| 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. |
AAAAATCTCTCTGGCTATTTATCAACCAAAAAAATCTCTCTTGCACACAC
AAACAACGAGAGAGAGATGCGGAGAGAGAGCGTGGACAGAAATCGCGCGT
GTCCCTGAAGCTTACGATCCCACCAATTTCGTTACTCTCCGGCGACACCC
AGATCCATGGTCCCACAATTCCCCCCACCCCTTCCCTTAAATTATTCATA
AACCCCTCTCCCTCCTTTTATTCTTTTCAAACTTTTTTCCAGATCGTACG
CACTCTTTTTATTTCACCTCTTCTAACTTCATCGATTAATTAATTATTAT
CAACAATTTATAATTTCTAACGCCGTGATTTCGTGTTAATTGAGCTCGAT
TCTATGCAATCCGGCGGCGCACATGGCCGGAACACGGCGGCGTCTGCCTC
CCAATCGCCGTCGTCTTCGTCGTCCGCCGTTCCGGATCAACACAGACCCC
ACCAGTTACTTAGGAAACCCGATGGGACTGAAGCTATGTTAGGATTCCAG
GGTGGACTTCATGGAGAGTTGGGAGGAAATATTGGGTCAAATTCTGGCTC
TATGCTTGTACAACCTAGAAGTAGGGAGGAAACACATAATAGGAATCATG
GATTTGACCTACAAATGCTGAACCCAGCACAGCACTCCTACTTGCAGTAT
CACTCAGCACAACAGAAGTCAGCTCCAGGGATGCAGTCTCAGCACCCAAG
CAAATTAGGAATGGCTGGGCCTTCTGTGCAAGACCATGACATGCGGATGG
GAAATATACAAATGCAGGATCTGATGTCCATTCAGGCTTCAGCATTGTTA
TCAAACAAGAAACCAGAGCATTTTGGTCATGATGAGAAGCTAAGTGAGGA
ACAGAGAAGTGATTCCAAGCCTCCTGTTCAAACATCACTTGGACAACTGA
TGCCTGGGAATATGACAAGCCCTATGCAGATACCACAATATCAGCAAAAC
ATCCAAAATATGGGTAATCAGTTTGCAATGGCCGCACAGATGCAGACAAT
TCAGGCTTTGGCACTTGATCGTAATATTGATATATCTGTTCCTGCAAATG
CAAATTTTATGGCACAACTTATGCAAATGCAATCCAGGATAGCTCCACAG
CATAATAAGCCAAATGAAACCAATTTAGGGGAAAAGTCTTTGTCCGTCAC
AATGCCAAAGCAGCAGGTAACTTCCCCACAAGTTGCAAATGAAAGTTCTC
CACGTGGTTGCTCATCCAGTGATGTGTTGGGCCATTCTTCTTCAGCTAAA
GTGATGAAACAGACAGGTCAACCTGGCCTGTTTTGTGCATCAACTGCTTC
CCTGGTTCCCAATGCCAATAACCACCCACTGCAAACATTTTCTGCTCATA
GCAGTGATAGTCAGTTGTTATCAAGACAGCGTACCATGATAGATAATGGA
GTTCCTCCCATGCATACTCCACAGTCATATGTTAACCAGAACCAACAAGT
AGATGCTAAGCCAATCCAGCGATCTTCTCCTCTCTCAGCAGCTTCACCAA
GTGAAGGGGGATTAGTGAATCCTTCATTTCAGGGTGGACCACTCACTCAC
TTGCCACAACAATTAGGATTTACAAAACAGCAATTACATGTTCTTAAAGC
TCAAATACTGGCTTTTAGGCGTTTAAAGAAAGGAGATGGAACACTTCCAC
ATGAATTACGACAGGCTATAGCTCCCCCACCTCTTGACGAACAGATGTTG
CAGGCATCACAGCCTGGGCCAACAGATGCATCTGGTGGGAGAAATGTACG
CATGGAAGATCATATTAAACGTGTGGAATGCAGTGAGAAAGATCTGCCCA
CTTTTTCATCAAATGACAGGCTTAGTAATGTCAAAAGAGAAGCAGTTGCT
GAAGATGAGAAAAGAAATTCTTCTAGACAAATTGTACGAGCTGTACTGAA
AGAGTCACCATCAGCTCCTCCTCAAGAAGAAGAGCATCAAACAACTATCT
CTTCTGCTAAAGTGGAAGAGGAAGATCATGGGATTCAAGGAGATGGTATT
GCAAGAAGTGATGTGCATGTGGATAAGGGTAAGGCAGGCTCTTCAGTAGC
TCCTCTCTCTGAAACAGTGCAAGTGAGAAAACCCTTCCAAGTAAGCACCA
CACCTCAACCGAAAGATACTGGACCTACTAGAAAGTATCATGGACCACTG
TTCGATTTTCCCTTCTTTACACGAAAACAAGATTCATATGGATCAGCAGC
AACAGTGAACAAACATAACAATATGACCTTGGCATATGATTTGAAGGATC
TTCTTTCTGAGGAAGGAAAGGAAGTTCTTATCAGGAAAAGGACAAAAAAT
ATTAAAAAGATTGGTGATCTGCTTGCAGTAAACTTAGAAAGAAAAAGAAT
CAGACCTGATCTTGTATTACGATTGCAAATTGAAGAGAAGAAGCTAAGGC
TCTTGGATGTGCAGGCACGCTTGAGGGATGAAGTTGATCAACAACAGCAG
GAAATAATGGCAATGCCAGACAGGCCTTATCGGAAATTCGTACGACTCTG
TGAGCGTCAACGTGCAGATCTCAGCAGGCAAGTTCAAGCCTCTCGAAAAG
CCATTAGGGAGAAGCAACTGAAATCAATATTCCAGTGGCGTAAGAAGCTA
CTTGAGGCTCACTGGGCCATGCGTGATGCTCGAATTGCACGTAATAGGGG
AGTTGCCAAGTATCATGAGAGAATGTTGAGGGAGTTCTCAAAACAGAAGG
ATGATGGTCACAATCAAAGGATGGAGGCTCTGAAGAATAATGATGTTGAA
AGGTATAGGGAGATGTTACTGGAGCAACAAACTAGTATTCCTGGTGATGG
TGCAGAGCGGTATGCTGTCCTCTCGTCATTTTTGTCTCAGACAGAAGAGT
ACCTTCACAAACTTGGCAGTAAAATAACTGCGACAAAGAGTCAGCAGGAG
GTTGAGGAGGCAGCAAATGCTGCTGCAGCTGCTGCAAGGGCTCAGGGTCT
ATCAGAAGAAGAAGCAAGAGCTGCGGCAGCTTGTGCTGGAGAGGAAGTAA
CAATAAGAAATCGTTTTACTGAGATGAATGCACCAAAAGATAGCTCCTCT
GTCAACAAGTATTATAATCTTGCGCATGCGGTGAACGAAAAGGTTTTCAG
GCAGCCATCAATGCTACGAGCGGGGACTTTACGGGATTATCAGATTGTTG
GTTTACAGTGGATGCTTTCCTTGTATAACAACAAGCTCAATGGAATTTTA
GCAGATGAGATGGGTCTAGGGAAGACGGTACAGGTCATGGCATTGATTGC
TTATCTGATGGAATTCAAAGGCAACTATGGCCCACATCTCATTATTGTTC
CCAATGCTGTGTTAGTCAACTGGAAGAGCGAGCTTCACAATTGGCTACCA
TCAGTATCCTGTATTTACTACGTTGGTCAAAAGGATCAGCGCGCAAAACT
ATTTTCACAAGAGGTCTGTGCTATGAAGTTTAATGTACTTGTGACGACGT
ATGAGTTTGTCATGTATGATCGTTCAAAACTCTCGAAGGTTGATTGGAAG
TACATTATAATTGATGAAGCGCAACGTATGAAGGACAGGGAATCTGTTCT
TGCCCGCGATCTTGATAGATATCGCTGCCAAAGGCGCTTGCTTCTTACAG
GAACGCCGTTGCAGAACGATCTTAAAGAGCTCTGGTCACTTTTGAACCTA
CTCCTTCCAGAAGTGTTTGATAATCGGAAAGCATTCCATGATTGGTTCTC
AAAACCTTTTCAACGGGAAGGTCCTGCACATAATGTTGAGGATGACTGGC
TCGAGACAGAGAAAAAAGTTATCATTATTCATCGGCTTCATCAAATTCTT
GAACCTTTTATGCTCAGACGTCGTGTTGAAGATGTGGAAGGTTCACTTCC
ACCAAAGGTGTCGATTATATTAAGATGTAAAATGTCAGCTATGCAAGGTG
CCATTTATGATTGGATCAAAGCTACTGGTACTTTACGTGTTGACCCTGAA
GATGAACTGCTGATGAGTCAGAGAAAACCTATGTATCAAGCTAAAGTATT
TAGAACGTTAGCTAATAGGTGTATGGAACTTCGTAAAACTTGCAATCACC
CTTTACTCAATTACCCATATTTTAATGATCTCTCCAAGGATTTTCTTGTT
AGATCATGTGGGAAATTGTTTGTTCTGGATAGGATCCTAGTAAAGCTTCA
GAGGACTGGGCACCGAGTATTGCTTTTTAGTACCATGACAAAACTCCTAG
ACATTTTGGAAGAATATTTACAGTGGCGGAGACTTGTTTACCGTCGAATA
GATGGAACGACTAGCTTAGAAGACAGAGAATCAGCTATTGTGGACTTCAA
TAGTCCTGATACTGATTGCTTTATTTTCTTGCTAAGCATTCGGGCTGCTG
GGAGAGGCTTAAATCTTCAGACTGCTGACACTGTTGTCATATATGATCCC
GATCCAAACCCTAAGAATGAGGAGCAAGCAGTTGCCAGAGCTCACCGCAT
TGGGCAGAAGAGAGAAGTTAAAGTAATCTATTTGGAAGCAGTAGTTGATA
AAATTCCGAGCTATCAGAAAGAAGATGACTACAGGAAAGGAGGTATGGTT
GATTCAGAGGATGACCTTGCTGGAAAGGATCGATATATAGGTTCTATCGA
GGGTCTCATACGGAATAATATTCAACAGTATAAGATTGACATGGCAGATG
AAGTCATCAATGCTGGTAGATTTGACCAGAGGACAACACATGAAGAGAGG
CGATTAACCTTAGAGTCAATGTTACATGATGAAGAGAGATATCAACAAAG
TGTTCATGATGTTCCTTCACTTCAGGAGGTGAATCGTATGATAGCAAGAA
GTGAAGAGGAGGTAGAACTATTTGATCAGATGGACGAGGAATTTGATTGG
GAAGAAGAGATGACTAGATATGACCAGGTTCCTAAGTGGCTTCATGCTAG
TAGTAAAGAAGTGGATGATACAATTGCTAAAAGATCTTCCAAGAAAAAGT
CATTACTTGGGGGAAATATAGGAGTGGAATCCAATGAAATTACTTCTGAA
GTATCTACTCAACTTGAGAAGAAAAGGGAAAGGAACAAGGCTAAAAAGTT
TCCTGTTTACACAGAATTGGATGATGATTTTTTTGAAGAGAGTTCCGAAG
AGAGGAATGGACACTCTGGTAATGAAGTAGAAGTTGAGGATCTGGAAGAT
GATGACTTTGTTGATTCTGGTGACTCACCTCCTGGCAATAAGGATCGCCT
GGAAGATGGTTCACTTACCGCTGAGGTCTCTGAGGATCCCCGGCCTTTAG
AAAGTCATAAACCTGATCATACACCAGAAAAAGCAGGTTCATCAGGGTCA
TCTTCAGGCAATCGAAGATTGATTCAAATGGCTTCTTCTTTATCTTCTCA
GAAATTTGGTTCACTCTCTGCGCTAGATGCAAGGCCAGGATCTGCTTCCA
GTAGGCTGCCTGATGACTTGGAGGAAGGAGAAATTGCCCTCTCCGGAGAT
TCTCGGGCAGACCGCCGGCATTCTGGTAGTTGGATCCATGATCGTGATGA
AGTTGAGGATGAACAAGTTGTGCAACCTAAAATAAAACGAAAGCGAAGCA
TCAGAATTAGACCTCGACTTACAACAGGAAAGCCAGAAGGGAAAACTGGT
GAGAAATCATCTCTCCTTCGTGGTGATTCCTCTCAGATACCACTGCAGAT
GGGTCATAAATACGATAGAGAACAAAATCTGGTCGTGGAGCCCAATTCTC
TGAAGCTGGAAAAACGTGATTTATCATTAAAGTGTAGTAGGGCTTTAGAT
TTACAGATAAAATCAAATTCTGGAAAAGTGCATGCATCACAAAAGCCTAG
CAAAGTCAATGTCTTGTCTGCGCCTTCGGAAGATGCCACTGAACACTCCA
AAGAAAGTCGGGATAGCAAAGTAAAGCATGGAGCAGGGAATTCAATTGGC
CATAGAATGTCAGATGGAGTTCAGCGCAGGTGCAAGAATGTGATGAAGAA
GTTCCAGAGGACACTAGACAAGGAAGGGCATCAAATAGTGCCACTTCTAA
CAGAACTTTGGAAGAAAAGTGAAGATACTGGTTACATGAGTGGGAACTGT
CAGATTCATATACAAAAGATTGACTATCAGCTTGAAAACTTTGGTTATAA
CGGAGTTATGGAGTTTGTTTCAGATGTGCAGCTTTTGTTAAAGGGCGCAG
TTCAGTATTATAAGTTTTCCCATGAGGTAAGGACTGAAGCAAGGAAGGTG
CATGATCTATTCTTTGATATATTAAAGAAGATTTTTCCAGAAACCGATTT
CCTAGAAGCCAGGGGTGCTGTCTCTTTCTCGGGCCATGGAGCTTCTACTT
CGGCTCCACCTTCAAAACAAATTCTTGCTGGTCAAGGCAAGCGAGCTAAA
CAAGCTACCATGGTGGATCCTGATCGTAGCCACAAACAGAAGCCGCTTTC
TCGTGGGCTTAGTAATGAAGACACTCGGATTAGAAGTCACATGCCTCACA
AAGAGACAAGGCTTGGAAATAGCAACAGGGAGCTAAACCAGCAAGAAGAT
TCCGGTCTCTTCTCTCATCCAGGAGAACTTGTCATATGTAAAAAGAAGAG
GAAGGATAGGGAAAAGTTTTCCGTAAAGTCGGGAAACGTTTCTGCTGGCC
CAATGTCACCTGCGAGTGTTGGCGGTAATATTAGAAGCCCAAGCTCAGGC
TCACTGTCAAAGGATACCAGATTGATTCAGCAAGGAAGGGATAATCAGCC
TCCTCATCAAGCAAATGTCAGTAGCAGCGGAGGCATTGGCTGGGCAAATC
CTGTGAAAAGAATGAGAACAGATACCGGAAAACGGCGCCCCAGCCATTTG
TAACTTGTCAAGTTAGTTTCTATAGTGAAAGTAAAGGGAAAAAATAAATT
GCTATCCGTCGGTGAATGTATAAATTTGCTCACATCTGCAGTCACATGTC
AATATATTTTATACACCTTGTTCATTGTCCAATATTCTCGAAATTTGGAT
GATCTCTGGGATTGTCTAGTAAGATTCTTCTTTGCGGTAACGATTAAATT
TCGTCTATTATCAGATTTGCAGGAAATACTCCTAGTTTCATA
MQSGGAHGRNTAASASQSPSSSSSAVPDQHRPHQLLRKPDGTEAMLGFQG
GLHGELGGNIGSNSGSMLVQPRSREETHNRNHGFDLQMLNPAQHSYLQYH
SAQQKSAPGMQSQHPSKLGMAGPSVQDHDMRMGNIQMQDLMSIQASALLS
NKKPEHFGHDEKLSEEQRSDSKPPVQTSLGQLMPGNMTSPMQIPQYQQNI
QNMGNQFAMAAQMQTIQALALDRNIDISVPANANFMAQLMQMQSRIAPQH
NKPNETNLGEKSLSVTMPKQQVTSPQVANESSPRGCSSSDVLGHSSSAKV
MKQTGQPGLFCASTASLVPNANNHPLQTFSAHSSDSQLLSRQRTMIDNGV
PPMHTPQSYVNQNQQVDAKPIQRSSPLSAASPSEGGLVNPSFQGGPLTHL
PQQLGFTKQQLHVLKAQILAFRRLKKGDGTLPHELRQAIAPPPLDEQMLQ
ASQPGPTDASGGRNVRMEDHIKRVECSEKDLPTFSSNDRLSNVKREAVAE
DEKRNSSRQIVRAVLKESPSAPPQEEEHQTTISSAKVEEEDHGIQGDGIA
RSDVHVDKGKAGSSVAPLSETVQVRKPFQVSTTPQPKDTGPTRKYHGPLF
DFPFFTRKQDSYGSAATVNKHNNMTLAYDLKDLLSEEGKEVLIRKRTKNI
KKIGDLLAVNLERKRIRPDLVLRLQIEEKKLRLLDVQARLRDEVDQQQQE
IMAMPDRPYRKFVRLCERQRADLSRQVQASRKAIREKQLKSIFQWRKKLL
EAHWAMRDARIARNRGVAKYHERMLREFSKQKDDGHNQRMEALKNNDVER
YREMLLEQQTSIPGDGAERYAVLSSFLSQTEEYLHKLGSKITATKSQQEV
EEAANAAAAAARAQGLSEEEARAAAACAGEEVTIRNRFTEMNAPKDSSSV
NKYYNLAHAVNEKVFRQPSMLRAGTLRDYQIVGLQWMLSLYNNKLNGILA
DEMGLGKTVQVMALIAYLMEFKGNYGPHLIIVPNAVLVNWKSELHNWLPS
VSCIYYVGQKDQRAKLFSQEVCAMKFNVLVTTYEFVMYDRSKLSKVDWKY
IIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDLKELWSLLNLL
LPEVFDNRKAFHDWFSKPFQREGPAHNVEDDWLETEKKVIIIHRLHQILE
PFMLRRRVEDVEGSLPPKVSIILRCKMSAMQGAIYDWIKATGTLRVDPED
ELLMSQRKPMYQAKVFRTLANRCMELRKTCNHPLLNYPYFNDLSKDFLVR
SCGKLFVLDRILVKLQRTGHRVLLFSTMTKLLDILEEYLQWRRLVYRRID
GTTSLEDRESAIVDFNSPDTDCFIFLLSIRAAGRGLNLQTADTVVIYDPD
PNPKNEEQAVARAHRIGQKREVKVIYLEAVVDKIPSYQKEDDYRKGGMVD
SEDDLAGKDRYIGSIEGLIRNNIQQYKIDMADEVINAGRFDQRTTHEERR
LTLESMLHDEERYQQSVHDVPSLQEVNRMIARSEEEVELFDQMDEEFDWE
EEMTRYDQVPKWLHASSKEVDDTIAKRSSKKKSLLGGNIGVESNEITSEV
STQLEKKRERNKAKKFPVYTELDDDFFEESSEERNGHSGNEVEVEDLEDD
DFVDSGDSPPGNKDRLEDGSLTAEVSEDPRPLESHKPDHTPEKAGSSGSS
SGNRRLIQMASSLSSQKFGSLSALDARPGSASSRLPDDLEEGEIALSGDS
RADRRHSGSWIHDRDEVEDEQVVQPKIKRKRSIRIRPRLTTGKPEGKTGE
KSSLLRGDSSQIPLQMGHKYDREQNLVVEPNSLKLEKRDLSLKCSRALDL
QIKSNSGKVHASQKPSKVNVLSAPSEDATEHSKESRDSKVKHGAGNSIGH
RMSDGVQRRCKNVMKKFQRTLDKEGHQIVPLLTELWKKSEDTGYMSGNCQ
IHIQKIDYQLENFGYNGVMEFVSDVQLLLKGAVQYYKFSHEVRTEARKVH
DLFFDILKKIFPETDFLEARGAVSFSGHGASTSAPPSKQILAGQGKRAKQ
ATMVDPDRSHKQKPLSRGLSNEDTRIRSHMPHKETRLGNSNRELNQQEDS
GLFSHPGELVICKKKRKDREKFSVKSGNVSAGPMSPASVGGNIRSPSSGS
LSKDTRLIQQGRDNQPPHQANVSSSGGIGWANPVKRMRTDTGKRRPSHL
| Relationships |
|---|
| The mRNA, XM_017362683.1, is a part of gene, LOC108195709. |
| The polypeptide, XM_017362683.1, derives from mRNA, XM_017362683.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |