| 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
ACCAGTCCTTCCATCAACAGTTACTTAGGAAACCCGATGGGACTGAAGCT
ATGTTAGGATTCCAGGGTGGACTTCATGGAGAGTTGGGAGGAAATATTGG
GTCAAATTCTGGCTCTATGCTTGTACAACCTAGAAGTAGGGAGGAAACAC
ATAATAGGAATCATGGATTTGACCTACAAATGCTGAACCCAGCACAGCAC
TCCTACTTGCAGTATCACTCAGCACAACAGAAGTCAGCTCCAGGGATGCA
GTCTCAGCACCCAAGCAAATTAGGAATGGCTGGGCCTTCTGTGCAAGACC
ATGACATGCGGATGGGAAATATACAAATGCAGGATCTGATGTCCATTCAG
GCTTCAGCATTGTTATCAAACAAGAAACCAGAGCATTTTGGTCATGATGA
GAAGCTAAGTGAGGAACAGAGAAGTGATTCCAAGCCTCCTGTTCAAACAT
CACTTGGACAACTGATGCCTGGGAATATGACAAGCCCTATGCAGATACCA
CAATATCAGCAAAACATCCAAAATATGGGTAATCAGTTTGCAATGGCCGC
ACAGATGCAGACAATTCAGGCTTTGGCACTTGATCGTAATATTGATATAT
CTGTTCCTGCAAATGCAAATTTTATGGCACAACTTATGCAAATGCAATCC
AGGATAGCTCCACAGCATAATAAGCCAAATGAAACCAATTTAGGGGAAAA
GTCTTTGTCCGTCACAATGCCAAAGCAGCAGGTAACTTCCCCACAAGTTG
CAAATGAAAGTTCTCCACGTGGTTGCTCATCCAGTGATGTGTTGGGCCAT
TCTTCTTCAGCTAAAGTGATGAAACAGACAGGTCAACCTGGCCTGTTTTG
TGCATCAACTGCTTCCCTGGTTCCCAATGCCAATAACCACCCACTGCAAA
CATTTTCTGCTCATAGCAGTGATAGTCAGTTGTTATCAAGACAGCGTACC
ATGATAGATAATGGAGTTCCTCCCATGCATACTCCACAGTCATATGTTAA
CCAGAACCAACAAGTAGATGCTAAGCCAATCCAGCGATCTTCTCCTCTCT
CAGCAGCTTCACCAAGTGAAGGGGGATTAGTGAATCCTTCATTTCAGGGT
GGACCACTCACTCACTTGCCACAACAATTAGGATTTACAAAACAGCAATT
ACATGTTCTTAAAGCTCAAATACTGGCTTTTAGGCGTTTAAAGAAAGGAG
ATGGAACACTTCCACATGAATTACGACAGGCTATAGCTCCCCCACCTCTT
GACGAACAGATGTTGCAGGCATCACAGCCTGGGCCAACAGATGCATCTGG
TGGGAGAAATGTACGCATGGAAGATCATATTAAACGTGTGGAATGCAGTG
AGAAAGATCTGCCCACTTTTTCATCAAATGACAGGCTTAGTAATGTCAAA
AGAGAAGCAGTTGCTGAAGATGAGAAAAGAAATTCTTCTAGACAAATTGT
ACGAGCTGTACTGAAAGAGTCACCATCAGCTCCTCCTCAAGAAGAAGAGC
ATCAAACAACTATCTCTTCTGCTAAAGTGGAAGAGGAAGATCATGGGATT
CAAGGAGATGGTATTGCAAGAAGTGATGTGCATGTGGATAAGGGTAAGGC
AGGCTCTTCAGTAGCTCCTCTCTCTGAAACAGTGCAAGTGAGAAAACCCT
TCCAAGTAAGCACCACACCTCAACCGAAAGATACTGGACCTACTAGAAAG
TATCATGGACCACTGTTCGATTTTCCCTTCTTTACACGAAAACAAGATTC
ATATGGATCAGCAGCAACAGTGAACAAACATAACAATATGACCTTGGCAT
ATGATTTGAAGGATCTTCTTTCTGAGGAAGGAAAGGAAGTTCTTATCAGG
AAAAGGACAAAAAATATTAAAAAGATTGGTGATCTGCTTGCAGTAAACTT
AGAAAGAAAAAGAATCAGACCTGATCTTGTATTACGATTGCAAATTGAAG
AGAAGAAGCTAAGGCTCTTGGATGTGCAGGCACGCTTGAGGGATGAAGTT
GATCAACAACAGCAGGAAATAATGGCAATGCCAGACAGGCCTTATCGGAA
ATTCGTACGACTCTGTGAGCGTCAACGTGCAGATCTCAGCAGGCAAGTTC
AAGCCTCTCGAAAAGCCATTAGGGAGAAGCAACTGAAATCAATATTCCAG
TGGCGTAAGAAGCTACTTGAGGCTCACTGGGCCATGCGTGATGCTCGAAT
TGCACGTAATAGGGGAGTTGCCAAGTATCATGAGAGAATGTTGAGGGAGT
TCTCAAAACAGAAGGATGATGGTCACAATCAAAGGATGGAGGCTCTGAAG
AATAATGATGTTGAAAGGTATAGGGAGATGTTACTGGAGCAACAAACTAG
TATTCCTGGTGATGGTGCAGAGCGGTATGCTGTCCTCTCGTCATTTTTGT
CTCAGACAGAAGAGTACCTTCACAAACTTGGCAGTAAAATAACTGCGACA
AAGAGTCAGCAGGAGGTTGAGGAGGCAGCAAATGCTGCTGCAGCTGCTGC
AAGGGCTCAGGGTCTATCAGAAGAAGAAGCAAGAGCTGCGGCAGCTTGTG
CTGGAGAGGAAGTAACAATAAGAAATCGTTTTACTGAGATGAATGCACCA
AAAGATAGCTCCTCTGTCAACAAGTATTATAATCTTGCGCATGCGGTGAA
CGAAAAGGTTTTCAGGCAGCCATCAATGCTACGAGCGGGGACTTTACGGG
ATTATCAGATTGTTGGTTTACAGTGGATGCTTTCCTTGTATAACAACAAG
CTCAATGGAATTTTAGCAGATGAGATGGGTCTAGGGAAGACGGTACAGGT
CATGGCATTGATTGCTTATCTGATGGAATTCAAAGGCAACTATGGCCCAC
ATCTCATTATTGTTCCCAATGCTGTGTTAGTCAACTGGAAGAGCGAGCTT
CACAATTGGCTACCATCAGTATCCTGTATTTACTACGTTGGTCAAAAGGA
TCAGCGCGCAAAACTATTTTCACAAGAGGTCTGTGCTATGAAGTTTAATG
TACTTGTGACGACGTATGAGTTTGTCATGTATGATCGTTCAAAACTCTCG
AAGGTTGATTGGAAGTACATTATAATTGATGAAGCGCAACGTATGAAGGA
CAGGGAATCTGTTCTTGCCCGCGATCTTGATAGATATCGCTGCCAAAGGC
GCTTGCTTCTTACAGGAACGCCGTTGCAGAACGATCTTAAAGAGCTCTGG
TCACTTTTGAACCTACTCCTTCCAGAAGTGTTTGATAATCGGAAAGCATT
CCATGATTGGTTCTCAAAACCTTTTCAACGGGAAGGTCCTGCACATAATG
TTGAGGATGACTGGCTCGAGACAGAGAAAAAAGTTATCATTATTCATCGG
CTTCATCAAATTCTTGAACCTTTTATGCTCAGACGTCGTGTTGAAGATGT
GGAAGGTTCACTTCCACCAAAGGTGTCGATTATATTAAGATGTAAAATGT
CAGCTATGCAAGGTGCCATTTATGATTGGATCAAAGCTACTGGTACTTTA
CGTGTTGACCCTGAAGATGAACTGCTGATGAGTCAGAGAAAACCTATGTA
TCAAGCTAAAGTATTTAGAACGTTAGCTAATAGGTGTATGGAACTTCGTA
AAACTTGCAATCACCCTTTACTCAATTACCCATATTTTAATGATCTCTCC
AAGGATTTTCTTGTTAGATCATGTGGGAAATTGTTTGTTCTGGATAGGAT
CCTAGTAAAGCTTCAGAGGACTGGGCACCGAGTATTGCTTTTTAGTACCA
TGACAAAACTCCTAGACATTTTGGAAGAATATTTACAGTGGCGGAGACTT
GTTTACCGTCGAATAGATGGAACGACTAGCTTAGAAGACAGAGAATCAGC
TATTGTGGACTTCAATAGTCCTGATACTGATTGCTTTATTTTCTTGCTAA
GCATTCGGGCTGCTGGGAGAGGCTTAAATCTTCAGACTGCTGACACTGTT
GTCATATATGATCCCGATCCAAACCCTAAGAATGAGGAGCAAGCAGTTGC
CAGAGCTCACCGCATTGGGCAGAAGAGAGAAGTTAAAGTAATCTATTTGG
AAGCAGTAGTTGATAAAATTCCGAGCTATCAGAAAGAAGATGACTACAGG
AAAGGAGGTATGGTTGATTCAGAGGATGACCTTGCTGGAAAGGATCGATA
TATAGGTTCTATCGAGGGTCTCATACGGAATAATATTCAACAGTATAAGA
TTGACATGGCAGATGAAGTCATCAATGCTGGTAGATTTGACCAGAGGACA
ACACATGAAGAGAGGCGATTAACCTTAGAGTCAATGTTACATGATGAAGA
GAGATATCAACAAAGTGTTCATGATGTTCCTTCACTTCAGGAGGTGAATC
GTATGATAGCAAGAAGTGAAGAGGAGGTAGAACTATTTGATCAGATGGAC
GAGGAATTTGATTGGGAAGAAGAGATGACTAGATATGACCAGGTTCCTAA
GTGGCTTCATGCTAGTAGTAAAGAAGTGGATGATACAATTGCTAAAAGAT
CTTCCAAGAAAAAGTCATTACTTGGGGGAAATATAGGAGTGGAATCCAAT
GAAATTACTTCTGAAGTATCTACTCAACTTGAGAAGAAAAGGGAAAGGAA
CAAGGCTAAAAAGTTTCCTGTTTACACAGAATTGGATGATGATTTTTTTG
AAGAGAGTTCCGAAGAGAGGAATGGACACTCTGGTAATGAAGTAGAAGTT
GAGGATCTGGAAGATGATGACTTTGTTGATTCTGGTGACTCACCTCCTGG
CAATAAGGATCGCCTGGAAGATGGTTCACTTACCGCTGAGGTCTCTGAGG
ATCCCCGGCCTTTAGAAAGTCATAAACCTGATCATACACCAGAAAAAGCA
GGTTCATCAGGGTCATCTTCAGGCAATCGAAGATTGATTCAAATGGCTTC
TTCTTTATCTTCTCAGAAATTTGGTTCACTCTCTGCGCTAGATGCAAGGC
CAGGATCTGCTTCCAGTAGGCTGCCTGATGACTTGGAGGAAGGAGAAATT
GCCCTCTCCGGAGATTCTCGGGCAGACCGCCGGCATTCTGGTAGTTGGAT
CCATGATCGTGATGAAGTTGAGGATGAACAAGTTGTGCAACCTAAAATAA
AACGAAAGCGAAGCATCAGAATTAGACCTCGACTTACAACAGGAAAGCCA
GAAGGGAAAACTGGTGAGAAATCATCTCTCCTTCGTGGTGATTCCTCTCA
GATACCACTGCAGATGGGTCATAAATACGATAGAGAACAAAATCTGGTCG
TGGAGCCCAATTCTCTGAAGCTGGAAAAACGTGATTTATCATTAAAGTGT
AGTAGGGCTTTAGATTTACAGATAAAATCAAATTCTGGAAAAGTGCATGC
ATCACAAAAGCCTAGCAAAGTCAATGTCTTGTCTGCGCCTTCGGAAGATG
CCACTGAACACTCCAAAGAAAGTCGGGATAGCAAAGTAAAGCATGGAGCA
GGGAATTCAATTGGCCATAGAATGTCAGATGGAGTTCAGCGCAGGTGCAA
GAATGTGATGAAGAAGTTCCAGAGGACACTAGACAAGGAAGGGCATCAAA
TAGTGCCACTTCTAACAGAACTTTGGAAGAAAAGTGAAGATACTGGTTAC
ATGAGTGGGAACTGTCAGATTCATATACAAAAGATTGACTATCAGCTTGA
AAACTTTGGTTATAACGGAGTTATGGAGTTTGTTTCAGATGTGCAGCTTT
TGTTAAAGGGCGCAGTTCAGTATTATAAGTTTTCCCATGAGGTAAGGACT
GAAGCAAGGAAGGTGCATGATCTATTCTTTGATATATTAAAGAAGATTTT
TCCAGAAACCGATTTCCTAGAAGCCAGGGGTGCTGTCTCTTTCTCGGGCC
ATGGAGCTTCTACTTCGGCTCCACCTTCAAAACAAATTCTTGCTGGTCAA
GGCAAGCGAGCTAAACAAGCTACCATGGTGGATCCTGATCGTAGCCACAA
ACAGAAGCCGCTTTCTCGTGGGCTTAGTAATGAAGACACTCGGATTAGAA
GTCACATGCCTCACAAAGAGACAAGGCTTGGAAATAGCAACAGGGAGCTA
AACCAGCAAGAAGATTCCGGTCTCTTCTCTCATCCAGGAGAACTTGTCAT
ATGTAAAAAGAAGAGGAAGGATAGGGAAAAGTTTTCCGTAAAGTCGGGAA
ACGTTTCTGCTGGCCCAATGTCACCTGCGAGTGTTGGCGGTAATATTAGA
AGCCCAAGCTCAGGCTCACTGTCAAAGGATACCAGATTGATTCAGCAAGG
AAGGGATAATCAGCCTCCTCATCAAGCAAATGTCAGTAGCAGCGGAGGCA
TTGGCTGGGCAAATCCTGTGAAAAGAATGAGAACAGATACCGGAAAACGG
CGCCCCAGCCATTTGTAACTTGTCAAGTTAGTTTCTATAGTGAAAGTAAA
GGGAAAAAATAAATTGCTATCCGTCGGTGAATGTATAAATTTGCTCACAT
CTGCAGTCACATGTCAATATATTTTATACACCTTGTTCATTGTCCAATAT
TCTCGAAATTTGGATGATCTCTGGGATTGTCTAGTAAGATTCTTCTTTGC
GGTAACGATTAAATTTCGTCTATTATCAGATTTGCAGGAAATACTCCTAG
TTTCATA
MQSGGAHGRNTAASASQSPSSSSSAVPDQHRPHQSFHQQLLRKPDGTEAM
LGFQGGLHGELGGNIGSNSGSMLVQPRSREETHNRNHGFDLQMLNPAQHS
YLQYHSAQQKSAPGMQSQHPSKLGMAGPSVQDHDMRMGNIQMQDLMSIQA
SALLSNKKPEHFGHDEKLSEEQRSDSKPPVQTSLGQLMPGNMTSPMQIPQ
YQQNIQNMGNQFAMAAQMQTIQALALDRNIDISVPANANFMAQLMQMQSR
IAPQHNKPNETNLGEKSLSVTMPKQQVTSPQVANESSPRGCSSSDVLGHS
SSAKVMKQTGQPGLFCASTASLVPNANNHPLQTFSAHSSDSQLLSRQRTM
IDNGVPPMHTPQSYVNQNQQVDAKPIQRSSPLSAASPSEGGLVNPSFQGG
PLTHLPQQLGFTKQQLHVLKAQILAFRRLKKGDGTLPHELRQAIAPPPLD
EQMLQASQPGPTDASGGRNVRMEDHIKRVECSEKDLPTFSSNDRLSNVKR
EAVAEDEKRNSSRQIVRAVLKESPSAPPQEEEHQTTISSAKVEEEDHGIQ
GDGIARSDVHVDKGKAGSSVAPLSETVQVRKPFQVSTTPQPKDTGPTRKY
HGPLFDFPFFTRKQDSYGSAATVNKHNNMTLAYDLKDLLSEEGKEVLIRK
RTKNIKKIGDLLAVNLERKRIRPDLVLRLQIEEKKLRLLDVQARLRDEVD
QQQQEIMAMPDRPYRKFVRLCERQRADLSRQVQASRKAIREKQLKSIFQW
RKKLLEAHWAMRDARIARNRGVAKYHERMLREFSKQKDDGHNQRMEALKN
NDVERYREMLLEQQTSIPGDGAERYAVLSSFLSQTEEYLHKLGSKITATK
SQQEVEEAANAAAAAARAQGLSEEEARAAAACAGEEVTIRNRFTEMNAPK
DSSSVNKYYNLAHAVNEKVFRQPSMLRAGTLRDYQIVGLQWMLSLYNNKL
NGILADEMGLGKTVQVMALIAYLMEFKGNYGPHLIIVPNAVLVNWKSELH
NWLPSVSCIYYVGQKDQRAKLFSQEVCAMKFNVLVTTYEFVMYDRSKLSK
VDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDLKELWS
LLNLLLPEVFDNRKAFHDWFSKPFQREGPAHNVEDDWLETEKKVIIIHRL
HQILEPFMLRRRVEDVEGSLPPKVSIILRCKMSAMQGAIYDWIKATGTLR
VDPEDELLMSQRKPMYQAKVFRTLANRCMELRKTCNHPLLNYPYFNDLSK
DFLVRSCGKLFVLDRILVKLQRTGHRVLLFSTMTKLLDILEEYLQWRRLV
YRRIDGTTSLEDRESAIVDFNSPDTDCFIFLLSIRAAGRGLNLQTADTVV
IYDPDPNPKNEEQAVARAHRIGQKREVKVIYLEAVVDKIPSYQKEDDYRK
GGMVDSEDDLAGKDRYIGSIEGLIRNNIQQYKIDMADEVINAGRFDQRTT
HEERRLTLESMLHDEERYQQSVHDVPSLQEVNRMIARSEEEVELFDQMDE
EFDWEEEMTRYDQVPKWLHASSKEVDDTIAKRSSKKKSLLGGNIGVESNE
ITSEVSTQLEKKRERNKAKKFPVYTELDDDFFEESSEERNGHSGNEVEVE
DLEDDDFVDSGDSPPGNKDRLEDGSLTAEVSEDPRPLESHKPDHTPEKAG
SSGSSSGNRRLIQMASSLSSQKFGSLSALDARPGSASSRLPDDLEEGEIA
LSGDSRADRRHSGSWIHDRDEVEDEQVVQPKIKRKRSIRIRPRLTTGKPE
GKTGEKSSLLRGDSSQIPLQMGHKYDREQNLVVEPNSLKLEKRDLSLKCS
RALDLQIKSNSGKVHASQKPSKVNVLSAPSEDATEHSKESRDSKVKHGAG
NSIGHRMSDGVQRRCKNVMKKFQRTLDKEGHQIVPLLTELWKKSEDTGYM
SGNCQIHIQKIDYQLENFGYNGVMEFVSDVQLLLKGAVQYYKFSHEVRTE
ARKVHDLFFDILKKIFPETDFLEARGAVSFSGHGASTSAPPSKQILAGQG
KRAKQATMVDPDRSHKQKPLSRGLSNEDTRIRSHMPHKETRLGNSNRELN
QQEDSGLFSHPGELVICKKKRKDREKFSVKSGNVSAGPMSPASVGGNIRS
PSSGSLSKDTRLIQQGRDNQPPHQANVSSSGGIGWANPVKRMRTDTGKRR
PSHL
| Relationships |
|---|
| The mRNA, XM_017362682.1, is a part of gene, LOC108195709. |
| The polypeptide, XM_017362682.1, derives from mRNA, XM_017362682.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |