| 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. |
CTCGTCACGTGCAAAACATATGTTTTGTACATAAACGTGTGTATATAAGT
ATATTTGTTCTCTTAGTATATTTGTTCCGCATTCACAGTCTTTCTTCTCC
TGTCTACTCCATCTCGAGTCAACCCAAGTCAAGCCCTCTCTCCGTTTAAC
CGCCGACATGGCCTCCGGTGACTCCAACTCCGAGGATCATCAAGATTTTG
ATGTGAAAGACCCCACACTCATTGCCAGAGAGTATCAGACAAAACTGTGT
CAGAAAGCTTTGAGTGAAAACACAATAGCCTATTTGGGAACTGGTTGTGG
GAAGACTCACATTGCTGTTCTATTAATTCATGAGATGCGACACTTGATAA
AGAAACCCCAGAATAACATATGTGTCTTTCTAGCTCCTTCAGTTGCTCTG
GTTGAGCAGCAAGCCAAAGTCATCAAGGACTCAATTGATGTTAAAGTTGG
CATCTACTGTGGGAGTTCTAAGCATTTGAAGCGTCATACCTATTGGGAGA
AAGAATTAGCACAACATGAGGTTCTTGTCATGACCCCTCCAGTACTTCTC
CAGAATTTATCGCATTGCTTCATCAGGATTGAATTGATTGCGCTTCTAAT
TTTTGATGAGTGCCATCATGCGCAACCTGAGAGCAATCATCCTTATGCTG
AAATCATGAAGGTATTTTACAATACCAGTGCAACAAAGCTTCCTCGTGTA
TTTGGTATGACCGCATCTCCAATATTGGGAAAAGGTGCTTCTATCCGTGG
CCTCGAGTCTTTACTACATGCTAAGGTTTATTCTGTTGAAGACAAGGAAG
AACTCGAACGGTTTGTGACACCTCCCAAAGTTAGTGTATATTATTATGAT
ACAGCAGCAGATGGACCATCTTCCCCTCTAGTTTATTCTAGTAAACTGCA
AGCGATAAAATCCCAGTGTGTATCAACACTGGTAGAGAATATCAGCGACA
TGGATAGCCTAATAAGCTCCAAAAAGATGCTCCAGAAACTGCACACTAAT
CTGTGTTTGTGTGTAGAGAAACTTGGTGTTTGGGGAGCATGTCAGGCTGC
TCAGATACTCTCAAAGGGTGACTGCCTTGTGCAAAATGAACTAATGGAGA
TGGAAGTGCAGAATTCGCATGTCTCTATATGCAACAGCTATCTTTCTCAA
GCTGCCATGATATTTTTGTCGGATTGCAAAAAAGATCGAACCAAGGAGAA
GTTAAATTCACCAGAAGTCCTAGAGGAGCCCTTTTTCTCCAAAAAGCTCT
TGCAACTTATTAACATCCTTACCAATTTCAGGTCCCAGCAAAACATGAAA
TGTATAATTTTTGTCGATAGAATTGTAACTGCCATATCTTTGTCGTCTAT
ACTTCAAAGCCTTCAATTTCTATCAGCTTGGAAATCTGATTTTTTGGTCG
GAGTCAACTCTGGACTAAAGCGTGTGTCACGAAAATCTACTAACGCTTTG
CTTGCTAAATTTCAATCCGGTGAGATAAATCTATTGGTTGCAACTAAAGT
TGGGGAGGAAGGTCTTGATATTCAAACGTGCTGCCTTGTAGTAAGGTTTG
ATCTTCCGGAAACTGTAGCCAGTTTCATACAATCTAGAGGACGTGCTCGC
ATGCCTCAGTCAGAATATGCATTTCTGGTAGACAGTGGCAATGAGAAGGA
GCAAAATCTTATTGACAGTTTTACTGAAGCTGAGGATAAAATGAATGAAG
AAATTGAATTCAGAACATCTACTGCCACTTTTTGTGATATTGAGGAGAAA
ACTTATAGAGTAGAATTGACGGGAGCCACAATCAGTTCTGGAAGTAGCAT
TTCATTGCTTTACCGCTATTGTTCGAAACTTCCACATGATGAATTTTTTA
AGCCCAAGCTGGAGTTCTCATACTTCGATGAGGCAGATGGAACAGTCTGC
CAGATAATTTTTCCCTCCAATGCTCCAATTTATCAACTGTCAAGTGCTCC
TCAATCTTCTAAGGATGCAGCAAAGAGAGATGCGTGCTTGGAAGCATGTA
AGCAATTACATCAATTGGGTGCTCTAACCCACTATCTCTTGCCCGAACGA
GATGATGAAAATGAGGACCTGGAATCTTCATCAGATTCAGATTGCTCTGA
TGACGAGGATACGAGAAGAGAATTGCATGAAATGCTTGTTCCTGCTGTCC
TCAAAGAGCCGTGGAGTGAGGCCGAGGATTCTGTCCACCTCAGGTCCTAC
TTTGTGAAGTTTAGACCCCATCCACCAGATAGGGATTATAGACCATTTGG
TCTCTTTGTAAAAGCATCTCTTCCTGGAGATGCTGAAAGAATGAAACTAG
ACCTTCATTTGGCACGTGGTAGATCTGTAGCAACAGAGCTTGTACCATTT
AGAACTCTGCTATTTAGTAGAGATCAGCTAGCTTTGGCCGAGAAGTTTCA
GGAAATGTTCCTCAAGGTCATCATTGACAGATCACAGTTCTGTTCTGAAT
TTGTTCCCTTGGGAAGAATTAATTCTGATATATTGGCTCCTAGAACATAT
TACCTCATGCTTCCTGTAATCTGCTATGAATTTGAGGAAGCAATGGTTGT
GGACTGGAACCTTGTCATGAAATGTTTATCGTCGCCGATATTTAACATGC
CAGAAGTTGCTAAGGCTAATGAGCTTCCTCAACCCAGCGAGAAATTACAT
CTCGCTAATGGTCCTAAAAGTGTCAATGATGTTGTGAATAGCTTGATTTA
TGTACCAAGCAAGAAATTGTTCTATTTTGTTTCTGATGTTTTGTCAGAGA
AGAATGCATACAGTGACTATAAAGCATCAAAAAGTCACGTTCACCACTTC
TCTGAGAGGTTTGGCGTTCATCTTTTACATCCTAAACAAGCTCTTTTAAA
AGCAAAGCAGCTCTTTAGTCTGGAGAACTTACTACGAAAGAAAGGAAATT
TGGCATCTCATGCAGAACCACGAGAAAAAGAGGAGCACTTTGTTGAATTA
CCTCCTGAAATTTGTGAATTAAAGATAATTGGGTTTTCGAAAGATGTTGG
AAGTTCATTATCTTTGTTACCATCAGTCATGCATCGTCTGGAAAGCTTGC
TTGTTGCTGTTGAACTAAAACATTTACTTTCTGTCTCATTTCCTGAGGGA
GCTGAAGTATCTGCTTCTCGTGTCCTTGAAGCACTTACTACTGAGAAATG
CAATGAACACTTCTCTCTTGAAAGGCTCGAAGTTCTTGGTGATGCATTCC
TCAAATATGCAGTTGGCAGGCGTCTTTTTGTCTTGCATGATGCCCTAGAT
GAGGGACAGCTTACAAGAAAACGTTCAAGTGTCGTCAATAACTCCAATTT
ACTGAAGCTAGCGATAGCAAACAGATTACAGGTATACATACGCGACCAAT
CATTTGACCCATGCCAATTTTTCGCATTGGGTCGGCCTTGTTCAGTTGTT
TGTAAATCTGAAACGGAAAAGACTATCCATTCATCACAATGTAGTAGGGC
TGCAAATCTCCATATGGAATTAAGATGCACTAAATCTCATCACTGGTTGC
ATAAGAAAACCATAGCCGATGTTGTGGAATCTCTTGTCGGTGCATTTATA
GTCGACAGTGGCTTCAAAGGTGCAGCTGCTTTTCTTAATTGGATGGGTAT
ACAAGTGGAATTTGAAGGTTCGAAGGTTAGCCATATCTGTTCAGCAAGTT
CAATCTATTTACCACTTGCTGCTCAAATAGATATAGCTGCTCTTGAAGAT
TCTATCGGGTATCAATTTAACAATAAAGGTTTGCTTGTGCAAGCTTTTGT
CCATCCATCATATACCTATCATTCCGGAGGCTGTTATCAGAGACTGGAGT
TTCTAGGAGATGCTGTGCTGGATTATCTAATCACTTCCTATCTCTATTCA
GTCTATCCAAACCTGAAGCCTGGCCAGCTGACCGATTTGAGATCCACATG
TGTCAACAATATTAGCTTTGCTAACATTGCAATACGTCGGTCATTCTATA
AATATATTATTTCCGAGTCTAGTGGCCTCTGCAAATCCATGGAGAAATAT
GTCATGTTTTCTAGAACCCATCAGCTTACTGGAAATTTAGTTGAAGCGCC
CCCATGCCCCAAAGCTCTTGGTGACATAGTGGAGTCATGTATCGGTGCCA
TTCTTCTGGACACGGGATTCAATTTAAACCATGTTTGGAAAACAATGCTC
TCCTTTCTCGATCCGGTCATTCACTTTTCCGGATTACAGCTTAATCCCAT
TCGAGAACTTCAAGAACTAAGTCAATCGTACAATATGGAATTGAAATTTG
CATCTTCAAAGAAGGATAATACTTATACTGTTGAAATAAAGGTGAATGGG
AAAGATGTTTGTGAACATTCTAGTGCTAGCAACTTCAGCAAAAAAGCTGC
CAAGAGAAGGGCTGCAAAGCAATTAATTCTGATTTTGAAGGAGCATGGTT
ACAAATCAAAGAGTAAATCGTTAGAGGAGGTTTTGAAGTTGACCCACAAG
ATGGAAGCAAAATTAATTGGTTACAATGAAGCACCAACAGATGTTAATGA
TCCATATGCCACAATTGCTTACAATGAAAAAACACCAACAGATGTTAGCG
CTCCATTTGCCACAATTGCTTACAATGAAAAAACACCAACAGACGTTAGC
GCTCCATTTGCCACAATTGGTTACAATGAAAAAACACCAACAGATGTTAG
CGCTCCATTTGCCACAATTGGTAACAATGAAACGCCAACAAATGTTAGCA
CTCCATATGCCAGAGGATTTGATATCTTGAAGGTGCAGGATTCCTGTACA
AGTGGTTCTTCATCATCCAAAGTAAATCCACTCGGTGTACAACTGCATAG
ATCTGGAGGCATCAAGATTAACCCAATTATGCAAAAATCATCTCTCTGTG
ACACTCGTGAATATCAGACAACAGACAAAAAAGATAGTGATAACTGCTCT
AGCGATTCTCAGAATCCAGGTCGTTCAGTGAAGAAGTCAGCAAAGTCACT
TTTGTTTGAAATTTGTGCGGCCAACGGTTGGAAACCACCTATATTTGTAT
GCTGCAAGGAGACAGGGGCAGATCACTTGAAAGAGTTTACTTTTACGGTG
ATCGTGAAGCCTGATAGTTTGGAAAAATGTTTCATTGAAGCAATCGGAAA
ACCAGCCGGTAAAAAGAAAGAAGCTGCAGAGCATGCAGCTGAAGGGGCTG
TTTGGCTGTTGCGAGAACGTTATGGAGTTTCAAAAGCCAAGCCGGGGTTG
TCTTACTTTGCTGATGCGGAAGGAACTGTTTGCCAAAAAGTTCTTCCTTC
CGACCCTCCAATTAGTCAAGTGTTGTGTGACACTCAATCTTCTCAGGAAG
CATGTAAGCAATTGCCTGAACAAGATGATGCAACTGAGGACCTGAAAACC
TCAACAGATTCTAATTGCCTTAATGATGATAATACCAGAAGAGAACTCGA
TAAAATTCTTGTCCCCACTGTACTTAAAGAGCAATGGAGTAATTCAGAGG
AAGTGTCATCTTTTCGTGACGCTCGTGAATGCCAGCTGATAGGAAAAAAA
GATGACAGCTGCTGTAGTGGTTCTGTGACTCCAGGTCATTCAATGAAGAA
GTCAGCAACGTCAATTTTGTTTGAATTCTGTGCTGCAAATCGTTGGAAAC
CGCCTCTATTTGTATGCTGCAAGGAGACGGGGGCCAGTCACTTGAAAGAG
TTCACATATAAGGTGATCGTGAAACCTGACAGTGTGGAAAAATGTATCAT
TGAAGCAATCGGAAGACCAGCAGGTAAAAAGAAAGAAGCTGCGGAGAATG
CAGCTAAAGGGGCTGTTTGGCTCTTGAAAGATCATCTTTTGTAGGTTGAA
ATCCATAAACATGCACTCTTAGATTGTCCAGTGAAAGTTGGTTTACTTGA
TAAGTGAATGCAGCTGTTTTAAACCTTCATCCATTTTGTTAGAAATTTCT
TGAGTAGTAAAATAGTAATGTTATGTGTGTCAGTAGCGGACCCAGGATTA
TACACGTTCGATATTTATTTTTTTCGACCAAAATATCAATTTTAGTACCT
GATTGTGCCGAAGACAATAGGCTGTAACATCGATTTCGTGGTTATAGTGC
ATGATCACTGTCAGACTATTTTTATTATTATTTGATATATTAGTTAAGAT
TTGTTTA
MASGDSNSEDHQDFDVKDPTLIAREYQTKLCQKALSENTIAYLGTGCGKT
HIAVLLIHEMRHLIKKPQNNICVFLAPSVALVEQQAKVIKDSIDVKVGIY
CGSSKHLKRHTYWEKELAQHEVLVMTPPVLLQNLSHCFIRIELIALLIFD
ECHHAQPESNHPYAEIMKVFYNTSATKLPRVFGMTASPILGKGASIRGLE
SLLHAKVYSVEDKEELERFVTPPKVSVYYYDTAADGPSSPLVYSSKLQAI
KSQCVSTLVENISDMDSLISSKKMLQKLHTNLCLCVEKLGVWGACQAAQI
LSKGDCLVQNELMEMEVQNSHVSICNSYLSQAAMIFLSDCKKDRTKEKLN
SPEVLEEPFFSKKLLQLINILTNFRSQQNMKCIIFVDRIVTAISLSSILQ
SLQFLSAWKSDFLVGVNSGLKRVSRKSTNALLAKFQSGEINLLVATKVGE
EGLDIQTCCLVVRFDLPETVASFIQSRGRARMPQSEYAFLVDSGNEKEQN
LIDSFTEAEDKMNEEIEFRTSTATFCDIEEKTYRVELTGATISSGSSISL
LYRYCSKLPHDEFFKPKLEFSYFDEADGTVCQIIFPSNAPIYQLSSAPQS
SKDAAKRDACLEACKQLHQLGALTHYLLPERDDENEDLESSSDSDCSDDE
DTRRELHEMLVPAVLKEPWSEAEDSVHLRSYFVKFRPHPPDRDYRPFGLF
VKASLPGDAERMKLDLHLARGRSVATELVPFRTLLFSRDQLALAEKFQEM
FLKVIIDRSQFCSEFVPLGRINSDILAPRTYYLMLPVICYEFEEAMVVDW
NLVMKCLSSPIFNMPEVAKANELPQPSEKLHLANGPKSVNDVVNSLIYVP
SKKLFYFVSDVLSEKNAYSDYKASKSHVHHFSERFGVHLLHPKQALLKAK
QLFSLENLLRKKGNLASHAEPREKEEHFVELPPEICELKIIGFSKDVGSS
LSLLPSVMHRLESLLVAVELKHLLSVSFPEGAEVSASRVLEALTTEKCNE
HFSLERLEVLGDAFLKYAVGRRLFVLHDALDEGQLTRKRSSVVNNSNLLK
LAIANRLQVYIRDQSFDPCQFFALGRPCSVVCKSETEKTIHSSQCSRAAN
LHMELRCTKSHHWLHKKTIADVVESLVGAFIVDSGFKGAAAFLNWMGIQV
EFEGSKVSHICSASSIYLPLAAQIDIAALEDSIGYQFNNKGLLVQAFVHP
SYTYHSGGCYQRLEFLGDAVLDYLITSYLYSVYPNLKPGQLTDLRSTCVN
NISFANIAIRRSFYKYIISESSGLCKSMEKYVMFSRTHQLTGNLVEAPPC
PKALGDIVESCIGAILLDTGFNLNHVWKTMLSFLDPVIHFSGLQLNPIRE
LQELSQSYNMELKFASSKKDNTYTVEIKVNGKDVCEHSSASNFSKKAAKR
RAAKQLILILKEHGYKSKSKSLEEVLKLTHKMEAKLIGYNEAPTDVNDPY
ATIAYNEKTPTDVSAPFATIAYNEKTPTDVSAPFATIGYNEKTPTDVSAP
FATIGNNETPTNVSTPYARGFDILKVQDSCTSGSSSSKVNPLGVQLHRSG
GIKINPIMQKSSLCDTREYQTTDKKDSDNCSSDSQNPGRSVKKSAKSLLF
EICAANGWKPPIFVCCKETGADHLKEFTFTVIVKPDSLEKCFIEAIGKPA
GKKKEAAEHAAEGAVWLLRERYGVSKAKPGLSYFADAEGTVCQKVLPSDP
PISQVLCDTQSSQEACKQLPEQDDATEDLKTSTDSNCLNDDNTRRELDKI
LVPTVLKEQWSNSEEVSSFRDARECQLIGKKDDSCCSGSVTPGHSMKKSA
TSILFEFCAANRWKPPLFVCCKETGASHLKEFTYKVIVKPDSVEKCIIEA
IGRPAGKKKEAAENAAKGAVWLLKDHLL
| Relationships |
|---|
| The mRNA, XM_017386100.1, is a part of gene, LOC108214228. |
| The polypeptide, XM_017386100.1, derives from mRNA, XM_017386100.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |