| 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. |
GTCACGTGCAAAACATATGTTTTGTACATAAACGTGTGTATATAAGTATA
TTTGTTCTCTTAGTATATTTGTTCCGCATTCACAGTCTTTCTTCTCCTGT
CTACTCCATCTCGAGTCAACCCAAGTCAAGCCCTCTCTCCGTTTAACCGC
CGACATGGCCTCCGGTGACTCCAACTCCGAGGATCATCAAGATTTTGATG
TGAAAGACCCCACACTCATTGCCAGAGAGTATCAGACAAAACTGTGTCAG
AAAGCTTTGAGTGAAAACACAATAGCCTATTTGGGAACTGGTTGTGGGAA
GACTCACATTGCTGTTCTATTAATTCATGAGATGCGACACTTGATAAAGA
AACCCCAGAATAACATATGTGTCTTTCTAGCTCCTTCAGTTGCTCTGGTT
GAGCAGCAAGCCAAAGTCATCAAGGACTCAATTGATGTTAAAGTTGGCAT
CTACTGTGGGAGTTCTAAGCATTTGAAGCGTCATACCTATTGGGAGAAAG
AATTAGCACAACATGAGGTTCTTGTCATGACCCCTCCAGTACTTCTCCAG
AATTTATCGCATTGCTTCATCAGGATTGAATTGATTGCGCTTCTAATTTT
TGATGAGTGCCATCATGCGCAACCTGAGAGCAATCATCCTTATGCTGAAA
TCATGAAGGTATTTTACAATACCAGTGCAACAAAGCTTCCTCGTGTATTT
GGTATGACCGCATCTCCAATATTGGGAAAAGGTGCTTCTATCCGTGGCCT
CGAGTCTTTACTACATGCTAAGGTTTATTCTGTTGAAGACAAGGAAGAAC
TCGAACGGTTTGTGACACCTCCCAAAGTTAGTGTATATTATTATGATACA
GCAGCAGATGGACCATCTTCCCCTCTAGTTTATTCTAGTAAACTGCAAGC
GATAAAATCCCAGTGTGTATCAACACTGGTAGAGAATATCAGCGACATGG
ATAGCCTAATAAGCTCCAAAAAGATGCTCCAGAAACTGCACACTAATCTG
TGTTTGTGTGTAGAGAAACTTGGTGTTTGGGGAGCATGTCAGGCTGCTCA
GATACTCTCAAAGGGTGACTGCCTTGTGCAAAATGAACTAATGGAGATGG
AAGTGCAGAATTCGCATGTCTCTATATGCAACAGCTATCTTTCTCAAGCT
GCCATGATATTTTTGTCGGATTGCAAAAAAGATCGAACCAAGGAGAAGTT
AAATTCACCAGAAGTCCTAGAGGAGCCCTTTTTCTCCAAAAAGCTCTTGC
AACTTATTAACATCCTTACCAATTTCAGGTCCCAGCAAAACATGAAATGT
ATAATTTTTGTCGATAGAATTGTAACTGCCATATCTTTGTCGTCTATACT
TCAAAGCCTTCAATTTCTATCAGCTTGGAAATCTGATTTTTTGGTCGGAG
TCAACTCTGGACTAAAGCGTGTGTCACGAAAATCTACTAACGCTTTGCTT
GCTAAATTTCAATCCGGTGAGATAAATCTATTGGTTGCAACTAAAGTTGG
GGAGGAAGGTCTTGATATTCAAACGTGCTGCCTTGTAGTAAGGTTTGATC
TTCCGGAAACTGTAGCCAGTTTCATACAATCTAGAGGACGTGCTCGCATG
CCTCAGTCAGAATATGCATTTCTGGTAGACAGTGGCAATGAGAAGGAGCA
AAATCTTATTGACAGTTTTACTGAAGCTGAGGATAAAATGAATGAAGAAA
TTGAATTCAGAACATCTACTGCCACTTTTTGTGATATTGAGGAGAAAACT
TATAGAGTAGAATTGACGGGAGCCACAATCAGTTCTGGAAGTAGCATTTC
ATTGCTTTACCGCTATTGTTCGAAACTTCCACATGATGAATTTTTTAAGC
CCAAGCTGGAGTTCTCATACTTCGATGAGGCAGATGGAACAGTCTGCCAG
ATAATTTTTCCCTCCAATGCTCCAATTTATCAACTGTCAAGTGCTCCTCA
ATCTTCTAAGGATGCAGCAAAGAGAGATGCGTGCTTGGAAGCATGTAAGC
AATTACATCAATTGGGTGCTCTAACCCACTATCTCTTGCCCGAACGAGAT
GATGAAAATGAGGACCTGGAATCTTCATCAGATTCAGATTGCTCTGATGA
CGAGGATACGAGAAGAGAATTGCATGAAATGCTTGTTCCTGCTGTCCTCA
AAGAGCCGTGGAGTGAGGCCGAGGATTCTGTCCACCTCAGGTCCTACTTT
GTGAAGTTTAGACCCCATCCACCAGATAGGGATTATAGACCATTTGGTCT
CTTTGTAAAAGCATCTCTTCCTGGAGATGCTGAAAGAATGAAACTAGACC
TTCATTTGGCACGTGGTAGATCTGTAGCAACAGAGCTTGTACCATTTAGA
ACTCTGCTATTTAGTAGAGATCAGCTAGCTTTGGCCGAGAAGTTTCAGGA
AATGTTCCTCAAGGTCATCATTGACAGATCACAGTTCTGTTCTGAATTTG
TTCCCTTGGGAAGAATTAATTCTGATATATTGGCTCCTAGAACATATTAC
CTCATGCTTCCTGTAATCTGCTATGAATTTGAGGAAGCAATGGTTGTGGA
CTGGAACCTTGTCATGAAATGTTTATCGTCGCCGATATTTAACATGCCAG
AAGTTGCTAAGGCTAATGAGCTTCCTCAACCCAGCGAGAAATTACATCTC
GCTAATGGTCCTAAAAGTGTCAATGATGTTGTGAATAGCTTGATTTATGT
ACCAAGCAAGAAATTGTTCTATTTTGTTTCTGATGTTTTGTCAGAGAAGA
ATGCATACAGTGACTATAAAGCATCAAAAAGTCACGTTCACCACTTCTCT
GAGAGGTTTGGCGTTCATCTTTTACATCCTAAACAAGCTCTTTTAAAAGC
AAAGCAGCTCTTTAGTCTGGAGAACTTACTACGAAAGAAAGGAAATTTGG
AACCACGAGAAAAAGAGGAGCACTTTGTTGAATTACCTCCTGAAATTTGT
GAATTAAAGATAATTGGGTTTTCGAAAGATGTTGGAAGTTCATTATCTTT
GTTACCATCAGTCATGCATCGTCTGGAAAGCTTGCTTGTTGCTGTTGAAC
TAAAACATTTACTTTCTGTCTCATTTCCTGAGGGAGCTGAAGTATCTGCT
TCTCGTGTCCTTGAAGCACTTACTACTGAGAAATGCAATGAACACTTCTC
TCTTGAAAGGCTCGAAGTTCTTGGTGATGCATTCCTCAAATATGCAGTTG
GCAGGCGTCTTTTTGTCTTGCATGATGCCCTAGATGAGGGACAGCTTACA
AGAAAACGTTCAAGTGTCGTCAATAACTCCAATTTACTGAAGCTAGCGAT
AGCAAACAGATTACAGGTATACATACGCGACCAATCATTTGACCCATGCC
AATTTTTCGCATTGGGTCGGCCTTGTTCAGTTGTTTGTAAATCTGAAACG
GAAAAGACTATCCATTCATCACAATGTAGTAGGGCTGCAAATCTCCATAT
GGAATTAAGATGCACTAAATCTCATCACTGGTTGCATAAGAAAACCATAG
CCGATGTTGTGGAATCTCTTGTCGGTGCATTTATAGTCGACAGTGGCTTC
AAAGGTGCAGCTGCTTTTCTTAATTGGATGGGTATACAAGTGGAATTTGA
AGGTTCGAAGGTTAGCCATATCTGTTCAGCAAGTTCAATCTATTTACCAC
TTGCTGCTCAAATAGATATAGCTGCTCTTGAAGATTCTATCGGGTATCAA
TTTAACAATAAAGGTTTGCTTGTGCAAGCTTTTGTCCATCCATCATATAC
CTATCATTCCGGAGGCTGTTATCAGAGACTGGAGTTTCTAGGAGATGCTG
TGCTGGATTATCTAATCACTTCCTATCTCTATTCAGTCTATCCAAACCTG
AAGCCTGGCCAGCTGACCGATTTGAGATCCACATGTGTCAACAATATTAG
CTTTGCTAACATTGCAATACGTCGGTCATTCTATAAATATATTATTTCCG
AGTCTAGTGGCCTCTGCAAATCCATGGAGAAATATGTCATGTTTTCTAGA
ACCCATCAGCTTACTGGAAATTTAGTTGAAGCGCCCCCATGCCCCAAAGC
TCTTGGTGACATAGTGGAGTCATGTATCGGTGCCATTCTTCTGGACACGG
GATTCAATTTAAACCATGTTTGGAAAACAATGCTCTCCTTTCTCGATCCG
GTCATTCACTTTTCCGGATTACAGCTTAATCCCATTCGAGAACTTCAAGA
ACTAAGTCAATCGTACAATATGGAATTGAAATTTGCATCTTCAAAGAAGG
ATAATACTTATACTGTTGAAATAAAGGTGAATGGGAAAGATGTTTGTGAA
CATTCTAGTGCTAGCAACTTCAGCAAAAAAGCTGCCAAGAGAAGGGCTGC
AAAGCAATTAATTCTGATTTTGAAGGAGCATGGTTACAAATCAAAGAGTA
AATCGTTAGAGGAGGTTTTGAAGTTGACCCACAAGATGGAAGCAAAATTA
ATTGGTTACAATGAAGCACCAACAGATGTTAATGATCCATATGCCACAAT
TGCTTACAATGAAAAAACACCAACAGATGTTAGCGCTCCATTTGCCACAA
TTGCTTACAATGAAAAAACACCAACAGACGTTAGCGCTCCATTTGCCACA
ATTGGTTACAATGAAAAAACACCAACAGATGTTAGCGCTCCATTTGCCAC
AATTGGTAACAATGAAACGCCAACAAATGTTAGCACTCCATATGCCAGAG
GATTTGATATCTTGAAGGTGCAGGATTCCTGTACAAGTGGTTCTTCATCA
TCCAAAGTAAATCCACTCGGTGTACAACTGCATAGATCTGGAGGCATCAA
GATTAACCCAATTATGCAAAAATCATCTCTCTGTGACACTCGTGAATATC
AGACAACAGACAAAAAAGATAGTGATAACTGCTCTAGCGATTCTCAGAAT
CCAGGTCGTTCAGTGAAGAAGTCAGCAAAGTCACTTTTGTTTGAAATTTG
TGCGGCCAACGGTTGGAAACCACCTATATTTGTATGCTGCAAGGAGACAG
GGGCAGATCACTTGAAAGAGTTTACTTTTACGGTGATCGTGAAGCCTGAT
AGTTTGGAAAAATGTTTCATTGAAGCAATCGGAAAACCAGCCGGTAAAAA
GAAAGAAGCTGCAGAGCATGCAGCTGAAGGGGCTGTTTGGCTGTTGCGAG
AACGTTATGGAGTTTCAAAAGCCAAGCCGGGGTTGTCTTACTTTGCTGAT
GCGGAAGGAACTGTTTGCCAAAAAGTTCTTCCTTCCGACCCTCCAATTAG
TCAAGTGTTGTGTGACACTCAATCTTCTCAGGAAGCATGTAAGCAATTGC
CTGAACAAGATGATGCAACTGAGGACCTGAAAACCTCAACAGATTCTAAT
TGCCTTAATGATGATAATACCAGAAGAGAACTCGATAAAATTCTTGTCCC
CACTGTACTTAAAGAGCAATGGAGTAATTCAGAGGAAGTGTCATCTTTTC
GTGACGCTCGTGAATGCCAGCTGATAGGAAAAAAAGATGACAGCTGCTGT
AGTGGTTCTGTGACTCCAGGTCATTCAATGAAGAAGTCAGCAACGTCAAT
TTTGTTTGAATTCTGTGCTGCAAATCGTTGGAAACCGCCTCTATTTGTAT
GCTGCAAGGAGACGGGGGCCAGTCACTTGAAAGAGTTCACATATAAGGTA
ATTGTGAAGCCTGATGGTTTGGAAAAATGTTTGATTGAAGCAATCGGAAA
ACCAGCTGGTAAGAAGAAAGAAGCTGCGACGCATGCAGCTGAAGGGGCTG
TTTGGTTGTTGCGAGAACATTTTGGAGTTTGTATGCCCAATCTAGAGTTA
TCATCCAAAGTGCATCCACTTGGTGGAGAACCGTATAGATCTGAAGGCAG
CAAGATCAAACAGACCGGGCAAATGTCGTCTTTTCATGAGACTCGCGAAT
GCCAGCAAATAGTAAAACAAGTCGATGATTGCCGCTCTAGTGATTCTCAG
ACTGCAGGTTGTTCAATGAAGAAGTCATCAAAATCACAATTGTTTGAAAT
CTGTGCTGCAAATCGTTGGAAACCACCTATTTTTGTATGCTGCAAGGAGA
CGGGGGCCAGTCACTTGAAAGAGTTCACATATAAGGTGATCGTGAAACCT
GACAGTGTGGAAAAATGTATCATTGAAGCAATCGGAAGACCAGCAGGTAA
AAAGAAAGAAGCTGCGGAGAATGCAGCTAAAGGGGCTGTTTGGCTCTTGA
AAGATCATCTTTTGTAGGTTGAAATCCATAAACATGCACTCTTAGATTGT
CCAGTGAAAGTTGGTTTACTTGATAAGTGAATGCAGCTGTTTTAAACCTT
CATCCATTTTGTTAGAAATTTCTTGAGTAGTAAAATAGTAATGTTATGTG
TGTCAGTAGCGGACCCAGGATTATACACGTTCGATATTTATTTTTTTCGA
CCAAAATATCAATTTTAGTACCTGATTGTGCCGAAGACAATAGGCTGTAA
CATCGATTTCGTGGTTATAGTGCATGATCACTGTCAGACTATTTTTATTA
TTATTTGATATATTAGTTAAGATTTGTTTA
MASGDSNSEDHQDFDVKDPTLIAREYQTKLCQKALSENTIAYLGTGCGKT
HIAVLLIHEMRHLIKKPQNNICVFLAPSVALVEQQAKVIKDSIDVKVGIY
CGSSKHLKRHTYWEKELAQHEVLVMTPPVLLQNLSHCFIRIELIALLIFD
ECHHAQPESNHPYAEIMKVFYNTSATKLPRVFGMTASPILGKGASIRGLE
SLLHAKVYSVEDKEELERFVTPPKVSVYYYDTAADGPSSPLVYSSKLQAI
KSQCVSTLVENISDMDSLISSKKMLQKLHTNLCLCVEKLGVWGACQAAQI
LSKGDCLVQNELMEMEVQNSHVSICNSYLSQAAMIFLSDCKKDRTKEKLN
SPEVLEEPFFSKKLLQLINILTNFRSQQNMKCIIFVDRIVTAISLSSILQ
SLQFLSAWKSDFLVGVNSGLKRVSRKSTNALLAKFQSGEINLLVATKVGE
EGLDIQTCCLVVRFDLPETVASFIQSRGRARMPQSEYAFLVDSGNEKEQN
LIDSFTEAEDKMNEEIEFRTSTATFCDIEEKTYRVELTGATISSGSSISL
LYRYCSKLPHDEFFKPKLEFSYFDEADGTVCQIIFPSNAPIYQLSSAPQS
SKDAAKRDACLEACKQLHQLGALTHYLLPERDDENEDLESSSDSDCSDDE
DTRRELHEMLVPAVLKEPWSEAEDSVHLRSYFVKFRPHPPDRDYRPFGLF
VKASLPGDAERMKLDLHLARGRSVATELVPFRTLLFSRDQLALAEKFQEM
FLKVIIDRSQFCSEFVPLGRINSDILAPRTYYLMLPVICYEFEEAMVVDW
NLVMKCLSSPIFNMPEVAKANELPQPSEKLHLANGPKSVNDVVNSLIYVP
SKKLFYFVSDVLSEKNAYSDYKASKSHVHHFSERFGVHLLHPKQALLKAK
QLFSLENLLRKKGNLEPREKEEHFVELPPEICELKIIGFSKDVGSSLSLL
PSVMHRLESLLVAVELKHLLSVSFPEGAEVSASRVLEALTTEKCNEHFSL
ERLEVLGDAFLKYAVGRRLFVLHDALDEGQLTRKRSSVVNNSNLLKLAIA
NRLQVYIRDQSFDPCQFFALGRPCSVVCKSETEKTIHSSQCSRAANLHME
LRCTKSHHWLHKKTIADVVESLVGAFIVDSGFKGAAAFLNWMGIQVEFEG
SKVSHICSASSIYLPLAAQIDIAALEDSIGYQFNNKGLLVQAFVHPSYTY
HSGGCYQRLEFLGDAVLDYLITSYLYSVYPNLKPGQLTDLRSTCVNNISF
ANIAIRRSFYKYIISESSGLCKSMEKYVMFSRTHQLTGNLVEAPPCPKAL
GDIVESCIGAILLDTGFNLNHVWKTMLSFLDPVIHFSGLQLNPIRELQEL
SQSYNMELKFASSKKDNTYTVEIKVNGKDVCEHSSASNFSKKAAKRRAAK
QLILILKEHGYKSKSKSLEEVLKLTHKMEAKLIGYNEAPTDVNDPYATIA
YNEKTPTDVSAPFATIAYNEKTPTDVSAPFATIGYNEKTPTDVSAPFATI
GNNETPTNVSTPYARGFDILKVQDSCTSGSSSSKVNPLGVQLHRSGGIKI
NPIMQKSSLCDTREYQTTDKKDSDNCSSDSQNPGRSVKKSAKSLLFEICA
ANGWKPPIFVCCKETGADHLKEFTFTVIVKPDSLEKCFIEAIGKPAGKKK
EAAEHAAEGAVWLLRERYGVSKAKPGLSYFADAEGTVCQKVLPSDPPISQ
VLCDTQSSQEACKQLPEQDDATEDLKTSTDSNCLNDDNTRRELDKILVPT
VLKEQWSNSEEVSSFRDARECQLIGKKDDSCCSGSVTPGHSMKKSATSIL
FEFCAANRWKPPLFVCCKETGASHLKEFTYKVIVKPDGLEKCLIEAIGKP
AGKKKEAATHAAEGAVWLLREHFGVCMPNLELSSKVHPLGGEPYRSEGSK
IKQTGQMSSFHETRECQQIVKQVDDCRSSDSQTAGCSMKKSSKSQLFEIC
AANRWKPPIFVCCKETGASHLKEFTYKVIVKPDSVEKCIIEAIGRPAGKK
KEAAENAAKGAVWLLKDHLL
| Relationships |
|---|
| The mRNA, XM_017386099.1, is a part of gene, LOC108214228. |
| The polypeptide, XM_017386099.1, derives from mRNA, XM_017386099.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |