| 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. |
CCCGGAAAATAAGTAACAGTCAATTTCTCTAAAACCCTTGTTAAGCCTCC
TCCGGCTTCTTCTAAACCCCAAAATGGCGCCTCCGGCAAAGAAATTTAAC
AATAACAAATCTGATAAAGCCTTCAAAAAGCCTCACAATCCGTCTTTCAA
ACGCAATAACGACGCCGTTTCGAAACCAGCTCCTCTTCCCCTAGACGACG
ACGTTCCTGACTTCCCGAGAGGTGGCGGAAGCTCACTGACGAGAGAGGAG
CGGAACGGAATTCGGGAGCAAGTCGATGCGGAGTTCGATTCCGAAGTTCG
AGATTCCAAGAGGAGGAAGAATAAGGTGCAGAGTAGAAGTTTTGGAGCGG
AGGATGATGAATTGGGATCGTTATTTGGTGAGGGACTTACCGGGAAATTA
CCGAGGTTTGCTAATAAAATTACCTTGAAGAATGTTTCTCCGGGAATGAA
GCTTTGGGGTGTAATTACTGAGGTGAATGAAAAAGATATTGTTATTGGTC
TGCCAGGGGGACTACGTGGGCTAGTTAATTCTTGTGAAGCACTTGATTCC
TTTTCAGATAATAAAGGAAGAGGGGAACCAGAAAGGAATATATTATGCAG
CATTTACCATACTGGACAGTTGGTTCCATGCATTGTGTTGAAATTGGACG
CTGACAAGAAAGACAATGGGAAACAAAAGCTGTGGCTTTCCTTGCGCCTG
TCTTTGCTGTACAAGAATTTAACATTAGATGCCATTCAAGATGGAATGGT
TCTTAGCGCGTATGTGAAAAGCATTGAAGACCATGGGTACATGCTTCATT
TTGGGCTGCCTTCATTTACAGGGTTTATGTCTGAAGAAATTCAGCCTGGA
AGAAGGGCTATTATGCACACTGGCAAACTCTTACAAGGAGTAGTTAAGAG
TGTTGATAGAAGTCGAAAAGTAGTTTATCTTTGTTCTGACAGTGATTTGA
TGTCTAAATGTTTGACTAGAGATATTAAGGGTATTTCAATTGATCATCTC
GTTCCTGGGATGATGGTCAATGCTCATGTGAAGTCAACCCTTGAGAATGG
CATATTGTTATCATTTCTTACATATTTTTCCGGAACAGTTGATATTTTTA
ATCTGGAGAATCCGTTCTGTAATTCAAAATGGAAAGAAGAGTACAATCAA
CATAAAAAGGTAAATGCTCGGATATTATTTGTTGATCCTTCAACAAGAGC
TGTTGGGTTGACTCTGAATCCCAATCTTATCCATAACAAAGCTCCACCTG
CACTTGTAAATGCAGGAGATATCTTTGATAATTCTAAGGTGATCAGGATT
GATAGAGGATTAGGCCTTCTTTTGGAAGTTCCCTCCTTACCAGTTCCAAC
TCCAGCGTATGTCCGTGTTTTCGATGTATCTGACAAAGAAATTCGCCAAT
TAGAGAAAAGTTTTAAGGAAGGAAGTCATGTTCGTGCTAGAGTTCTTGGG
TTCAGGCACCTGGAGGGCTTAGCTACTGGTGTTTTGAAGACTAGTGCTTT
TGAAGGGTCTGTCTTCACCCACTCCGATGTTAAGCCTGGTATGGTTGTCA
AGGGAAAAGTTATTGTCGTTGATAGTTTTGGTGCCATCGTACAACTTGCT
AGCGGGGTGAAGGCACTTTGTCCTCTACGTCATATGTCGGAACTCGACAT
AGCTAAGCCTAGAAAAAAGTTTCAGGTTGGAGCGGAACTAATCTTCCGTG
TTCTTGGTTGCAAGTCCAAAAGAATTACCGTTACTCACAAGAAAACACTT
GTTAAATCAAAGCTTGAAATCCTTTGCTCCTATGCTGATGCAACTGAAGG
ATTAATAACCCATGGATGGATAACGAAAATTGAGAAACATGGTTGTTTCG
TCAGATTTTACAATGGAGTGCAAGGGTTTGCTCCCAGATCTGAACTAGGG
TTGGATAAAGGGAGTGAAATAAGCTCGATCTATCATGTTGAGGAGGTGGT
GAAATGTAGAGTCATAAGTTCTCTTCCTGCTTCACGACGGATCAACCTTA
GTTTTATAATGTCGCCTTCAAGGATTTCCGAAGATGATGTGGTCAAACCA
GGAAGGCTCATTTCTGGTGTTGTTGAACGGGTTACTCCTAATTCAATTAT
AATTAGTAGTGACGTTAATGGTTACATGAAGGGCACTCTTTCTACTGAAC
ATCTAGCTGACAACCAAGGGCTTGCTGCCATAATGAAGTTAGCTTTGAAG
CCAGGATACCAGTTTGATCGACTCTTGGTCCTTGATGTTGAAAGCAGCAG
CCTGATTCTCACTGCTAAACATTCGCTCATTAATTCGAGCGACCAACTTC
CTCTGGATGTCAGTCAGATTCGCCCTCATTCAGTTGTCCATGGATATGTG
TGCAACATAATTGAAACGGGTTGCTTTGTCCGCTTTATGGGGCGCTTGAC
TGGTTTTGCTCCAAAAAGCAAGGCCACTGATGACTGGAGGGTTAATCTGT
CCACAGTATTTAATATTGGACAATCTGTTCGGAGTAACATACTTGAGATA
AATAGCGAAACTGGTAGAATGACACTATCTTTGAAGCAATTGATGTGCTC
CTCAACGGATGGGTCCTTTATTCAGGAGTATTTTATTTTGGAAGAAAAGA
TTGCAAAGCTGCAATCATTGAACTCGAATGGTTCGGAGTTGAAATGGGTT
GAAGAATTCAGTATTGGTAGCCTTATAGAGGGCGAGGTGCAAGAGACCAA
GAACATCGGAGCTGTTATCCGCTTTAAGAACCATGATGATGTTTTTGGCT
TTATAACTCCATATCAATTGGGTGGACATTCTGTGGAGATTGGATCCATT
GTTAAAGCTGTGGTTCTTGATATCTCCAAGATGGAACGCCTTGTGGATGT
ATCTTTGAAGCCAGATTTTGTTAATAGGTTAAAAGAGAGCACTTCTAGCC
TTAAATCTCAGAAAAAGAAACGCAAACGGGAAGCACACAAAGACATGGAG
TTGCACCAAGCTGTAAATGCAGTAGTTGAGATTGTAAAAGAGAATTATTT
GGTTCTTTCAATACCCGAGTATAACTTTGCCCTGGGTTATGCGTCTGTAA
AGGACTACAACACTCAGTTGTTGCCTCCTAAACACTTTGTTCCTGGACAA
AGTTTAAGTGCGACAGTAGTAGCTCTTCCAAGTCAATCAACAGCAGGAAG
ATTGTTGCTACTTCTTAACTCTATAAGTGAACAGAAGGAGACTTCCAGTT
CAAAGAGGGCGAAAAAAAAATTGAGTTATGATGTGGGAACCCTTGTTCAG
GCGGAGATTACTGAGATAAAGTCTCTTGAATTGAGAGTCAAATTTGGACC
TAGTTTGCATGGGAGAGTACACATAACTGAGGCAAATGATGATACTGTTG
AAGATCCATTTAGCAACTTTAAGGTTGGGCAGATGCTAACTACAAAGATT
GTCTCAAAGCCTAAGAAGTTAGAAAGTTCTAAGAAACTTTCTAATTGGGA
GCTTTCTATCAAACCTTCATTACTTGCAGTTGATACAGGGGCCCAAATTA
CTGCTGAAGAATTCAGTTATGTGATTGGCCAAAGTGTTGCGGGATTTGTG
TACAAGGTGGATACTGACTGGGTTTGGTTATCAATAACTCGTGATGTAAG
GGCTCGGCTGTATGTTCTTGACAGTGCATGTGAACCTCATGAGCTTCAGG
AATTTCAGAAGCGTTTTCATGTGGGTCAAGCTCTGAATGGCTACATTTTG
AGTACTGATAAGGAGAAAAAGATTTTACGTGTGGTGATGCAGCCGTTGGT
TGTTCCTGAGAAAGAAAATGGAGATGTATCGAACCCTACTTCGAGAGAAA
TTTCGGCTCATTTATGTGAAGGTCAGGCTGTTGGAGGCCGGATTTTTAAA
ATTTTACCGGGTATCGGTGGCCTGCTTGTGCAGATCGATCCTCACCTTTA
TGGTAAGGTTCATTACACAGAACTGACAGATGATTGGGTACCAGATCCAT
TATCTGGATATAGGGAAGGGCAATTTGTTACATGCAAAGTCCTAGAAATC
AGCCGCTCAGTTACAGGTACTACCCACATTGAGCTGTCACTACGTTCATC
TTCAGCCGGCATGGAGAGTCAGAAACCAGCTGAAATGGGGCAGCCTATTT
CTAAACGTGTGGAGAAATTGGAAGATATTCGTCCTAATGAAGCAGTGCAG
GGCTATGTTAAGAATGTTACACCCAAGGGATGTTTCATCATGCTATCACG
CAAGTTTGATGCAAGAATAATTATTTCAAATTTGTCTGATGGATTTGTTG
AAAATCCTGAAAGGCAGTTCCCAACTGGAATGCTCGTCAATGGGAAGGTA
ATATCTGTTGAGCCTCTGTCAATGCGAATTGAAGTCACTCTTAGGACAAG
CAACACACCGAAAGCCTCAAATAAAGGAATAGCTGATTCAAGCAGCCTTA
GTGTTGGAGATATCATTTCTGGGTATATAAGGGGTGTTGCCTCCTTTGGC
TTATTTATCTCTATTGATCAGACAAACTGTGTTGGACTGTGCCATCTTTC
ACAGCTTCCAGAGGAAAATAGTAAAGATATTGAAGCTAAATACAGAGTTG
GAGAGAGAGTTAGTGCGAAGATTTTGAAGGTGGACAAAGATAGAGACAGG
ATTTCTCTTGGGATGAAAGATTCAGACTTGAGTGATGATGCACATATCCA
GACACCTTTAAACCAAATGTCTGATGATGCTTCCGAGGAGAACCTTATGG
TAGAGGATGAACAAATAATGTCTAATGATGCTTCTGTAAAGGCTGTTATT
CTTTCTGAAGCGGAATCCAGGGCATCAGTCCTTTCTAAAGTGGAATCCAG
GGCCTCGGTCCTTCCCCTCGAGGTTGCTCTAGATGATGCAGAGAACTCCC
TTGTAAGTAGCAATGCAGATGGTCAAAGTCTTGAGAATGTTGATAACAAT
GACACCATGGAACAAAGGAACAAATTGGCAAAGAAAAAAGCAAAAAAAGA
GAGGAAAAGAGAAATTAGTGCTGCTGAGGAAAGACTGATCGAGGAAGATG
TACCGAGGACTCCTGATGAATTTGAGAAGCTAATTAGAAATTCCCCTAAT
AACAGCTTTCTCTGGATAAAATATATGGAGTTTATGATATCTTTATCTGA
TGTTGAGAAGGCCCGGTCAATTGCTGAAAGGGCCCTGAGAACAATCAACA
TCCGTGAAGAATCTGAAAAGCTAAATATCTGGGTTGCTTTTTTTAATCTT
GAGAATGAATATGGAAATCCGCCAGAGGATGCTGTAGCAAAAATTTTTCA
AAGAGCATTGCAGTATTGTGATCCTAAGAAAGTGCATTTAGCTTTACTTG
GTATGTATGAGAGAACCGAAAGACCAGAGCAGCAAAAGTTGGCTGATGAA
CTTATCGAGAAAATGGTGAAGAAGTTTAAACATTCTTGCAAGGTTTGGCT
TAGGCGAATTCAGATACTTCTAAAACAAAAACAGGATGGTGTTCAGCCCC
TTGTAAGTCGTGCTCTTATGAGCCTTCCTCGGCACAAGCATATAAAGTTC
ATCTCACAGGCAGCTATTCTTGAATTTAAAGGCGGAGTACCTGATAGAGG
ACGATCTATGTTTGAGGGAATGCTTAGGGAGTATCCAAAAAGGACAGATT
TGTGGAGCATTTATCTTGATCAAGAAATTCGACTCGGTGACATGGATGTC
ATCCGTTCATTATTCGAGAGAGCAATAAGTTTAAGCCTTCCACCAAAAAA
GATGAAGTTTTTGTTCAAGAAGTATCTGGAGTATGAGAAATCTCTTGGTC
ACGAAGAACGCATCGAATATGTAAAAAGAAAGGCAATGGAATATGTGGAT
AGCACCAGTGCTTGATACAATCATATATAACGAGAGGATTTGAGCAAGAG
CCAGCACAGGCAGGTTTCAAACAATTAAATTTTAACAGGAGGCAATGATG
TGTGGCGAGAACGCCCAAGCTTGATATCTTTATATAGACCGGAGGTGGCC
AATGATGGCTGAAATTTTGTACTGCCAAAATAGATGTGTTGTAATCTAAT
TGTATCACAGTCTATGATAATAAAGGTTTTTTTTCTTCCATAATTATGTA
TTTTATTCTTATTCTGTAAACAGCTTGTGTAATTATCCTGCTGGATCTTC
TAACTATATATTTGTACTTTTCTTCTTTGCCTAGAATCAGGCTTGCAAAG
GCAATGTTACTTCCA
MAPPAKKFNNNKSDKAFKKPHNPSFKRNNDAVSKPAPLPLDDDVPDFPRG
GGSSLTREERNGIREQVDAEFDSEVRDSKRRKNKVQSRSFGAEDDELGSL
FGEGLTGKLPRFANKITLKNVSPGMKLWGVITEVNEKDIVIGLPGGLRGL
VNSCEALDSFSDNKGRGEPERNILCSIYHTGQLVPCIVLKLDADKKDNGK
QKLWLSLRLSLLYKNLTLDAIQDGMVLSAYVKSIEDHGYMLHFGLPSFTG
FMSEEIQPGRRAIMHTGKLLQGVVKSVDRSRKVVYLCSDSDLMSKCLTRD
IKGISIDHLVPGMMVNAHVKSTLENGILLSFLTYFSGTVDIFNLENPFCN
SKWKEEYNQHKKVNARILFVDPSTRAVGLTLNPNLIHNKAPPALVNAGDI
FDNSKVIRIDRGLGLLLEVPSLPVPTPAYVRVFDVSDKEIRQLEKSFKEG
SHVRARVLGFRHLEGLATGVLKTSAFEGSVFTHSDVKPGMVVKGKVIVVD
SFGAIVQLASGVKALCPLRHMSELDIAKPRKKFQVGAELIFRVLGCKSKR
ITVTHKKTLVKSKLEILCSYADATEGLITHGWITKIEKHGCFVRFYNGVQ
GFAPRSELGLDKGSEISSIYHVEEVVKCRVISSLPASRRINLSFIMSPSR
ISEDDVVKPGRLISGVVERVTPNSIIISSDVNGYMKGTLSTEHLADNQGL
AAIMKLALKPGYQFDRLLVLDVESSSLILTAKHSLINSSDQLPLDVSQIR
PHSVVHGYVCNIIETGCFVRFMGRLTGFAPKSKATDDWRVNLSTVFNIGQ
SVRSNILEINSETGRMTLSLKQLMCSSTDGSFIQEYFILEEKIAKLQSLN
SNGSELKWVEEFSIGSLIEGEVQETKNIGAVIRFKNHDDVFGFITPYQLG
GHSVEIGSIVKAVVLDISKMERLVDVSLKPDFVNRLKESTSSLKSQKKKR
KREAHKDMELHQAVNAVVEIVKENYLVLSIPEYNFALGYASVKDYNTQLL
PPKHFVPGQSLSATVVALPSQSTAGRLLLLLNSISEQKETSSSKRAKKKL
SYDVGTLVQAEITEIKSLELRVKFGPSLHGRVHITEANDDTVEDPFSNFK
VGQMLTTKIVSKPKKLESSKKLSNWELSIKPSLLAVDTGAQITAEEFSYV
IGQSVAGFVYKVDTDWVWLSITRDVRARLYVLDSACEPHELQEFQKRFHV
GQALNGYILSTDKEKKILRVVMQPLVVPEKENGDVSNPTSREISAHLCEG
QAVGGRIFKILPGIGGLLVQIDPHLYGKVHYTELTDDWVPDPLSGYREGQ
FVTCKVLEISRSVTGTTHIELSLRSSSAGMESQKPAEMGQPISKRVEKLE
DIRPNEAVQGYVKNVTPKGCFIMLSRKFDARIIISNLSDGFVENPERQFP
TGMLVNGKVISVEPLSMRIEVTLRTSNTPKASNKGIADSSSLSVGDIISG
YIRGVASFGLFISIDQTNCVGLCHLSQLPEENSKDIEAKYRVGERVSAKI
LKVDKDRDRISLGMKDSDLSDDAHIQTPLNQMSDDASEENLMVEDEQIMS
NDASVKAVILSEAESRASVLSKVESRASVLPLEVALDDAENSLVSSNADG
QSLENVDNNDTMEQRNKLAKKKAKKERKREISAAEERLIEEDVPRTPDEF
EKLIRNSPNNSFLWIKYMEFMISLSDVEKARSIAERALRTINIREESEKL
NIWVAFFNLENEYGNPPEDAVAKIFQRALQYCDPKKVHLALLGMYERTER
PEQQKLADELIEKMVKKFKHSCKVWLRRIQILLKQKQDGVQPLVSRALMS
LPRHKHIKFISQAAILEFKGGVPDRGRSMFEGMLREYPKRTDLWSIYLDQ
EIRLGDMDVIRSLFERAISLSLPPKKMKFLFKKYLEYEKSLGHEERIEYV
KRKAMEYVDSTSA
| Relationships |
|---|
| The mRNA, XM_017396847.1, is a part of gene, LOC108222887. |
| The polypeptide, XM_017396847.1, derives from mRNA, XM_017396847.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |