| 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. |
TAACTCTCTTTCCTTTGCTCAGATTTCATGTCTTTGATTAATCTGTAGCT
CTCAATTGCTTTGAATGATTCTAGGTCAATTGGTGAATTGATTTTACAAT
ACACTGTTTGGTTATGATTGGGAGTTGAAGCTTAAGCCCTAGACTAGATT
TGTTTAAAATGAAAGCGGGGAGTGCCGCTAAGCTCATCGTTGATGCTCTT
CTCCAACGCTTCCTTCCACTTGCTCGTCGTCGTATCGAAACTGCTCAAGC
TCAGGATGGACAGTATCTTCGGCCATCTGATCCAGCGTACGAGCAGGTAT
TGGATTCCTTGGCTATGGTGGCACGACATACTCCCGTGCCTCTACTTGAA
GCTCTTTTAAGATGGAGAGAAAGTGAATCACCGAAGGGGGCAAATGATGC
ATCTACATTCCAGCGGAAGCTTGCAGTGGAGTGCATTTTTTGCTCAGCAT
GTATCCGCTTTGTAGAGTGTTGCCCTCAAGAGGGGCTTACAGAGAAGCTA
TGGAATGGACTAGAAAATTTTGTCTTCGACTGGCTGATCAATGCTGATCG
GGTTGTCAGTCAAATTGATTATCCTTCCCTTGTAGATTTACGCAGTCTTC
TTCTCGATCTAGTAGCTCAACTTTTAGGGGCGCTGTCTCGGATCAGATTT
AGTTCTGTTACTGAGCGTTTTTTCATGGAACTCAATACTCGTCGAATTGA
TACAAGTGGTGCTAGGGGGGAGACTCTTAGCATCATTAATGGGATGCGTT
ACTTGAAGCTTGGGGTTAAGACTGAGGGTGGATTGAATGCATCAGCGTCA
TTTGTGGCTAAAGCGAACCCTCTTAATCGTGCTCCTCATAAGCGAAAGAG
TGAACTACACCATGCACTTTGCAATATGCTTTCAAATATTCTAGCACCAC
TTGCAGATGGTGGAAAGGGCCAATGGCCTCCTTCGGGTGTTGAACCAGCA
CTTACCCTATGGTATGAAGCCATTGCGAGAATAAGAGTGCAACTTATGCA
TTGGATGGACAAGCAAAGCAAACATATTGCTGTTGGTTACCCGCTTGTGA
CTCTTCTTCTTTGTCTTGGCGACCCAAAAGTTTTCCTCAATAACTTTGGC
TCTCACATGGAGCAGCTGTACAAGCACCTTCGTGACAAGAACCAGCGGTT
CATGGCGTTGGATTGTCTTCATCGTGTTCTTAGGTTTTATCTGAGTGTTC
ACGGGGACTCACAGCCTCCAAATCGAGTATGGGACTACCTGGACAGTGTG
ACTGCGCAGCTCCTAACAATTCTGAGGAAAGGAATGCTTACCCAGGATGT
CCAACATGACAAACTTGTAGAATTCTGTGTGACTATAGCAGAACATAACC
TTGATTTTGCCATGAATCATACAATACTGGAATTACTCAAGCAAGATAGT
CCAAGTGAAGCGAAGGTTATTGGTCTCCGTTCTCTGCTTTCAATTGCTAT
GTCTCCTACCAGCCAGCACGTTGGTCTGGAAATTCTTCATGTTCATAACA
TCGGTCACTACATTCCAAAGGTGAAGGCTGCTATTGAGGCTATTTTAAGG
TCATGTCATCGAACCTACAGTCAGGCTCTTCTTACCTCATCAAGGACAAC
CATAGATGCTGTTACAAAAGAGAAATCTCAGGGTTATCTTTTTCGATCAG
TTTTAAAGTGCATTCCGTATCTGATAGAAGAAGTTGGGCGAAGTGATAAG
ATCTCTGAAATAATACCTCAGCATGGTATTAGTATTGATCCTGGTGTCCG
TGAAGAAGCAGTTCAAGTACTTAATCGTATTGTGAGATATCTTCCTCATC
GCCGCTTTGCAGTTATGAAAGGAATGGCGAACTTCATTTTACGCCTTCCT
GATGAGTTCCCTCTTCTCATTCAAACATCATTGGGGCGCTTACTGGAACT
TATGCGTTTCTGGAGAGCTTGTCAAGCTGATGATAAATTACACCATGATG
ATAAGATTACGAAGCGTGTGCAGAGGAATGAAGGGTTCAAGAAATCTTCT
TTCTATCAATCTGGAGAAGCAATTGAATTTCGGTCCTCGGAGATAGATGC
AGTTGGCCTTATTTTTCTTGGTTCTGTAGATAGCCAGATCAGACATACAG
CATTGGAGTTACTCCGCTGTGTTCGGGCTCTGCGCAATGATATTCGGGAG
ATTGCACTGCTTGATCGCCCAGATCATCTGAAAAATGAAGCTGAGCCAAT
TTTTATAATTGATGTTTTGGAAGAGAATGGGGATGACATAGTTCAAAGCT
GCTATTGGGATTCTGGCCGTCCATTTGATTTGAGACGTGAATCTGATTCT
GTACCTCAAGATGTGACCCTTCAGTCTATACTCTTTGAAAGCCCTGATAA
AAATCGATGGGCACGTTGTCTTAGTGAGCTTGTCAAGTATGCCGCTGAGC
TGTGCCCAAGCTCTGTTCAGGAGGCAAAGCTAGAGGTAATCCAGCGTCTT
GCTCATATCACACCTGTTGAGTTGGGTGGAAAAGCTCATCAGACACAGGA
TGCAGACAACAAACTAGACCAATGGCTTATGTATGCAATATTTGCATGTT
CTTGTCCAACTGATATTAGGGAAGGTGGCGGATTAGCAGCTACTAGAGAA
CTTTTTCATCTCATCTTTCCTTCACTAAAATCTGGTTCAGAAACACACGT
ACATGCTGCCACTATGGCTCTTGGCCATTCACATTTAGAAGTGTGTGAAA
TAATGTTCAGCGAGCTTGCATCTTTCATCGATGAAGTCTCTTTAGAAACT
GAGGGAAAAGCAAAGTGGAAGAATCAGAAGTCCCGCCGTGAAGAACTTCG
AATCCACATCGCAAATATATACCGTGTTGTTGCAGAAAAAATTTGGCCTG
GCATGCTAGGCCGAAAGCCAGTTTTCCGCCTCCATTATCTAAAGTTTATT
GAAGAAACAACTAGACAGATCTTAACAGCACCAAACGAGAACTTCCAGGA
AACCCAACCCCTTCGTTATGCTCTTGCTTCTGTTTTAAGATCACTAGCCC
CCGAATTTGTGGAGTCAAAATCAGAAAAATTTGATCTTAGAACAAGAAAG
CGATTGTTTGATCTTCTTCTCTCCTGGTGTGATGACACAGGTAATACATG
GAGTCAGGACGGTGTCAGTGATTACCGGCGTGAGGTTGAACGATATAAAT
CTACACAGCATGTTCGTTCAAAAGATTCTGTTGATAAACTTTCATTTGAT
AAAGAAATCAGTGAACAAGTCGAGGCTATTCAGTGGGCTTCCATGAATGC
CATGGCTTCCCTGTTATATGGCCCTTGCTTTGATGACAATGCCAGAAAAA
TGAGTGGCAGGGTAATATCTTGGATTAATAGTCTTTTTATTGAGCCTGCC
CCTCGGGCTCCATTTGGTTATTCACCCGCCGATCCAAGAACACCATCATA
TTCCAAATATACAGGAGAAGGTGGACGAGGAGCAACTGGACGTGATCGGC
ATAGAGGTGGGCATTTGCGTGTGGCCCTTGCAAAAACGGCTTTAAAGAAT
CTTCTACTAACAAATTTGGACCTGTTTCCTGCTTGCATTGATCAGTGCTA
CTACTCTGATGCTGCTATAGCTGATGGATACTTCAGTGTCTTGGCCGAAG
TCTACATGCGTCAAGAGATACCGAAGTGTGAAATTCAGAGGCTGTTGAGC
CTGATCCTCTACAAAGTGGTGGATCCATCTAGACAAATTCGTGATGATGC
CCTTCAGATGCTTGAAACGCTTTCCGACCGGGAATGGGCTGGGGAGGGCA
TCGAGGGTTCGGGAAGTTATCGAGCTGCTGTTGTTGGTAACCTTCCTGAC
TCGTACCAACAGTTCCAATACAAACTTTCATGCAAACTCGCAAAAGATCA
TCCTGATCTGAGCCAGCTTCTTTGTGAGGAGATCATGCAAAGACAACTTG
ATGCTGTTGATATAATTGCACAGCATCAAGTTTTAACATGCATGGCTCCC
TGGATCGAAAATCTCAATTTTTGGAAACTCAAGGACTCCGGATGGAGTGA
AAGGTTATTGAAAAGCCTTTACTATGTGACATGGCGACATGGTGACCAGT
TTCCTGATGAAATTGAGAAGCTTTGGAGCACTATTGCTAGCAAGCCCAGG
AACATTAGTCCAGTTCTCGATTTTTTAATCACCAAAGGAATTGAAGATTG
TGATTCAAATGCATCTGCAGAAATTAGTGGGGCATTTGCAACATACTTTT
CTGTTGCAAAACGAGTAAGCTTATATCTAGCTCGAATATGTCCACAACGC
ACCATTGATCACTTGGTTTACCAGTTAGCTCAGCGAATGTTAGAGGACAG
TGTCGAACCACTCAGACCCAGCGTAAGCAAGGGTGATCCAGGTGCAAATT
TTGTATTAGAGTTCTCTCATGGGCCTGCAGTGACCCAGATTGCATCTGTT
GTGGACATCCAGCCTCACATGTCACCCTTGCTTGTTCGAGGATCTCTAGA
TGGTCCCCTTAGGAATACCAGTGGCAGCTTAAGCTGGAGAACAGCAGCCG
TTGGAGGTCGAAGTGCTTCAGGTCCATTGAGTCCAATGCCTCCGGAGTTG
AACATTGTTCCTGTAACTGCAGGCCGATCCGGCCAACTACTTCCTTCCTT
GGTAAACATGTCAGGACCCTTGATGGGGGTCCGAAGTTCAACAGGGAGCT
TGCGCAGCCGCCATGTGTCTCGAGACAGTGGAGACTACATTATAGACACT
CCAAATTCCGGAGAAGATGGTTTACATACTGGCCTTGGGCTGCATGGTAT
CAGTGCTAAAGAACTTCAATCAGCCTTACAAGGGCATCAACAGCATTCAC
TGACTCATGCAGATATAGCATTAATTCTACTTGCCGAAATTGCATATGAA
AATGATGAAGATTTCCGCGAGCACCTACCCTTGCTTTTTCATGTCACATT
TGTCTCAATGGACAGCTCTGAAGATATTGTACTGGAGCACTGCCAGCACC
TACTTGTTAATTTGCTGTATTCTCTGGCTGGACGTCACCTGGAGTTGTAT
GAGGTTGAGAATATCGATGGGGAGAACAAGCAACAGGTTGTTAGTCTGAT
CAAGTATGTGCAGTCAAAGCGAGGGAGCATGATGTGGGAGAATGAGGATC
CCACAGTTGTGAGGACTGAACTTCCAAGTGCAGCCCTTTTGTCAGCTCTT
GTACAGAGTATGGTAGATGCTATCTTCTTCCAAGGAGACCTTCGAGAGAC
TTGGGGACAAGAGGCACTCAAGTGGGCTATGGAGTGCACATCAAGACACC
TTGCATGCCGCTCACACCAAATTTACCGTGCATTGAGGCCTCATGTCACA
AGCGATGCATCAGTATCGCTCCTCCGCTGTATCCACAGATGTTTGGGAAA
TCCTGTGCCAGCAGTTTTAGGATTCATCATGGAAATTTTGTTGACTTTAC
AAGTAATGGTAGAGAATATGGAGCCTGAAAAAGTGATCCTCTACCCACAG
CTATTTTGGGGATGTGTAGCTATGATGCATACAGACTTTGTTCACGTTTA
CTGCCAGGCGCTGGAGTTGTTCTCTCGTGTAATTGATCGTCTATCATTTC
GTGACCGAACAACAGAAAATGTACTCTTATCTAGCATGCCGCGTGATGAG
CTCGATACCAGTGTTTCTGACACCAGTGATTTTCAAAGGGATTTAAGAAA
TACTCGTGAATCAACATCATCAAGTGGGAAGGTTCCAGCCTTTGAAGGAG
TGCAGCCACTTGTTCTTAAGGGACTAATGTCAACAGCAAGTCATGGTGTC
TCTATTGAGGTCCTTTCACGGATCACAGTTCACTCTTGCGATTCAATATT
TGGGGACGCAGAAACACGACTCTTAATGCACATCACAGGTTTGCTTCCCT
GGCTGTGCTTGCAGCTAAACCAGGAAGCAGTGGTGGGCATTGCTTCACCA
CTCCTACAACAGCATCAAAAGGCCTTCTCTGTTGCAACCAATATTGCAAT
TTGGTGTCGAGCACGGTCAATGGATGAACTAGCCACTGTTTTTATGGCAT
ACTCTGGTGGTGAGATAAAGAGTATAGATAACCTACTTTCTTGTGTATCA
CCACTATTATGCAATGAATGGTTCCCAAGACATTCGGCATTGGCATTTGG
TCATCTGCTACGGCTCCTAGAGAGAGGACCTGTTGAATACCAGCGTGTGA
TACTTCTTATACTAAAAGCATTGCTCCAGCACACTCCCATGGATGCTGCT
CAAAGCCCACATATGTATGCAATTGTGTCTCAGCTAGTTGAAAGCACCTT
ATGCTGGGAGGCACTTAGTGTACTGGAAGCCCTTCTGCAGAGCTGCAGTT
CATTGCCAGGCTCTCATCCACATGATCCTGCTTCATTTGAAAACGGGCTT
AGTGGGGCAGATGAGAAGATGCTCGCTCCACAGACCTCGTTCAAGGCTCG
AAGCGGGCCCTTACAGTATGCAATGGGACTAGGGTTTGGGACGGGCTCCA
CGCCCACTGCTCAAGGCAGCGCAACGGAATCCGGGATTTTGCCGAGAGAG
TTAGCTCTTCAAAACACACGCCTGATCCTTGGTCGTGTGCTAGAAAACTG
TGCGCTTGGGAGGAGGAGAGATTACAGAAGACTGGTGCCATTCGTGACCA
GCATCGGAAATTCATAGCCTAGCACTTTTTGTTCATGTTTTATGGCTGAG
CTCATTCTTCTTGCACATGTCTAGTTAACAGAAGGCTGGGTTCTGTGTAT
ATTGTGTAGTCATTTTAATTTAATTTATGTAGATTGTGTATTTAGAATGT
ATACCTTACCTGCTGCTAATTCATACAAAGTTATGTATATTTCTTTTGTT
GTTTTTAGCAGTGTTCTATGGAAGTGTTAGTGATTTGGGAAATGTTTGTC
CTTGGTTACCTCTAGTAAATTTTAAACTTTTATAA
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_017385965.1, is a part of gene, LOC108214150. |
| The polypeptide, XM_017385965.1, derives from mRNA, XM_017385965.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |