| 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. |
GAGCGGAAGCGATGAGATTAAGGAGTGTAGTGTAATAACAGTGGAAAGGA
AACAGAAACCGAGAGCAGCAACATTTAAATAAATCTGATAAACCCCTCTT
CCTAAGCTACTTGTTGTCCAAAACCCTAGAATATCTCTGTCTCTATCTAT
CTGTATCACTAGCACACGGACACAAATATCTTGGCTCTCTCTCATCGTAG
CATGTCCTCCTCCTCCATATGGTTAGGTCTAGTAGTAGTAGTGGTGGTGT
TGTTGGTGAGCAATGCGGCGTCGTATTCTAAGTCCGAATCTTCTAATTCA
GGGAGTAGAGGACCCCACATAGCTGATGTGAATATATTGTTGCCTCCCAA
GATGACTCATCCTGTTCACTATAGACTTCAAGCAAGTGATGGCTGCTTCA
AATGGTCATGGGATCATCATGATATCTTGTCTGTTTTACCCGAGTACAAT
TCGAGTAATCACTGCTCCACGAGTGCCCACTTGAAGTCGATAGCACCCTA
TAGTGGGCGCAAGGAGACGGCCGTGTATGCTACGGATGTGGATACTGGGA
GGGTCATTCGTTGCAAGGTTTATATTGATAATGTTTCTAGAATTCAAATA
TTTCATAGTTCTGTCAAACTTGATTTAGACGGGCTTGCCACTTTACGTGT
TCGTGCCTTTGACAGCGAAGAAAATGTGTTTTCATCCCTAGTGGGCATAC
GGTTCATGTGGCAACTCGAGCCTGAAACCGATGAATCAGCTCATCACCTT
GTTCATGTACCTTTAAAGCTCTCTCCACTAAGTGATTGTGGTGGCTTGTG
CGGTGATCTCGACGTCCAAATAAAGCTTGAAGATAGTGGAGTTTTTTCAG
ACCTTTATGTTGTAAAAGGAACTGAAATCGGTCATGAACGCGTTTCAGTA
GATCTGCTTGAGCCAATGTATGATCAGATGGCTGATAGTATTGTTCTAAC
TGTTGCAGAAGCTATGTCTCTTTATCCACCATCCCCTGTTTTTGTTCTTG
TTGGTGCTGTTGTGCAATATCTACTAACAGTTGTGCGCGGGAATATTCCT
CGAGCAGTAACTTTACCATCTCCGTATCATCAATGGTCGGTTTTGAATTC
TTCAGTTTCTCGGATAGACAAAACGATGGGTATAGCTCATGCACTGAACT
TAGGTGTCACAACTGTTAGTGTTGAAGATACAAGAGTTGCTGGTCACATC
CAACTGTCATCACTACATGTAGTGCTTCCAGATTCTTTATATATATACAT
ATCGCCTTTGTCACATTCTGGTGATATTCTCGAAGGTGCAGCACCTAATC
CATCTGTTTCACGTTGGTATGTTGTTACTGGTAGACAATATCTTCTTGAA
ATGAAAGTTTTCTCGCGAGTACCTGAGTCACAAGAGATATATATAACGGA
GACTGATGATATAAAGTTGTATGATGACCATTCTGAGTTTTGGAATATAT
TCCCAGTTTCAGATACTACTACTTCCAAACTTGTGTGTTTGAATTCTAAA
ATTCTGAAAGCAATGTCATATGGATTGGGTAAACTAACTGCAACTTTAAC
CTACAGTAATGGGGTTCATGAGGTGAATCAGGCTCTCAAGGTTGTGCAAG
AAATCATGGTTTGTGAGCAAGTAAAGTTTAGTAAGGACAAAAGAAGTGCA
TCTGGGAGTATTCTCCTTCCATGGGCCCCTTCTGTCCACCAGGAGGTGGA
GCTAAAGGCAACAGGAGGTTGTGCCATATCATCCAGTGACTACAAATGGT
TTTCTTCAGATATGTCCATTGTGTGTGTATCAGCACATGGTATTGTTCAG
TCAAAAAGACCAGGGAAAGTTACTATTAAAGTGGTATCTAGTTTTGATTC
TTTCAATTACGATGAGTTGGAAATTGAAGTTTCCATTCCTTCCTCTATGA
TCATGCTGCAACAATTTCCTGTAGAGACTGTTGTGGGATCAAATCTTGCA
GCTTCCGTGACACTTAAAGATTCTAATGGTGATAATTATTTCAGATGTGA
TGCTTTCAGTTCAGCCATACAGTGGAATACCGGAAGCGATTCTTTTACGA
TTGTCTATACAGAGAGAGAATCATTCTTATTTGATGAGCAAGACGTCCCT
GATTTGCTTGCATCATTATATAGCCCGCCATGTGCCTGGGCCCGTATATA
TGCTTCTGCTACTGGGCGAACAATGCTACATGCTTCACTTAAAAAGGATT
ATCATCCTCTTGATCATTCGCTCACCGGATCTATCGATTTAAAAGCATCA
GCTCTCATTTCAGCATATCTACCACTCTTCGTGCATCAGGCAGGTGATGG
GAACCAGTATGGTGGTTATTGGTTTAATTTGTCTTATGCTGAGGCTAATA
ACCATTTAGAGAATTTGAAAATCTTGAATCTTGTTCCTGGCACACATATG
GATGTCACTCTGTCCGGGGGACCAGATCAGTGGGGAGGAGGTGTTGAATT
CACTGAAACTGTGGAAATTTTACCTCAGGAACAGACTAAGCAGAAAGGGG
TTTTGGTCCATAATATAACTACCATTTATGGTAGCTCATATAGAATATCA
TGCGAGAATTGGGGAGAATTTAAAGTTCTTTTCAAACGTGGAAACTTGGC
TGGCGATGATCATATACTACCTGCTGTGGCGGAGGCTGAACTATTGCTCT
CATGTATCTTACCATCTTCAATCTCAATAGTAGTTGATAGTTCTGTCAAT
GCCCTTGATGTGATACACACAGCTATGCAGGCTGACCGGAATTCAGAGCA
AGTTCGGGCCCTTCCAATCACTGTGGCTAATGGGCGAACTATTAGAGTAT
CTGCTGTTGGTATTAGTGACTCTGGGAATGCTTTTGGGAACTCTTCTTCT
CTTAGTATAAGTTGGGAAGCGAGAAATTGTGATGGATTGGCCTTCTGGGA
TGCTGCTGCTACATCCATATCAAATTGGGAGAGGTTTTTGGTCTTGCAAA
ACTCAACAGGACTTTGCACTGTTCGTGCCACAGTTGGTGGATTCATAGAG
ACCTTGAGTAATCATCGCTTTATTAAATCCTATGGAAGTTCAAAATCTCT
TACCGATGCCGTACAACTACAACTTGTCTCTACTTTAAAAGTCACTCCAG
AGTTCAGCTTGTTATTATTCAGTCACTTGGCTATATTAGATCTCTCAATT
AGTGGAGGGAGTTGTGCACTGACTACTGTGGTTAATGATACCCAAGTTGC
AGAATTAATTGATCGTACACCAGATTTGCATTGCTCTCAACTATCACTAG
CGCCTAAAAGTTTAGGGACTGCACTTGTTACGGTTTATGATATGGGACTT
TCTCCCCCACTTGCTGCCACCTCCGTGGTTCAAGTTGCTGATGTAGATTG
GCTTAAGATTACTTCGGGAGAACTAATAAGCCTCGTGGAAGGAAGTTCCC
AATCTATAGATCTTCTGGCTGGGGTAAATAATGGACGCACTTTTGACTTC
TCCCAGTACATGTATATGAAAATTCGTGTGCATATTGAAGATCATAATAT
TGTTAGTCTGTTAGATGGTATTAGCGATGGATATCTGAAGGCTCCAAAAT
TTATCCTTCAGGCCAAAAATCACGGTATTACGACTCTTTATGTAAGTGCT
AGGCAACAATCTGGACGTGAAATATTGAGCCAATTTATTAAGGTTGAAGT
TTATGCCCCACTTAGTATACGTCCTTCTAATATATATCTTGTACCCGGTG
CTTCTTATGTGCTTACCGTGGAAGGAGGCCCAACTATTGGTGGTTATGTT
GAATATGGAAGTATGAATGATGAGACTGCAATAATTCATAAATCTTCTGG
GCGGCTGATTGCAATTGCTCCAGGGAATACAACTCTCGTGGCTAGAATTT
ATAGCAAAGGTGATGAAGTGATGTGTCATGCATTTGGATATGTAGTAGTT
GAGATCCCTTCTTCAGCAATGTTAAATGTGCAGAGTGAGCAACTTGCCAT
TGGTAGCGAACTACAAATATATCCTTCGTTTACCAACGGTAATTTGTTTT
CTTTGTATGAGGTGTGCAAGAATTATGAATGGAGCGTTGAAGATGAAGAC
GTATTGACTTTCAAAGTAGTAGATCTCTTGCATGGTTACAAGCTTGGTGC
CTCTTCCATTGTTTTGGAAGCAAGTGGATCTAATGAGAAGCTTGACCTAA
GGTTTATCCGCGAGTTTTATGGAAAGTCTTCTGGCCAGACTCATGTCAGC
GTTTCATTTTCTTGTAATTTTGTATCCCGTTCATTTTCACAGTCCAGGTT
ATATACTGCATCCATATTGCTCTCTGTGGTGCCTGATCTCCCTCTTGCTC
TTGGAAAACCAGTGACATGGGTACTTCCTCCTCATTATATAACATCAAAT
CTCTTACCATCATCTTCAGGGTCCTACAGTCAGGGAGATGCTCAGAGCAG
CAAAGGAACCATTACTTACACTTTGTTAAAAGAATATGGGGGTCAGAAAG
ATATAGAGTTGGTAAATGAAGCAATATCCATCCAAGGTGTTAAAATACAA
ACAAGAGAGAGTAATAATATTGGGTGCATTCAGGCGAAAGATAGATTGAC
TGGAAGATTTGAGATTGCATCTTGTGTTAGAGTCGCTGAGGTAGCTCAAA
TCAGAGTGAGCAGGCATGCGTTTCCATTTTACAGCGTTAACCTTGCTGTT
GGAGCTGAACTCAGTATTCCGCTGATATATTACGATGCTTTTGGATACCC
TTTCTACGAGGCTTATAACATTGTTTTGTATGATGTTGAGACTAACTATG
GCGACATTGTCTCCATCAATGACACACATGACGGTAATATATATCTGAAA
GCATTACAATTTGGTAGAGCACTGGTCCGAATATCCTTAAAAAATAACTC
AACCAAGTCGGACTACTTGTTGATCACAATTGGTGCTCGTTTGTACCCTC
ATAATCCACTCCTCCAATTGGGTAATCGTCTTAATTTCAGTATTGAAGGC
CTCACTGATCAAGTATCTGGCTGGTGGACGAGTGTTAATACAAGTACTGT
TTCAATAGACAGGGTGTCTGGAGAAGCTGAAGCCATTGGGGAAGGAAGTA
CTCAAGTCATCTATGAAAGCTCAGATTTCAAGTTGCTGACGTTTGTTACA
GTCTCAAAGGGGCATATGATAACTGTTAATGCTCCAAAAGGGATTCTAAC
AAATGCTCCTTTCTCAATGAGAGGTTATAAATTCCTTGTGACATTTAGTG
ATGCGTTTGAACCCATCCGTGAACCAGGGGGGGCTGTTAAAACACTCCTG
CATGAGTGTGAAGTGGAGCCACATTTTGTTGGGTATGCAGACCCATGGAT
GGATTTTGAGAGTGGAATGTCATATTGTCTCTTCTTTCCATACTCACCAG
GACACTTGGTTCGTTCAGTTGGAAATTTGAAGGATACAAGGCGGGATATA
AGTGTTACCATCAATGCTTTTGTGCGAGGAACAAACAATATATCTGGATC
TGCTTCTGCTTTTTTTGTTGGTGGATTTGCTATACTGGACATGGACCACA
ACTCATTACATTTGAATTTGACTTCCAAGTCTAACAAGTCTGTCATAACT
GTAGTCGGTAATACAGATGTTGTTGTTGACTCGCAAGGTCGGAATCAGTT
GCTAATCACACCTATACACAGAGAAAATAATGGAGTAGCAGGGCGGGCAG
AATACGAGGTCAAAGTTCTCAGCTCTTGGAGGTTCAAAGATAAATTGATA
ATTTCACTCGCAGCAAATGGCCAGAGAGTCGAAATTGATGTAAACTATGA
ACCTGAGAAGATACCCGCACTGCCTTCATCCACTAAAGTCAGCAACTGGA
TGGTTATACTTGTGTGTTCCTCTGTTCTAATATCAACACTAATTCTGTTT
CTCTGTTACCTGGATAGATCAAATAGATATCAAGCAAATGCGGCACCTAC
CACCCGAACTGCCACAGTTCAATCACCGGCAACCCCTCCTCGGAGCAGTC
CATCCGTCGTGAATGAACACTCTCCACAAACGCCTCAAGCTTTCATAGAC
TATGTAAGGAGAACAGTTGATGAGACTCCTTACTACAGGAAAGATCCGCG
CAGGAGGTTTAATGCACAAAATACCTTTTAGATTGTATGAGCACTTTATT
AGTTCTCTCCTTTCCCCTTTCCCCTTTCTAAGTTGTTGTATCAGTTTGGA
TGAATATATAGTCACACTAGAAAAGGGTTGTAGTCATGTAAGGCAACTGT
TGTATTAATGCCATTTTTCTGGCTACAAATTTAAGCCCCACCCTTTTGTG
CTC
MSSSSIWLGLVVVVVVLLVSNAASYSKSESSNSGSRGPHIADVNILLPPK
MTHPVHYRLQASDGCFKWSWDHHDILSVLPEYNSSNHCSTSAHLKSIAPY
SGRKETAVYATDVDTGRVIRCKVYIDNVSRIQIFHSSVKLDLDGLATLRV
RAFDSEENVFSSLVGIRFMWQLEPETDESAHHLVHVPLKLSPLSDCGGLC
GDLDVQIKLEDSGVFSDLYVVKGTEIGHERVSVDLLEPMYDQMADSIVLT
VAEAMSLYPPSPVFVLVGAVVQYLLTVVRGNIPRAVTLPSPYHQWSVLNS
SVSRIDKTMGIAHALNLGVTTVSVEDTRVAGHIQLSSLHVVLPDSLYIYI
SPLSHSGDILEGAAPNPSVSRWYVVTGRQYLLEMKVFSRVPESQEIYITE
TDDIKLYDDHSEFWNIFPVSDTTTSKLVCLNSKILKAMSYGLGKLTATLT
YSNGVHEVNQALKVVQEIMVCEQVKFSKDKRSASGSILLPWAPSVHQEVE
LKATGGCAISSSDYKWFSSDMSIVCVSAHGIVQSKRPGKVTIKVVSSFDS
FNYDELEIEVSIPSSMIMLQQFPVETVVGSNLAASVTLKDSNGDNYFRCD
AFSSAIQWNTGSDSFTIVYTERESFLFDEQDVPDLLASLYSPPCAWARIY
ASATGRTMLHASLKKDYHPLDHSLTGSIDLKASALISAYLPLFVHQAGDG
NQYGGYWFNLSYAEANNHLENLKILNLVPGTHMDVTLSGGPDQWGGGVEF
TETVEILPQEQTKQKGVLVHNITTIYGSSYRISCENWGEFKVLFKRGNLA
GDDHILPAVAEAELLLSCILPSSISIVVDSSVNALDVIHTAMQADRNSEQ
VRALPITVANGRTIRVSAVGISDSGNAFGNSSSLSISWEARNCDGLAFWD
AAATSISNWERFLVLQNSTGLCTVRATVGGFIETLSNHRFIKSYGSSKSL
TDAVQLQLVSTLKVTPEFSLLLFSHLAILDLSISGGSCALTTVVNDTQVA
ELIDRTPDLHCSQLSLAPKSLGTALVTVYDMGLSPPLAATSVVQVADVDW
LKITSGELISLVEGSSQSIDLLAGVNNGRTFDFSQYMYMKIRVHIEDHNI
VSLLDGISDGYLKAPKFILQAKNHGITTLYVSARQQSGREILSQFIKVEV
YAPLSIRPSNIYLVPGASYVLTVEGGPTIGGYVEYGSMNDETAIIHKSSG
RLIAIAPGNTTLVARIYSKGDEVMCHAFGYVVVEIPSSAMLNVQSEQLAI
GSELQIYPSFTNGNLFSLYEVCKNYEWSVEDEDVLTFKVVDLLHGYKLGA
SSIVLEASGSNEKLDLRFIREFYGKSSGQTHVSVSFSCNFVSRSFSQSRL
YTASILLSVVPDLPLALGKPVTWVLPPHYITSNLLPSSSGSYSQGDAQSS
KGTITYTLLKEYGGQKDIELVNEAISIQGVKIQTRESNNIGCIQAKDRLT
GRFEIASCVRVAEVAQIRVSRHAFPFYSVNLAVGAELSIPLIYYDAFGYP
FYEAYNIVLYDVETNYGDIVSINDTHDGNIYLKALQFGRALVRISLKNNS
TKSDYLLITIGARLYPHNPLLQLGNRLNFSIEGLTDQVSGWWTSVNTSTV
SIDRVSGEAEAIGEGSTQVIYESSDFKLLTFVTVSKGHMITVNAPKGILT
NAPFSMRGYKFLVTFSDAFEPIREPGGAVKTLLHECEVEPHFVGYADPWM
DFESGMSYCLFFPYSPGHLVRSVGNLKDTRRDISVTINAFVRGTNNISGS
ASAFFVGGFAILDMDHNSLHLNLTSKSNKSVITVVGNTDVVVDSQGRNQL
LITPIHRENNGVAGRAEYEVKVLSSWRFKDKLIISLAANGQRVEIDVNYE
PEKIPALPSSTKVSNWMVILVCSSVLISTLILFLCYLDRSNRYQANAAPT
TRTATVQSPATPPRSSPSVVNEHSPQTPQAFIDYVRRTVDETPYYRKDPR
RRFNAQNTF
| Relationships |
|---|
| The mRNA, XM_017373605.1, is a part of gene, LOC108204254. |
| The polypeptide, XM_017373605.1, derives from mRNA, XM_017373605.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |