTTGCAGATCCTTGGACGAAGGGTTGACCAAATTGTTTTAGAGCACGA
GGAGGAACTATATAAGCAAGAAAGGATGAAAACACGATTATGGAAGTATA
TATCAACTTTTTCGAATTTGTCTGGAGAGGGACTGTATCAGATTTATTCC
AAACTAAAGCAGGAGCAGGTAGGACTAGCACCTTCACATGTTAACGGTTC
TTCACGTGGTTACAGACATGAAGCCTCCAACCAGATTTCTGGAGTAGTTC
AAAGGGGTGTTGATACAGGAAAATTTGAAGCGTGGAAACGAATGAAAAGA
GCTGAGGCTGATATGAACTCTCTAGTTCAACCCCTGCATGAAAGATCTTC
AAGTAATGCTACATCTGGGATTCTAGGATCAGGACCATCTAACAGCCGAT
ACTCTGGTAATGAGAAGTCTTATAATATGCGTCAAACTGGTCAACCTCCG
CGACAAGGCTTTCCGTCGGGTGTAAAGTAGCCTTGATACCTTATTGAAGG
AAATCTGTCTCGGAAAGTGGAATGCAAAAAATTTCCCCTTCCATTCAATT
CAGCTGCTTTGGCCATTAAATTTTTTCTGGGTTCTTTTCCCTTGCTGGGA
ATAAACAATTGCAGATCTTGTGGAGAATGTTTTAAAATCATCTCAAGCCT
GCATCAGAAAGTGGGCCCCAAGCTTTTGAGAGTGGAAAAAATGTCAACAA
AAATACATATAATCTTGGGACCAAAGTATATTATTGAACTTTATTTAAAC
AGCTCCCCAATTTCTTGAAAGTACATAGTGAATAGGCAAAGAATCAGCTG
CTCACCAGTTGGTATGAGGAAGACAACGAATGTAACATCCTTTGGATAGT
GTAAATTACCCAGTTTTGCTTCTTAAATGTCTGAACACAGAGATTACTAA
AGTTGATCGCATATTTTTATGAAAAGAATGATAGAATATTGAATGTCTTA
MAFYRNYSREPVSDGVLDEKGPGPDVEKGDSIVGNEDGNLSDRDFDINLN
AQYRSDGEADDVGKFQEDVGAGGALLDLQPSTGKMASSGRWGSTFWKDCQ
PMRHGSESGQESKSSSEYKNGEGSEDESLGVREDKSESEDPETVRRHQAD
VPVDEMLSDDYYEQDGDEPSNDLMHHRLGNSSAAFISNIKPRPVAANIHQ
SRKAKALNDDVYGDDDADYEDGDDPDDADFDPDFTSERLNQDDDWEGENM
DEDFNDVDDLDILDEDDDFPRKSKGRQRGKGGLVSKHARVGKSITSSSQR
KRGGLALEDDESSANDSDNESDEGFSSKVRRGASLRKKNVARATSYISSR
GREIRTSRRSVRKVTYAESEDSEENDESKKGKSQKEEIEEEDGNSIERVL
WHQPRGMAEEALANNKSTEPVLLSHLYDYEPDWNEMEFYIKWKGQSHLHC
EWKSFFELQNLSGFKKVINYTKKVMEDVKYRKSVSREEIEVHDVSKEMDL
DLIKQNSQVERVIAERVSKDSLDDVVPEYLVKWQGLSYAEATWEKYLDIS
FAQEAIDEFKAREAAVAIQGKMVDVQRRKSKESLRKLDEQPEWLKGGKLR
DYQLEGLNFLVNSWRNDTNVILADEMGLGKTVQSVSMLGFLQNAQQIHGP
FLVVVPLSTLSNWAKEFRKWLPQMNVIIYVGARASREVCQQYEFYSDKKN
GRGIKFDALLTTYEVLLKDKEVLSRLKWNYLMVDEAHRLKNSEAALYITL
AEFSTKNKLLITGTPLQNSVEELWALLHFLDSNKFKSKDEFVQNYKNLSS
FNENELANLHMELRPHILRRVIKDVEKSLPPKIERVLRVEMSPLQKQYYK
WILERNFQDLNKGVRGNQVSLLNIVVELKKCCNHPFLFESADHGYGGETN
ITGSSKLERVILSSGKLVILDKLLDRLNETNHRVLIFSQMVRMLDILAEY
LSIKGFKFQRLDGSTKAEVRHQAMEHFNAPGSDDFCFLLSTRAGGLGINL
ATADTVIIFDSDWNPQNDLQAMSRAHRIGQQDVVNIYRFVTSKSVEEDIL
ERAKKKMVLDHLVIQKLNAEGKLEKKETKKGSSFDKNELSAILRFGAEEL
FKEDKNEEESKKRLLSMDIDEILERAEKVEEKGANDEEGNELLSAFKVAN
FCTAEDDGSFWSRWIKPESVNQAEEALAPRAARNSKSYAEANLPEKLDKR
KKKGVETQERFSKRRKADATYFSVPAIDGAAAQVRGWSHGNLPKRDATRF
FRAVKKFGNDSQIDLIAAEVGGSVEAAPTDAQIELFDALIDGCREAVDGM
NLDPKGPVLDFFGVPVKADELLTRVEELQLLAKRVSRYEKPISQFQALMY
LKPATWSKGCGWNQKDDARLLLGIHYHGFGNWEKIRLDEKLGLTKKIAPV
ELQHHETFLPRAPQLKERASQLLEMEFTAVSGSNSNAKASRKATKKQKEN
SLGISLSRSKGKQGKQGSPKYNPQVIKVKTARTQKVEPLVKEEGEMSDTE
EVYEQFKEVKWMEWCEDVMADETKTLTRLQRLQTTSAELPKEKVLSRIRN
YLQILGRRVDQIVLEHEEELYKQERMKTRLWKYISTFSNLSGEGLYQIYS
KLKQEQVGLAPSHVNGSSRGYRHEASNQISGVVQRGVDTGKFEAWKRMKR
AEADMNSLVQPLHERSSSNATSGILGSGPSNSRYSGNEKSYNMRQTGQPP
RQGFPSGVK
| Relationships |
|---|
| The mRNA, XM_017401781.1, is a part of gene, LOC108226771. |
| The polypeptide, XM_017401781.1, derives from mRNA, XM_017401781.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |