| 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. |
AAACCAAACTGGTTCGTTAACTTTTTCAACTCTCTCTCTCCCAACTCTCG
CTACCCATCTCTCTCTCTCTCATATCCTTTCCCCAAACTATACGCACAAA
CAATCGTAAGTATATTTCTTATTTCTGATATCTAACCCGGCAGGGTTACA
AATCGATGGAGAACAGCACCAAATCATTCCTCCAAATCGATCTCAACGAA
GCTCCCCCGACCGTCTCATCTCCCCGCGACCCGCCCGGTCCAGCCCCCTC
CGGTCCGGTTCTCTGCGGTTCGTGCGGGAACCGCCAAGTACACGGAGAAA
TGCTGGTGTGTGTCAACTGTGGGAGAGGGTTTCACATGAAATGTATGGGG
ACTAAGAGGAGAAGCAGTGATTGGAAGTGTTTTAGCTGCTTGTTTGTCGG
AAAAGGCGGCGAGTCGTGTTCCGAGAGGTTTCGAGACGGTGGTGATGGCG
GAGGAGAGGGGCTTTTGGATATGAATGCGCCTCCGCCTGAGGAGGAGGAG
GAGGTGCAGTTTTTGAGAGCTCAGAGGACTGCTGGAGGGGTGCAGGCAGT
TTTTGATAAGTCAGGTCTTCGCCATCCATTTAATATTCCAGTTGCATATT
CACAATTTCAACATATTGGTAGCAGTATTCATGTTCACCAGGCTTCTCAA
TATGCGACAAAAGATGCTATGTCACTGTGTGAAGTTCCACTTCATTGCAG
ATGGAACCATAATGGAATGCCAAGTGATACAGATATGAGGTTCATGACTG
GTGCAAGACTTCAAAGTAGTCACTACGAACCACAAAAACTGCCTCCTACG
AGTGCAAATTATTTGTATTTACAAGATCTTAAAGATTTTGTTACTGAAAG
GAGAGGTGTATTAGGTGATGGTTGGCATGTTGAATTTCACTATTGCCCTG
TCAGATGCAAAACATCTGCAATATATTGTGCCCCAGATGGAAGAAAGTTT
GAGTCGATGTCGTCTGTTGCAGATTGTCTTGGGCTTGTACCTAGTGGACA
TGCATTAGAAGATGATAATAGAGGTAATGGAGTTCCTCCAGGACAAAAAA
GCCATAAAAGAAAGGAAGGTACCAGGTATTCGGGTGCCAAATATAGTAGA
GAAAATAAGATTGCTCGAAGGAGCATTCTTGGCGGGAAGTCCCCCCCTAG
CGCAGAGGTCGTAAGTGCTGATATCAGAAGATCAAACCAAAGCAAAAGGC
CGGAGCCTGACCAAAACAAGATTGATGACACTGAACATCAACATTTTTGT
GATGGTTTCCCAGTCCAGTTTGAAGACTTGTATATTATCCATGCAGGCAA
AGTTGATCTGCGAAATTTATATCATGACTCTGGGCACATATGGCCTGTAG
GTTACAAGTCTTGCTGGCATGACCGGATTACTGGATCTATTTTTGTCTGT
GAAGTTTTAGATGGTGGTGATGATGGCCCAGTTTTTAAGGTGCAAAGGTA
TCCATGCACCAAGCATCATATCCCTAGTAGCGCAACAGTCCTTCGGAAGC
AAAATGGGGAAAGTAGAGAGAAAAAAGATGATATGGCTTTAATGGATTTT
GATGACGATGAATGTACAAGTTTGCAAATGATATTAACAGAATGTAATCC
ACCATGTCTGGACAGCAGTATCTCATCAAGTTCCCCTTCTATTGCGGACT
CTGTTTCTCGTGAAGCGAATTGCACAATGCCTGGAATTAAAAATTCTAAT
GGCTTCGTGCGGGAGGATAGTATTGGAGAATTTTCGGTGGAAGCGAGGTC
ATCATTATCTGCATGGAAAATGGTCTCTGTAGTTTTTCTTGATGCTTGCT
GTGAGGCATATAAGCAAACAGGCGTTCTTGGATTTTGGTGTGAGCATGAT
ATGGATAAAACTGATGTGAAAGCAAGTGAAAATATAGGTTTGTTATCAAA
GTTCTCTTATAGTGCTGGTCCTATTAATACCCCACACTTAATTGAGAGTG
ATGAAGATTACAAGGTTTTTTCGGAGGTGCTGGTGAAGTGGGTGCAGCAG
GATAGATTTGGACTAGACCTTGAATTTGTTCAAGAGTTACTGGAACAGCT
TCCCGAGGCACGTTCTTGTTCAGATTATGTATCTTTGAATAAAAGAATTC
CAAAGTCAATGCTGCATACAGTTGGAAGTGGGTTTCTAATTTCAGAAAGG
ATATGTGATATGCCTGTCAAGAAACTATCAAACGGTTTTGTCCAAAGTTG
TGGAACTCCTAGAAAGAAGCTAAGTGAAGACACTGAAACAAAAACTCCTC
GTCCTTCAGGAAAACCTGTTAGCTCTAAGCTTCCTGCATATTTAATTGGT
GATGTTCTACAGGTTTGGGAATTCTTAAGGCGTTTCTCAGATATTTTAGG
ACTTGAGGAACCCGTTTCATTCCAGGAACTTGAGTGTGAACTTTTGAATC
CATGGTTAGATGATCTTAATCCTGCACAAGAGAATATTGCAAACCGATCA
AGGGATGATGAAGATGCCAATTCCTGCAGAAACTCTGTTACAGCAGTGAA
CGGGGAAACATCTGCATATAAACTCACTACTGATACTCATGGTAATTGTA
CTGGTATGATATTGACCACAGCTCATAGCTCACTGCTGAACTTGTTGATA
GGGGAGTTACTTGTCAGGGTTAAGCCATATGTGGATCCTGATTTTGATGC
TAGAGAAATTAAGTCAAAGCGAGGTAGGAAAAAAGATATCGAGAACTCAG
TTATTGCAAAGAAGTCAAAACTTGATATGCCTACAATTAATGACATCACA
TGGCCGGAGTTAGCTAGAAGATACGTTTTGGCTGTATTGTCCATGGAAGG
AAACCTGGACTCGACAGAGGTCATGTCCAGAGAGAGTGGAAAGGTATTCC
ATTGCTTACAAGGTGATGGTGGAATTCTTTGTGGTTCTCTTGCAGGAGTT
GCTGCAATAGAGGCAGATGCACTGCTTCTTGCAGAGGCCACTAAAAAAAT
CTTTGGTTCGTTGAAGAGTACAAATGATGTTTTTAGCGTAGATCAGAATG
ATTCTGATGCAGCAGATGCTTCAAACTTAACCACTAACAAAGATACTGAA
GTCCCCGACTGGGCGCAAGTGCTAGAACCCGTAAGAAAGCTACCTACCAA
TGTAGGAGCCAGAATTAGAAAGTGTGTAAATGAAGCCTTGGGAAAAGATC
CACCTGAATGGGCAAAGAAGATACTGGAGCATTCTATAAGCAAGGAAGTA
TACAAGGGAAATGCCTCCGGACCTACAAAGAGAGCAGTAGTGTCGGTGCT
TGAAGACCCTAGATGTGAGAGGCCACAGCCAAAACCAGAGACAAAAGAAA
AGGGGAAGACAGTTAGTATTATTTTATCAGATTTGGTAATGAAACAATGT
CGTCATGTTTTAAGGCATGCTGCAGCAGCAGACAAAGATGGGGTTTTTTG
CAATCTTTTGGGAAGAACACTTCTGAATTTGAATGATAATGATGACGAGG
GACTTCTCGGATATCCTGCAATGGTTTCTCGTCCTTTGGATTTTAGGACT
GTTGATCTGAGATTGGCTGCCGGAGCCTACGGTGGATCACATGAAGCTTT
TTTCGAGGATGTTCAAGAGGTGTGGTATAATATTCGTAAGGCATATGGAA
ACCATTCAGAATTGATTGATCTAGCTGAAACATTGTCCAGCAAATTTGAG
GACATGTATGAAGAAGAGGTTCTTACACTGGTCCACAAAATAAGGGAGAA
TGCTAATTCTCAAAGCGATGAAGACAAGAAAGAGTTAATTGATGTGCTTG
CGAGTGCAACTGAGTCCTTGCTTCCTAAAGCTCCCTGGGAAGAAGGAGTT
TGCAAAGTTTGTGGCATGGATAAAGATGATGTCAGTGTTCTGTTGTGTGA
TACATGTGATTCAGAATATCATACATACTGTTTAAATCCGCCGCTTGTGA
GAATTCCTGAGGGAAATTGGTACTGCCCTTCTTGTATTGCTGGAAAACGG
ATTTCTCATGGGGTTTCTTTTGGTACACAGATCAGCAATTTACACAGAAG
AAAGAGATATCAGAGGGATTTAACAAACAATTATTTGGATGCCCTGGTCA
ATATGGCAAACACAATGGAGATGAGAGAGTATTGGGAGTTCAGTGTGGAG
GAGAGGATTTTCCTTATCAAACTCTTGAGCGATGAGGTGCTCAACTCAGC
CATCTTCCGTGACCATCTTGACCGATGCGTCTCAGTTTCTGCTGATTTGC
AGCAAAAACTGCGTTCGTCTACCTCGGAATGGAATGTTTTGAAATACAAA
GAGGAGAGTTTGGCTGAAAGTCTGGCAGCACGAAGTATGGAGGTGCAACG
GAGTGAGTTGGATATATTATCTAAACAAAAGAGCCAGTCCATTTCAGAAA
GTTTGATGGAGAAAGCCTCTCCAAGTGGCATTCAAATTATAAAGGCAGCT
GATGCAAGCGATCTATTTCTTCATCAACATGGAAAGGGTCTGCCAGGTTC
TCATAATTGTTCCGTACAAGAACATCCTACTACAAAAAGTAATAGTGGAG
AGCATGGTCCCTCTATGTCTACTTGGCTTCACAATATCAATTCCACCGCA
GACAAAGCTCAGACCAATATGAACTTGCGGGGACAAGATTGTGGTGGTTG
TAATGGTTCTTCGCTATCTACTGGTAAAGTTTTTACAAGCCATATCTCAT
CCGACACCATTGACGCAGATCCAGCTGACAGTATATCTGATGTGAATGTC
TCAAAAGCCCCCGATCTAGAAGCTAGCTGTTCCCTGAAAACCGAGATTTC
TAATCTGCAGAACACAATTTCAACTCTGGAATCAGAGATGTTCAAGGCTT
CTGTTCGGAAACAGTGTCTTGGAAGGGATTCTGCTGGGAGATTGTATTGG
GTCTTTGGCTGCGGTAGTTCTCCACAAGCATTTGTTAATGGGAATTCGGT
AGCACAACGGAATAAAGTTCCTGAGTATGGGAGAGAAACTCAATGTGGTC
CATGCCTGAGGAATCCTGTTCTTGTAGTAGAGAGTCCTTCAAGCTCAAAA
GGAATAAGCTTTTCTAATATGCATCCATCTGAGCAAGTTATGCATAGTCC
AGAATCTTCTTCTTGGGCTTGTTATCAAAGTGATTCTGAAATTCAAGAGC
TCGTTGCATGGCTTGGAGATGATGCAAGAGAGAGAGAGCTAAGAGATTCT
ATTTTGTATTGGCAGCGGATGAAGCTCCATGATTCAGTTAATGTGAAAAA
TTATTTTCAAGGTCAGTATCAACCAATTTCCTTAAATTCTACCCTTAATG
ATAAACTTTTGGATTCTCACTTTCTGGTCTCAAAAGCATTGACCGTCCTA
GAAAAGAAGCTTGGTTCTCGCCTGGAATTGCAGACCAGTGATAATTTGAA
GCAGAAAAAACACAAAGTTGAGACATGTTTCCCTGGCAGAATTGACAGAT
GTGAGTGCTTGGAACTACTGTGGACCTCTAGACAGCACTGCCTCACATGT
CACAAAACGTTTGCAATCCCTGAGGATCTTGACAAGCACGCCAATGGAAC
ATGTAGCATGAGCGTGGCTGTCCCTGAGAGTAATAAGAATTCTTTAAAAC
ACAAAAGGATGAGAATGGAACCTTTACCAGAGAATAACTCTGATTTAAGA
AACGTCAAGGCATTAAAAGCCGAGAAACAAAATATTGCGTCATGTTTTGA
TGAGCAAAGAAATTTTGGATGTCCTTTTGACTTTGAAGAGATCAAAAGAA
AGTTTGTTACTCAAAACTCCCTCGCAGGATTGGTGAAAGATATAGGACTC
ATTGATTCTGCCGGGACCCCGTCATTTGTTCCACAAATAGCGCATTATCT
GGTCAGCCCTACCCTATCCTTGGTCCCTACAAGTTCACCAGGCCTATTTT
CAGAATTTGAAGATGGGCAGCGATTTTCAAAGAAAAGAATCAACAATGCA
ACTGGTATAAACTCTAGTCGTAGTTCTTATACCTCTAGAAACCCAGAGAA
TGGTATGGATCAAGAGCCATTGAAAGGTGGCAAATTACGTTTTAGGTGCA
TGACTGAATTGGATCAGTTTTCTGCTACTAAGAACATGCTTTGGGGTGGC
AAGGGGGCCATTCTTCATGAATCTTCACTAAGACCAATAGGAGGTAGGCC
TTCTGCAATTCTTAGGCAGCTCAAAATTAATTTGCTTGATATGGATGCTG
CATTACCTGAAGAAGCTTTAAGACCATCGAGGGCAAAGTCCGAGAAAAGA
TGTGTCTGGCGTGGATTTGTTAAATCTGCAGAGTCCATATATGAGATGAG
CCAAGCAACAATTGTACTAGAGGATATGATCAAGACAGACTACTTGAAAA
AAGATTGGTGGTATTGGTCATCACCTTCTGTTGCAGCTAAGATTTGTACA
ATTTCTGGTCTTGCTCTTCGCATATATGCGTTAGATGCAGCCATAATGTA
TGAGAAAAATCTCCCTGATCGGGATCCATCAGAGGGGTGCAAGTCCATGC
CTCCACAATCCAAGGATGTCAAATCAGATTCCTTAGACCTTCCTAGACTA
AGGAGTGGAAAAGCGAGATAAGAAAAGAGTCGTGTTCCTTCACGTCAAGT
GTAAAGACGTATAAACATTGAATGCCTTGTGCATTACGGAAAGATGCATA
TGCTGATACCTCCAAGTCGTCATTCCAAGCGTATGCTGGGAAGCTTTGGT
AGTACTCGACCTCAAAGAAAAGATTTTGTTGTCACGTATGGTTGCATGTT
TATATTGAGCAGAAGCCGAAAATAATTGGTGAATGGTTGAACAGAATTTA
CCCTTGCGGAGTAAACCTGTTCATTTTCTTAAACAGAAAGTTAACAAAAC
TGACAGCCAGCTAGATCTTCAGAATCTGCTGACAGTCCTCTACTTACTGT
GGCTGCTCCGGAACCTTACAATTTTGCATCAGACTAATCACAGCCGACAG
CTAGCTTCTTTTGAGTTGTTACCTCTTTCCTGTATTTTGTGTCCATACTT
AGTAGTAGAAAATCAACCTTCATATCGAAAAGAAAGTGTTTTTGTTCTGT
TTGTACAAACAGGGGCGACCGCCTAGCCAACCGAGCAGGGTATTATGTTT
CAGAATCAAGGCTTCTCGAGTTCATTTTACAATCCCTGGCTGGCCTCCAT
GGTAATCCTGCATTAAGTTTCGACATAGAATGAAATCTTGCAATCTTTAC
AGCGGACTACCTCTGTGGAAGCTTTCAAGCACAAATCCAAGTTCAAAGAG
CCTCTATTCTCGTTTGTAGTTTTTACTATTGGATGTTTTAAAAATCTATA
TAGATTGGCATATTGTAGACTGTCAACACTTTTATGAGAAATGTTCTGGC
CAGAAATAGTGTTATTATTCCTCGTACTCGAGGCCATTTCTGTCCGACAA
GTAAAAGTTTTGCCACAAACATTTAGACA
MENSTKSFLQIDLNEAPPTVSSPRDPPGPAPSGPVLCGSCGNRQVHGEML
VCVNCGRGFHMKCMGTKRRSSDWKCFSCLFVGKGGESCSERFRDGGDGGG
EGLLDMNAPPPEEEEEVQFLRAQRTAGGVQAVFDKSGLRHPFNIPVAYSQ
FQHIGSSIHVHQASQYATKDAMSLCEVPLHCRWNHNGMPSDTDMRFMTGA
RLQSSHYEPQKLPPTSANYLYLQDLKDFVTERRGVLGDGWHVEFHYCPVR
CKTSAIYCAPDGRKFESMSSVADCLGLVPSGHALEDDNRGNGVPPGQKSH
KRKEGTRYSGAKYSRENKIARRSILGGKSPPSAEVVSADIRRSNQSKRPE
PDQNKIDDTEHQHFCDGFPVQFEDLYIIHAGKVDLRNLYHDSGHIWPVGY
KSCWHDRITGSIFVCEVLDGGDDGPVFKVQRYPCTKHHIPSSATVLRKQN
GESREKKDDMALMDFDDDECTSLQMILTECNPPCLDSSISSSSPSIADSV
SREANCTMPGIKNSNGFVREDSIGEFSVEARSSLSAWKMVSVVFLDACCE
AYKQTGVLGFWCEHDMDKTDVKASENIGLLSKFSYSAGPINTPHLIESDE
DYKVFSEVLVKWVQQDRFGLDLEFVQELLEQLPEARSCSDYVSLNKRIPK
SMLHTVGSGFLISERICDMPVKKLSNGFVQSCGTPRKKLSEDTETKTPRP
SGKPVSSKLPAYLIGDVLQVWEFLRRFSDILGLEEPVSFQELECELLNPW
LDDLNPAQENIANRSRDDEDANSCRNSVTAVNGETSAYKLTTDTHGNCTG
MILTTAHSSLLNLLIGELLVRVKPYVDPDFDAREIKSKRGRKKDIENSVI
AKKSKLDMPTINDITWPELARRYVLAVLSMEGNLDSTEVMSRESGKVFHC
LQGDGGILCGSLAGVAAIEADALLLAEATKKIFGSLKSTNDVFSVDQNDS
DAADASNLTTNKDTEVPDWAQVLEPVRKLPTNVGARIRKCVNEALGKDPP
EWAKKILEHSISKEVYKGNASGPTKRAVVSVLEDPRCERPQPKPETKEKG
KTVSIILSDLVMKQCRHVLRHAAAADKDGVFCNLLGRTLLNLNDNDDEGL
LGYPAMVSRPLDFRTVDLRLAAGAYGGSHEAFFEDVQEVWYNIRKAYGNH
SELIDLAETLSSKFEDMYEEEVLTLVHKIRENANSQSDEDKKELIDVLAS
ATESLLPKAPWEEGVCKVCGMDKDDVSVLLCDTCDSEYHTYCLNPPLVRI
PEGNWYCPSCIAGKRISHGVSFGTQISNLHRRKRYQRDLTNNYLDALVNM
ANTMEMREYWEFSVEERIFLIKLLSDEVLNSAIFRDHLDRCVSVSADLQQ
KLRSSTSEWNVLKYKEESLAESLAARSMEVQRSELDILSKQKSQSISESL
MEKASPSGIQIIKAADASDLFLHQHGKGLPGSHNCSVQEHPTTKSNSGEH
GPSMSTWLHNINSTADKAQTNMNLRGQDCGGCNGSSLSTGKVFTSHISSD
TIDADPADSISDVNVSKAPDLEASCSLKTEISNLQNTISTLESEMFKASV
RKQCLGRDSAGRLYWVFGCGSSPQAFVNGNSVAQRNKVPEYGRETQCGPC
LRNPVLVVESPSSSKGISFSNMHPSEQVMHSPESSSWACYQSDSEIQELV
AWLGDDARERELRDSILYWQRMKLHDSVNVKNYFQGQYQPISLNSTLNDK
LLDSHFLVSKALTVLEKKLGSRLELQTSDNLKQKKHKVETCFPGRIDRCE
CLELLWTSRQHCLTCHKTFAIPEDLDKHANGTCSMSVAVPESNKNSLKHK
RMRMEPLPENNSDLRNVKALKAEKQNIASCFDEQRNFGCPFDFEEIKRKF
VTQNSLAGLVKDIGLIDSAGTPSFVPQIAHYLVSPTLSLVPTSSPGLFSE
FEDGQRFSKKRINNATGINSSRSSYTSRNPENGMDQEPLKGGKLRFRCMT
ELDQFSATKNMLWGGKGAILHESSLRPIGGRPSAILRQLKINLLDMDAAL
PEEALRPSRAKSEKRCVWRGFVKSAESIYEMSQATIVLEDMIKTDYLKKD
WWYWSSPSVAAKICTISGLALRIYALDAAIMYEKNLPDRDPSEGCKSMPP
QSKDVKSDSLDLPRLRSGKAR
| Relationships |
|---|
| The mRNA, XM_017370828.1, is a part of gene, LOC108202446. |
| The polypeptide, XM_017370828.1, derives from mRNA, XM_017370828.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |