| 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. |
ACAAACACGTTTCATTTACAAAAACCCTCACACAAACACACTATATATAA
ACACACAGTTGTACACCCTCCCAAAACCCTCTGAATCTTTCGGTTCTTGA
ATATACATACAAATACTTACACACCCTTTTCATATCTTGTTCTTTCTTGT
GAACTTGATGTGTTTTTCTTGCCAAAAAGTGTAAAAGATTGCAACTTTCT
TGGTGGGTTTTTTGTTTAACAATGGATGGAAGTGATATATACAATGCAAG
CAATAGTTTTAGAAAAAGTGGCAATCTTGGAAATCTTTCTTCAGTGTGGA
GGAATAATGGCATGGATGTTTTCTCAAAGTCATCAAGAAAAAGTGACTTT
TTTGATGATGAGGAGGCTCTGAAATGGGCTGCTCTGCAGAAGCTGCCTAC
TTATAATCGCCTGAGAAAAGGGCTTATTCTTGATCCTAGTGGGGAGGGTG
GACATGGGGTTCTTGAGGTTGATGTGGAGAGTCTTGATGTGCAGCAGAGA
AAGGAGTTGTTGGAGAGGCTGGTGAAGGTTTCTGAGGGTGAGAATGAGAA
GTTCTTGATGAGACTTAGGGAGAGGCTTGACAGAGTTGGGATTGCATTGC
CCCAAATTGAAGTTAGATTTGAGCATTTAAGTGTTGATGCAAAGGTTTAT
GTAGGGAGCAGGGCGTTGCCTACTTTCTTGAATTTTGTAGGGAATGTAAT
TGAGGGCTTTCTGAACTACCTCCACATACTACCAAATAGAAAGAAGGATT
TGTCTATACTTCGTGATATCAGTGGAATTGTCAAGCCTTGCAGAATGACA
TTGCTTCTTGGGCCGCCAAGTTCTGGCAAGACAACATTGCTGCTGGCTTT
GGCTGGAAAGCTTGATTCTGATCTTAAAACTTCTGGGAGTGTGACTTACA
ATGGTTATGGCATGCACGAATTCGTACCCCAGAGAACTGCTGCCTATATC
AGTCAATATGATTGCCATATAGGAGAGATGACTGTGAGAGAAACCTTTGC
TTTTTCTGCAAGGTGCCAGGGAGTCGGATCTCGCTATGAGATGCTAGCTG
AACTGTCAAGAAGAGAGAAAGAAGCAAACATTAAGCCCGATCCTGACATT
GATCTCTTTATGAAGGCTGCTGCAACTGAAGGACAAGAGGCCAGTGTGGT
TACAGATTATATTATAAAGCTTTTGGGACTAGAAATCTGTGCAGATACTG
TGGTTGGAAGTGAAATGATAAGGGGTATTTCTGGTGGACAAAGGAAGCGT
GTTACTACAGGTGAAATGTTGGTTGGACCATCAAACGCACTTTTTATGGA
TGAGATATCTACTGGTTTGGACAGTTCAACAACATATCAGATTGTAAATT
CACTACGCCATGCAGTCCACATTCTTCAAGGAACTGCTCTCATCTCCCTT
TTGCAGCCAGCCCCAGAAACTTATGATTTATTTGATGATATTATCCTCCT
ATCTGATGGCCTTATAGTTTACCAAGGTCCTCGAGAAAATGTGCTTGAAT
TTTTTGAATCAATGGGTTTCAAATGTCCAGAGAGGAAAGGAGTTGCAGAC
TTCTTGCAAGAAGTAACATCAAAACAGGATCAGAAGCAATACTGGTTGCA
TAAAGATGAACCTTACAGATATGTTACAGCCCAGGAATTTTCCGAAGCTT
ACCTATCATTCCATGTGGGGCGGAGACTCGGTGATGAACTTGGAACTCCA
TATCACAAGAGCAAAAGTCACCCAGCTGCTTTGACAACCAATAAGTATGG
TGTAAGAAAGATGGAGCTCTTAAAAGCATGTACCTCAAGGGAAATTTTGC
TTATGAAACGAAATGCATTCGTTTACATCTTCAAATCGGCCCAACTTTTC
ATTGTGGCATTGATTACGATGACATTATTCCTGAGAACTGAGATGCACAG
AGAATCACTAAATGATGGAAGCATATACATGGGTGCTTTGTTTTTTACCG
TAAGTACGATCATGTTTAACGGAATGGCCGAGCTGTCTATGACCATAGCA
AAGCTTCCTGTCTTTTATAAGCAAAGGGATCTTCTGTTTTTTCCCCCTTG
GGCGTATGCACTGCCTTCATGGATCATCAAAATCCCTATTTCATTTATTG
AAGCTTTCATCTGGGTACTTCTTACTTATTACGTTATTGGGTTAGATCCA
AATGCTGGAAGATTGTTTAAACAGTACCTGCTTTTAGTACTCATCAACCA
GATGGCTTCGGCATTGTTCCGGACTATTGCAGCAGCGGGAAGGAGTTTGA
TTGTTGCAAGCACGTTTGGTTCATTTGCATTGCTTATACTATTTGCACTT
GGGGGCTTCGTGTTGTCACGAGTTAACGTAAAGCAATGGTGGGTATGGGG
CTACTGGACATCGCCAATGATGTATGGGATGAATGCCATTGCAGTGAATG
AATTTCTTGGGCACCAGTGGAATCATGTTCTTCCTAACACTACAGAGCCA
CTAGGAGTCTTGATCTTGAAATCACGAGGGTTCTTCCCCTATGGATATTG
GTACTGGATAGGAGTTGGGGCATTGCTTGGATATATATTTCTTTTCAATT
TCTCCTTCACCCTGGCTCTGAATTTTCTTAACCCTCTTGGAAAGCCTCAA
GCTATTATACCAGCAGAAAGCTACAAAGGAAGAACTAAAGAGGGCGTTAA
TCAGCAGTCATTTAAAGATGGAAGTGATCATATGGCAAAAAATTCACCTC
CATTTTTATCTGCTAGAACAGAAGATACTGCGGAGGCTCATAACAAGAGG
AAAGGAATGGTTCTACCTTTTGAACCACACTCAATTACGTTTAACGAAAT
CAAATATTCTGTAGACATGCCTCAGGAAATGAAAGAGCAAGGTATAAGTG
AGGATAAGTTGATGCTCTTAAAAGGTGTGAGTGGTGCTTTCAGGCCCGGT
GTTCTTACTGCTTTAATGGGTGTAAGTGGTGCTGGAAAAACAACACTGAT
GGATGTACTGGCGGGTAGAAAAACAGGTGGATATATTGACGGTCATATTA
CAATATCTGGTTATCCAAAGAAACAAGAAACCTTTGCTCGGATATCTGGA
TACTGTGAACAGAATGACATTCACTCACCTCATGTTACTGTCTATGAATC
TTTGCTCTACTCAGCGTGGTTGCGACTGCCTATAGAAGTTGATTCGAGGA
GTAGAAAGATGTTTGTTGATGAGGTCATGGAACTTGTTGAACTAAACACT
TTGAAGGATGCACTTGTTGGCTTGCCAGGTGTAAGCGGACTATCGACCGA
GCAGCGCAAGAGACTAACTATTGCAGTTGAGCTGGTGGCAAACCCATCAA
TAATATTTATGGATGAGCCAACTTCAGGTCTGGATGCAAGAGCTGCTGCT
ATTGTTATGAGAACAGTGAGAAACACAGTAGACACAGGAAGAACAGTTGT
TTGCACCATCCATCAACCAAGCATAGACATTTTCGAAGCTTTCGATGAGT
TATTACTGATGAAACAAGGAGGGCTGGAGCTGTATGTTGGACCAGTGGGA
CGGCATTCTTGCGAGCTAATTAAGTACTTTGAGGAAATAGAAGGAATAAG
TAAAATCAGTGAGGGATATAATCCAGCCACCTGGATGTTGGAAATCACTA
GTCCTAAGCAAGAAATGATTCTTGGGATTGATTTCACTGAAGTGTATAAG
AATTCGGATCTGTACAGGAGAAACAAAGCTTTAATTACTGAATTAAGTAC
CCCTCGTCCGGGGTCAAGGGATTTAACTTTCTCTACTCAGTATGCTCAAT
CATTCCTTAGCCAGTTTGTAGCTTGTCTGTGGAAACAGAGAGCATCATAC
TGGCGGAATCCTTCCTACACTGCAGTCAGATTTCTCTTCACAACCTTCAT
AGCATTGATGTTTGGGACGATGTTCTGGGATCTTGGTACCAAGGGGAAAA
CTAGGCAAGATCTCTTCAATGCAATGGGATCTATGTATACTGCGGTTATC
TTTATTGGAATCCAAAATGCTTCATCGGTGCAGCCAGTAGTGGCTGTCGA
ACGGACAGTGTTTTACAGAGAGAGAGCTGCTGGAATGTACTCGTCTTTGG
CATATGCATTAGCTCAGGTTCTGGTAGAAATACCATACATTTTTGTGCAA
ACTGTGGTATATGGTGCTATTGTATACTCAATGATCGCATTTGAGTGGAC
AGCTGCAAAATTCCTATGGTACTTGTTCTTCATGTTTGCCACTTTATTGT
ACTTCACCTATTATGGCATGATGACCGTGGCTCTGACTCCCAACCCAAGC
ATCGCTGCTATTATAGCCGGTGCTTTTTACGGACTATGGAATTTATTTTC
CGGATTTATCATCCCCAGAACTAGGATGCCAATATGGTGGAGATGGTATT
ACTGGGCCTGCCCTGTCTCGTGGACACTGTATGGAATGCTGGCTTCTCAG
TTTGGAGACGTGCAGGATGTGCTGGTTGATGCAAATATCAGTGTCGCAGA
ATTTCTGGAAACATTCTTTGGATTTCACCACGACTTTGTTGGAGTTGTCG
CAGCTGTCGTCTCTGGTTTTGCACTTCTTTTTGCTTTCATTTTCGCGTAT
TCCATCAGAGTACTGAACTTCCAAAATCGATAGTCGTTACTCACCTGACT
GAGTTTAGGCAAAGTATGACAACCTCTTACATGGATATAGTTCAGATCAA
GTTTTGGTTACGAAATTCGCATTCTTTTTTTACATTTCAGAAACATCATT
CATGTCTCAGAGCTCAAGTCCTTGTAGACAATATTGTCTTCCTACATAAA
TATTTGCATGAAGTTCATTTGATAATCACAACATTAGACATTCTGGTATA
AATTTTTTGTTCTGAAATGTAATCAGATATCGAAATTTTTTGTTCAAGTT
MDGSDIYNASNSFRKSGNLGNLSSVWRNNGMDVFSKSSRKSDFFDDEEAL
KWAALQKLPTYNRLRKGLILDPSGEGGHGVLEVDVESLDVQQRKELLERL
VKVSEGENEKFLMRLRERLDRVGIALPQIEVRFEHLSVDAKVYVGSRALP
TFLNFVGNVIEGFLNYLHILPNRKKDLSILRDISGIVKPCRMTLLLGPPS
SGKTTLLLALAGKLDSDLKTSGSVTYNGYGMHEFVPQRTAAYISQYDCHI
GEMTVRETFAFSARCQGVGSRYEMLAELSRREKEANIKPDPDIDLFMKAA
ATEGQEASVVTDYIIKLLGLEICADTVVGSEMIRGISGGQRKRVTTGEML
VGPSNALFMDEISTGLDSSTTYQIVNSLRHAVHILQGTALISLLQPAPET
YDLFDDIILLSDGLIVYQGPRENVLEFFESMGFKCPERKGVADFLQEVTS
KQDQKQYWLHKDEPYRYVTAQEFSEAYLSFHVGRRLGDELGTPYHKSKSH
PAALTTNKYGVRKMELLKACTSREILLMKRNAFVYIFKSAQLFIVALITM
TLFLRTEMHRESLNDGSIYMGALFFTVSTIMFNGMAELSMTIAKLPVFYK
QRDLLFFPPWAYALPSWIIKIPISFIEAFIWVLLTYYVIGLDPNAGRLFK
QYLLLVLINQMASALFRTIAAAGRSLIVASTFGSFALLILFALGGFVLSR
VNVKQWWVWGYWTSPMMYGMNAIAVNEFLGHQWNHVLPNTTEPLGVLILK
SRGFFPYGYWYWIGVGALLGYIFLFNFSFTLALNFLNPLGKPQAIIPAES
YKGRTKEGVNQQSFKDGSDHMAKNSPPFLSARTEDTAEAHNKRKGMVLPF
EPHSITFNEIKYSVDMPQEMKEQGISEDKLMLLKGVSGAFRPGVLTALMG
VSGAGKTTLMDVLAGRKTGGYIDGHITISGYPKKQETFARISGYCEQNDI
HSPHVTVYESLLYSAWLRLPIEVDSRSRKMFVDEVMELVELNTLKDALVG
LPGVSGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVR
NTVDTGRTVVCTIHQPSIDIFEAFDELLLMKQGGLELYVGPVGRHSCELI
KYFEEIEGISKISEGYNPATWMLEITSPKQEMILGIDFTEVYKNSDLYRR
NKALITELSTPRPGSRDLTFSTQYAQSFLSQFVACLWKQRASYWRNPSYT
AVRFLFTTFIALMFGTMFWDLGTKGKTRQDLFNAMGSMYTAVIFIGIQNA
SSVQPVVAVERTVFYRERAAGMYSSLAYALAQVLVEIPYIFVQTVVYGAI
VYSMIAFEWTAAKFLWYLFFMFATLLYFTYYGMMTVALTPNPSIAAIIAG
AFYGLWNLFSGFIIPRTRMPIWWRWYYWACPVSWTLYGMLASQFGDVQDV
LVDANISVAEFLETFFGFHHDFVGVVAAVVSGFALLFAFIFAYSIRVLNF
QNR
| Relationships |
|---|
| The mRNA, XM_017359753.1, is a part of gene, LOC108193196. |
| The polypeptide, XM_017359753.1, derives from mRNA, XM_017359753.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |