| 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. |
AATGAAAAACCGGAGTAATGTTAAAAAAAAAGCAGAAGCAAAGCAGGAGA
AGAAAAGCGTGGGAATTGTCTGAAATCTCCTCCCCACCTGTATCATATGA
CGGGGAAACAACCTGTCAATTGGTGAATTGATTTTACAATACACTGTTTG
GTTATGATTGGGAGTTGAAGCTTAAGCCCTAGACTAGATTTGTTTAAAAT
GAAAGCGGGGAGTGCCGCTAAGCTCATCGTTGATGCTCTTCTCCAACGCT
TCCTTCCACTTGCTCGTCGTCGTATCGAAACTGCTCAAGCTCAGGATGGA
CAGTATCTTCGGCCATCTGATCCAGCGTACGAGCAGGTATTGGATTCCTT
GGCTATGGTGGCACGACATACTCCCGTGCCTCTACTTGAAGCTCTTTTAA
GATGGAGAGAAAGTGAATCACCGAAGGGGGCAAATGATGCATCTACATTC
CAGCGGAAGCTTGCAGTGGAGTGCATTTTTTGCTCAGCATGTATCCGCTT
TGTAGAGTGTTGCCCTCAAGAGGGGCTTACAGAGAAGCTATGGAATGGAC
TAGAAAATTTTGTCTTCGACTGGCTGATCAATGCTGATCGGGTTGTCAGT
CAAATTGATTATCCTTCCCTTGTAGATTTACGCAGTCTTCTTCTCGATCT
AGTAGCTCAACTTTTAGGGGCGCTGTCTCGGATCAGATTTAGTTCTGTTA
CTGAGCGTTTTTTCATGGAACTCAATACTCGTCGAATTGATACAAGTGGT
GCTAGGGGGGAGACTCTTAGCATCATTAATGGGATGCGTTACTTGAAGCT
TGGGGTTAAGACTGAGGGTGGATTGAATGCATCAGCGTCATTTGTGGCTA
AAGCGAACCCTCTTAATCGTGCTCCTCATAAGCGAAAGAGTGAACTACAC
CATGCACTTTGCAATATGCTTTCAAATATTCTAGCACCACTTGCAGATGG
TGGAAAGGGCCAATGGCCTCCTTCGGGTGTTGAACCAGCACTTACCCTAT
GGTATGAAGCCATTGCGAGAATAAGAGTGCAACTTATGCATTGGATGGAC
AAGCAAAGCAAACATATTGCTGTTGGTTACCCGCTTGTGACTCTTCTTCT
TTGTCTTGGCGACCCAAAAGTTTTCCTCAATAACTTTGGCTCTCACATGG
AGCAGCTGTACAAGCACCTTCGTGACAAGAACCAGCGGTTCATGGCGTTG
GATTGTCTTCATCGTGTTCTTAGGTTTTATCTGAGTGTTCACGGGGACTC
ACAGCCTCCAAATCGAGTATGGGACTACCTGGACAGTGTGACTGCGCAGC
TCCTAACAATTCTGAGGAAAGGAATGCTTACCCAGGATGTCCAACATGAC
AAACTTGTAGAATTCTGTGTGACTATAGCAGAACATAACCTTGATTTTGC
CATGAATCATACAATACTGGAATTACTCAAGCAAGATAGTCCAAGTGAAG
CGAAGGTTATTGGTCTCCGTTCTCTGCTTTCAATTGCTATGTCTCCTACC
AGCCAGCACGTTGGTCTGGAAATTCTTCATGTTCATAACATCGGTCACTA
CATTCCAAAGGTGAAGGCTGCTATTGAGGCTATTTTAAGGTCATGTCATC
GAACCTACAGTCAGGCTCTTCTTACCTCATCAAGGACAACCATAGATGCT
GTTACAAAAGAGAAATCTCAGGGTTATCTTTTTCGATCAGTTTTAAAGTG
CATTCCGTATCTGATAGAAGAAGTTGGGCGAAGTGATAAGATCTCTGAAA
TAATACCTCAGCATGGTATTAGTATTGATCCTGGTGTCCGTGAAGAAGCA
GTTCAAGTACTTAATCGTATTGTGAGATATCTTCCTCATCGCCGCTTTGC
AGTTATGAAAGGAATGGCGAACTTCATTTTACGCCTTCCTGATGAGTTCC
CTCTTCTCATTCAAACATCATTGGGGCGCTTACTGGAACTTATGCGTTTC
TGGAGAGCTTGTCAAGCTGATGATAAATTACACCATGATGATAAGATTAC
GAAGCGTGTGCAGAGGAATGAAGGGTTCAAGAAATCTTCTTTCTATCAAT
CTGGAGAAGCAATTGAATTTCGGTCCTCGGAGATAGATGCAGTTGGCCTT
ATTTTTCTTGGTTCTGTAGATAGCCAGATCAGACATACAGCATTGGAGTT
ACTCCGCTGTGTTCGGGCTCTGCGCAATGATATTCGGGAGATTGCACTGC
TTGATCGCCCAGATCATCTGAAAAATGAAGCTGAGCCAATTTTTATAATT
GATGTTTTGGAAGAGAATGGGGATGACATAGTTCAAAGCTGCTATTGGGA
TTCTGGCCGTCCATTTGATTTGAGACGTGAATCTGATTCTGTACCTCAAG
ATGTGACCCTTCAGTCTATACTCTTTGAAAGCCCTGATAAAAATCGATGG
GCACGTTGTCTTAGTGAGCTTGTCAAGTATGCCGCTGAGCTGTGCCCAAG
CTCTGTTCAGGAGGCAAAGCTAGAGGTAATCCAGCGTCTTGCTCATATCA
CACCTGTTGAGTTGGGTGGAAAAGCTCATCAGACACAGGATGCAGACAAC
AAACTAGACCAATGGCTTATGTATGCAATATTTGCATGTTCTTGTCCAAC
TGATATTAGGGAAGGTGGCGGATTAGCAGCTACTAGAGAACTTTTTCATC
TCATCTTTCCTTCACTAAAATCTGGTTCAGAAACACACGTACATGCTGCC
ACTATGGCTCTTGGCCATTCACATTTAGAAGTGTGTGAAATAATGTTCAG
CGAGCTTGCATCTTTCATCGATGAAGTCTCTTTAGAAACTGAGGGAAAAG
CAAAGTGGAAGAATCAGAAGTCCCGCCGTGAAGAACTTCGAATCCACATC
GCAAATATATACCGTGTTGTTGCAGAAAAAATTTGGCCTGGCATGCTAGG
CCGAAAGCCAGTTTTCCGCCTCCATTATCTAAAGTTTATTGAAGAAACAA
CTAGACAGATCTTAACAGCACCAAACGAGAACTTCCAGGAAACCCAACCC
CTTCGTTATGCTCTTGCTTCTGTTTTAAGATCACTAGCCCCCGAATTTGT
GGAGTCAAAATCAGAAAAATTTGATCTTAGAACAAGAAAGCGATTGTTTG
ATCTTCTTCTCTCCTGGTGTGATGACACAGGTAATACATGGAGTCAGGAC
GGTGTCAGTGATTACCGGCGTGAGGTTGAACGATATAAATCTACACAGCA
TGTTCGTTCAAAAGATTCTGTTGATAAACTTTCATTTGATAAAGAAATCA
GTGAACAAGTCGAGGCTATTCAGTGGGCTTCCATGAATGCCATGGCTTCC
CTGTTATATGGCCCTTGCTTTGATGACAATGCCAGAAAAATGAGTGGCAG
GGTAATATCTTGGATTAATAGTCTTTTTATTGAGCCTGCCCCTCGGGCTC
CATTTGGTTATTCACCCGCCGATCCAAGAACACCATCATATTCCAAATAT
ACAGGAGAAGGTGGACGAGGAGCAACTGGACGTGATCGGCATAGAGGTGG
GCATTTGCGTGTGGCCCTTGCAAAAACGGCTTTAAAGAATCTTCTACTAA
CAAATTTGGACCTGTTTCCTGCTTGCATTGATCAGTGCTACTACTCTGAT
GCTGCTATAGCTGATGGATACTTCAGTGTCTTGGCCGAAGTCTACATGCG
TCAAGAGATACCGAAGTGTGAAATTCAGAGGCTGTTGAGCCTGATCCTCT
ACAAAGTGGTGGATCCATCTAGACAAATTCGTGATGATGCCCTTCAGATG
CTTGAAACGCTTTCCGACCGGGAATGGGCTGGGGAGGGCATCGAGGGTTC
GGGAAGTTATCGAGCTGCTGTTGTTGGTAACCTTCCTGACTCGTACCAAC
AGTTCCAATACAAACTTTCATGCAAACTCGCAAAAGATCATCCTGATCTG
AGCCAGCTTCTTTGTGAGGAGATCATGCAAAGACAACTTGATGCTGTTGA
TATAATTGCACAGCATCAAGTTTTAACATGCATGGCTCCCTGGATCGAAA
ATCTCAATTTTTGGAAACTCAAGGACTCCGGATGGAGTGAAAGGTTATTG
AAAAGCCTTTACTATGTGACATGGCGACATGGTGACCAGTTTCCTGATGA
AATTGAGAAGCTTTGGAGCACTATTGCTAGCAAGCCCAGGAACATTAGTC
CAGTTCTCGATTTTTTAATCACCAAAGGAATTGAAGATTGTGATTCAAAT
GCATCTGCAGAAATTAGTGGGGCATTTGCAACATACTTTTCTGTTGCAAA
ACGAGTAAGCTTATATCTAGCTCGAATATGTCCACAACGCACCATTGATC
ACTTGGTTTACCAGTTAGCTCAGCGAATGTTAGAGGACAGTGTCGAACCA
CTCAGACCCAGCGTAAGCAAGGGTGATCCAGGTGCAAATTTTGTATTAGA
GTTCTCTCATGGGCCTGCAGTGACCCAGATTGCATCTGTTGTGGACATCC
AGCCTCACATGTCACCCTTGCTTGTTCGAGGATCTCTAGATGGTCCCCTT
AGGAATACCAGTGGCAGCTTAAGCTGGAGAACAGCAGCCGTTGGAGGTCG
AAGTGCTTCAGGTCCATTGAGTCCAATGCCTCCGGAGTTGAACATTGTTC
CTGTAACTGCAGGCCGATCCGGCCAACTACTTCCTTCCTTGGTAAACATG
TCAGGACCCTTGATGGGGGTCCGAAGTTCAACAGGGAGCTTGCGCAGCCG
CCATGTGTCTCGAGACAGTGGAGACTACATTATAGACACTCCAAATTCCG
GAGAAGATGGTTTACATACTGGCCTTGGGCTGCATGGTATCAGTGCTAAA
GAACTTCAATCAGCCTTACAAGGGCATCAACAGCATTCACTGACTCATGC
AGATATAGCATTAATTCTACTTGCCGAAATTGCATATGAAAATGATGAAG
ATTTCCGCGAGCACCTACCCTTGCTTTTTCATGTCACATTTGTCTCAATG
GACAGCTCTGAAGATATTGTACTGGAGCACTGCCAGCACCTACTTGTTAA
TTTGCTGTATTCTCTGGCTGGACGTCACCTGGAGTTGTATGAGGTTGAGA
ATATCGATGGGGAGAACAAGCAACAGGTTGTTAGTCTGATCAAGTATGTG
CAGTCAAAGCGAGGGAGCATGATGTGGGAGAATGAGGATCCCACAGTTGT
GAGGACTGAACTTCCAAGTGCAGCCCTTTTGTCAGCTCTTGTACAGAGTA
TGGTAGATGCTATCTTCTTCCAAGGAGACCTTCGAGAGACTTGGGGACAA
GAGGCACTCAAGTGGGCTATGGAGTGCACATCAAGACACCTTGCATGCCG
CTCACACCAAATTTACCGTGCATTGAGGCCTCATGTCACAAGCGATGCAT
CAGTATCGCTCCTCCGCTGTATCCACAGATGTTTGGGAAATCCTGTGCCA
GCAGTTTTAGGATTCATCATGGAAATTTTGTTGACTTTACAAGTAATGGT
AGAGAATATGGAGCCTGAAAAAGTGATCCTCTACCCACAGCTATTTTGGG
GATGTGTAGCTATGATGCATACAGACTTTGTTCACGTTTACTGCCAGGCG
CTGGAGTTGTTCTCTCGTGTAATTGATCGTCTATCATTTCGTGACCGAAC
AACAGAAAATGTACTCTTATCTAGCATGCCGCGTGATGAGCTCGATACCA
GTGTTTCTGACACCAGTGATTTTCAAAGGGATTTAAGAAATACTCGTGAA
TCAACATCATCAAGTGGGAAGGTTCCAGCCTTTGAAGGAGTGCAGCCACT
TGTTCTTAAGGGACTAATGTCAACAGCAAGTCATGGTGTCTCTATTGAGG
TCCTTTCACGGATCACAGTTCACTCTTGCGATTCAATATTTGGGGACGCA
GAAACACGACTCTTAATGCACATCACAGGTTTGCTTCCCTGGCTGTGCTT
GCAGCTAAACCAGGAAGCAGTGGTGGGCATTGCTTCACCACTCCTACAAC
AGCATCAAAAGGCCTTCTCTGTTGCAACCAATATTGCAATTTGGTGTCGA
GCACGGTCAATGGATGAACTAGCCACTGTTTTTATGGCATACTCTGGTGG
TGAGATAAAGAGTATAGATAACCTACTTTCTTGTGTATCACCACTATTAT
GCAATGAATGGTTCCCAAGACATTCGGCATTGGCATTTGGTCATCTGCTA
CGGCTCCTAGAGAGAGGACCTGTTGAATACCAGCGTGTGATACTTCTTAT
ACTAAAAGCATTGCTCCAGCACACTCCCATGGATGCTGCTCAAAGCCCAC
ATATGTATGCAATTGTGTCTCAGCTAGTTGAAAGCACCTTATGCTGGGAG
GCACTTAGTGTACTGGAAGCCCTTCTGCAGAGCTGCAGTTCATTGCCAGG
CTCTCATCCACATGATCCTGCTTCATTTGAAAACGGGCTTAGTGGGGCAG
ATGAGAAGATGCTCGCTCCACAGACCTCGTTCAAGGCTCGAAGCGGGCCC
TTACAGTATGCAATGGGACTAGGGTTTGGGACGGGCTCCACGCCCACTGC
TCAAGGCAGCGCAACGGAATCCGGGATTTTGCCGAGAGAGTTAGCTCTTC
AAAACACACGCCTGATCCTTGGTCGTGTGCTAGAAAACTGTGCGCTTGGG
AGGAGGAGAGATTACAGAAGACTGGTGCCATTCGTGACCAGCATCGGAAA
TTCATAGCCTAGCACTTTTTGTTCATGTTTTATGGCTGAGCTCATTCTTC
TTGCACATGTCTAGTTAACAGAAGGCTGGGTTCTGTGTATATTGTGTAGT
CATTTTAATTTAATTTATGTAGATTGTGTATTTAGAATGTATACCTTACC
TGCTGCTAATTCATACAAAGTTATGTATATTTCTTTTGTTGTTTTTAGCA
GTGTTCTATGGAAGTGTTAGTGATTTGGGAAATGTTTGTCCTTGGTTACC
TCTAGTAAATTTTAAACTTTTATAA
MKAGSAAKLIVDALLQRFLPLARRRIETAQAQDGQYLRPSDPAYEQVLDS
LAMVARHTPVPLLEALLRWRESESPKGANDASTFQRKLAVECIFCSACIR
FVECCPQEGLTEKLWNGLENFVFDWLINADRVVSQIDYPSLVDLRSLLLD
LVAQLLGALSRIRFSSVTERFFMELNTRRIDTSGARGETLSIINGMRYLK
LGVKTEGGLNASASFVAKANPLNRAPHKRKSELHHALCNMLSNILAPLAD
GGKGQWPPSGVEPALTLWYEAIARIRVQLMHWMDKQSKHIAVGYPLVTLL
LCLGDPKVFLNNFGSHMEQLYKHLRDKNQRFMALDCLHRVLRFYLSVHGD
SQPPNRVWDYLDSVTAQLLTILRKGMLTQDVQHDKLVEFCVTIAEHNLDF
AMNHTILELLKQDSPSEAKVIGLRSLLSIAMSPTSQHVGLEILHVHNIGH
YIPKVKAAIEAILRSCHRTYSQALLTSSRTTIDAVTKEKSQGYLFRSVLK
CIPYLIEEVGRSDKISEIIPQHGISIDPGVREEAVQVLNRIVRYLPHRRF
AVMKGMANFILRLPDEFPLLIQTSLGRLLELMRFWRACQADDKLHHDDKI
TKRVQRNEGFKKSSFYQSGEAIEFRSSEIDAVGLIFLGSVDSQIRHTALE
LLRCVRALRNDIREIALLDRPDHLKNEAEPIFIIDVLEENGDDIVQSCYW
DSGRPFDLRRESDSVPQDVTLQSILFESPDKNRWARCLSELVKYAAELCP
SSVQEAKLEVIQRLAHITPVELGGKAHQTQDADNKLDQWLMYAIFACSCP
TDIREGGGLAATRELFHLIFPSLKSGSETHVHAATMALGHSHLEVCEIMF
SELASFIDEVSLETEGKAKWKNQKSRREELRIHIANIYRVVAEKIWPGML
GRKPVFRLHYLKFIEETTRQILTAPNENFQETQPLRYALASVLRSLAPEF
VESKSEKFDLRTRKRLFDLLLSWCDDTGNTWSQDGVSDYRREVERYKSTQ
HVRSKDSVDKLSFDKEISEQVEAIQWASMNAMASLLYGPCFDDNARKMSG
RVISWINSLFIEPAPRAPFGYSPADPRTPSYSKYTGEGGRGATGRDRHRG
GHLRVALAKTALKNLLLTNLDLFPACIDQCYYSDAAIADGYFSVLAEVYM
RQEIPKCEIQRLLSLILYKVVDPSRQIRDDALQMLETLSDREWAGEGIEG
SGSYRAAVVGNLPDSYQQFQYKLSCKLAKDHPDLSQLLCEEIMQRQLDAV
DIIAQHQVLTCMAPWIENLNFWKLKDSGWSERLLKSLYYVTWRHGDQFPD
EIEKLWSTIASKPRNISPVLDFLITKGIEDCDSNASAEISGAFATYFSVA
KRVSLYLARICPQRTIDHLVYQLAQRMLEDSVEPLRPSVSKGDPGANFVL
EFSHGPAVTQIASVVDIQPHMSPLLVRGSLDGPLRNTSGSLSWRTAAVGG
RSASGPLSPMPPELNIVPVTAGRSGQLLPSLVNMSGPLMGVRSSTGSLRS
RHVSRDSGDYIIDTPNSGEDGLHTGLGLHGISAKELQSALQGHQQHSLTH
ADIALILLAEIAYENDEDFREHLPLLFHVTFVSMDSSEDIVLEHCQHLLV
NLLYSLAGRHLELYEVENIDGENKQQVVSLIKYVQSKRGSMMWENEDPTV
VRTELPSAALLSALVQSMVDAIFFQGDLRETWGQEALKWAMECTSRHLAC
RSHQIYRALRPHVTSDASVSLLRCIHRCLGNPVPAVLGFIMEILLTLQVM
VENMEPEKVILYPQLFWGCVAMMHTDFVHVYCQALELFSRVIDRLSFRDR
TTENVLLSSMPRDELDTSVSDTSDFQRDLRNTRESTSSSGKVPAFEGVQP
LVLKGLMSTASHGVSIEVLSRITVHSCDSIFGDAETRLLMHITGLLPWLC
LQLNQEAVVGIASPLLQQHQKAFSVATNIAIWCRARSMDELATVFMAYSG
GEIKSIDNLLSCVSPLLCNEWFPRHSALAFGHLLRLLERGPVEYQRVILL
ILKALLQHTPMDAAQSPHMYAIVSQLVESTLCWEALSVLEALLQSCSSLP
GSHPHDPASFENGLSGADEKMLAPQTSFKARSGPLQYAMGLGFGTGSTPT
AQGSATESGILPRELALQNTRLILGRVLENCALGRRRDYRRLVPFVTSIG
NS
| Relationships |
|---|
| The mRNA, XM_017385964.1, is a part of gene, LOC108214150. |
| The polypeptide, XM_017385964.1, derives from mRNA, XM_017385964.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |