| 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. |
CGACCGGATAACTAACCAAGACAAGTCAGTGGCGCCAATCAACGACGACG
ATGAGTAGTGTGTGCGTCTCTCTCCCTTTACCCGCGAAAACCCCCCTGAA
ACCAATTAACATAAACCCTAATTTCAAACCCCCCAATTTCGACGACAATC
TAATTCATCTAGCCAATACTGCCCAAATCCACAAAGCAATGCATTTAATA
ACAACCCATCAACACAAACTCACCCCAGACCTCAATACATACTCCACTCT
CCTCAAATCTTGCATTCGAACCCGTAATTTCGATCTCGGTAAGCTCCTAC
ACAACAATCTCATTAGTTCTGGTCTTGTATTTGATGATCATGTCATTATG
CTTAATTCACTTATTACTTTGTATTCTAAGTCTGGTGATTTAGTTACTGC
TAAATGTTTATTTGATAGTGTGGGGGATAGGAGGGACTTGGTATCGTGGA
GTGCGATAATTTCTGGTTTTGCACATAATGGGATGGAGAGGGAGAGTGTT
TGTATGTTTGTTGATATGATTAAGTCTGGGGAACGCCCGAATCAGTTTTG
TTTTTCGGGGGTTATTCATGCGTGTTGTAGTCGGGGGAATGTGGATGTTG
GGTTGGGGATATTTGGGTTCGTGATTAAGACGGGGTATTTTGAGGCTGAT
TTGTGTGTTGGGTGTGCTTTGATTGATTTGTTTGCCAAGGGGTTGAGTGA
TATGAAGTTGGCGAGGGTAGTGTTTGATCGAATGCCTGAAAGGAATGCGG
TTACTTGGACGTTGATGATTACTAGGTATGCGCAGATGGGTTTTTCAGGT
GATGCTTTGGAATTGTTTTTGAGTATGGTAGAGAATGGTTTTGTTGCTGA
TCGGTTTACTTTCAGTAGTGTTATTTCTGGGTGTGCTGAATTAGGATGGT
TAGATGTAGGTAAACAATTGCATTCTTTGGTGGTCAAATCTGGTTTGTCT
ACGGATGTTTGTGTCGGCTGTAGTTTGCTAGACATGTATGCAAAATCTGG
TGGATCTTTAATTGATTCAAGGAATGTGTTTAATAGGATGTCTGAACAAA
ATATCATGTCATGGACAGCAATGATTACTGGATATGTACTAAGTGGAGGA
TTTGATAGAGAAGCTATCGAGATGTACATTAAGATGATAGAAAGTCGGGT
ATTACCCAACGAGATCACATTTTCCAGCCTTCTTAAAGCATGTGGAAACC
TTGCTGATACGAAAGCAGGAGAGCAGATATACAGCAATGCTGTCAAGTTG
GGATTCTCATCTGTAAATTGTGTAGGAAATTCTCTTGTTAGTATGTATGC
TCGGTCGGGTAGTATTGAAGATGCTCAAAAAGCCTTTGAGATTTTGTTTG
AAAAGAACTTGATTTCTTACAACATACTTGTTGATGCCTATGCTAAGAAT
TTGAATTCAGATGAAGCCTTTGATATTTTTAATCAAATTGAGGATACTGA
AATTGGGGTTGATGCCTTTACGTATGCTAGTCTGTTGAGTGGAGCTGCAA
GTGTTGGTGCAGTTGGCAAGGGCGAGCAGCTCCATGCGCGGTTACTAAAA
TCTGGGTTCGAGTCTAACCAGTTTATCCGTAATGCTTTGATCTCTATGTA
CTCTAAATGTGGGAACATCGTAGCTGCATATCAAGTTTTTGATGACATGG
AAGATCGGAATGTAATATCTTGGACATCGATCATCACAGGTTTTGCAAAA
CATGGTTTAGCAAAAAGAGCTCGGGAAATGTTTGAACAAATGCTCCTAGC
TGGTGTTAAGCCGAATGATGTCACCTATGTTGCTGTTTTATCAGCCTGCA
GCCATGCAGGCTTGATGGATGAGGGATGGAAACACTTCAATAATATGTAC
AAAGAGCATGGAATAAATCCTAAGATGGAGCACTATGCATGCATAGTTGA
TTTATTAGGAAGATTGGGATATCTTGAAAGTGCAGTGCAGTTTATTGAGT
CAATGCCATACACTGCTGATCCTCTGGTCTGGCGAACATTGCTCGGAGCT
TGTCATGTTCATCGTAACACAGAGATAGGAAAATATGCTGCAGAAATGAT
TCTTAAGCAGGATCCAAGTGATCCAGCTGCTCATGTATTACTTTCTAATT
TGTATGCGTCGAAGAGTCAGTGGGATCATGTTACAGAGATAAGGAAAGGA
ATGAAACAGAGAAATGTGGTCAAGGAAGTGGGTTGTAGCTGGATAGAGAC
AGGAAACACGGTGCACAAGTTTTATGTAGGGGATACTTCTCATCCACAGG
CTCGGGATATATATGGACAACTAGATCAGTTGGCAGTTAAGATAAAAAAG
CTTGGATACATTCCAGATACGAATTTTGTTCTACATAATGTGGTAGAGGA
GCAGAAGGAGCAGTACTTGTTTCAACACAGTGAAAAAATTGCTGTAGCAT
TTGGTCTTATTAGCACAGCTAAACCAAAGCCCATTAGGATCTTCAAGAAT
TTACGTATCTGTGGAGACTGTCACACTGCAATGAAGTATATATCCTTAGC
AACTGGGAGAGACATAGTAGTTAGGGATTCAAACCGGTTTCATCATTTTG
TAGATGGATCGTGTTCCTGCAATGAATACTGGTGATAATTTGGTGCAGGA
TGAACAGTTTATTTTAATTGGCAAAGCAAGATGAGTTGATAAATCATAAG
GGCATCAGTATGACATGCAACTTTCTGCCAAATGTGACAGTACAACACTC
AAAGTCTCAAAGTGCCCTCAAAACAAGGGTTGATTTGCATTACATCTGTT
ATACCAGTGATGAGTTATGACTTATAAGTTGTTGGCTTCAATAAAAGTCT
ATGCATGAAAGATATTATGATGGCCGGTCATCTATGAGATCTAAACACTT
GTACAGGGCCCATAGTTCCCTGCTGAGGACTTGAGACTGTAGATCGGACC
TTTGCCACAGATGTCTAGCAGCCGCACAGACACCAAATGTAATGATAATG
AAAATAAAGGAACCAGAACTCCATATAAAAGGGTGTGTGTAATGACCCTA
TCTAACTCAGTTTTTTCATAAAATTATACTCAATTAATTGATGAGGATAA
GTCTACCTCAAGAATCTGTTAATATTGCTGGTCACCAGACAAAAATACTT
GAAGAAAAGAGTATATATTGCAGCTGATTTAATAGGAGCAACTCCAAGGT
AGTATCCCCACCTATATTTGACCAGCTGGACACTTTCAGGGATTTTGCTT
CAAAAAGCATTCTTCAACCATTCCCTCCCTTCAGGGATTTTGCTCCCCTA
TTTTTGCCAGGTCATCTCCCACAGTGCCACTATATTTCTCCCTTCCCGTC
TATTTTTCCTCTCTGTGTCTTCTTCTTCACTTCTGTGCATCAATTGTTTC
AGGACTTCTCCACATCAATTCATTTGATTTCTGAGGATTGCAGCGCATCA
CGATGAGAACAAAACATTTTCAAGTGACGGACTTCTTCGTTGTCTCATCA
GTGTTCCGTCATAAATACTTCTGTGTCCAAATTTATCAGGTATTTTAAGC
AATGGACATAAATCCAACCCTTTAAAAAAGAGTTACATTTGGTACATTGT
TGGATAGAGTCAGAAACTGCCTGAAATTTAGTGCTCCTGTTGCAAAAGAA
TCTGGGGAATCTCCGGGTATAGTCCAATATCTTTTGCCAGTGCTCGAAGT
CCATTTATTAGTAATCAGATCCCAGAAAGTGAAGAAAGATTAATAGACCA
ACGGGAAAAAAGAAGAAGCTGCAAAGTGTTTAAACAAGACGAAACATGAT
GCAAAGGTGATGGATTCATTAAAACTTCAAGACAAGTGAAAGATACCGTG
AGCATGTTGTCTGAAGTGAGAAATGAAACAATATAGCAGCTGATGATTGA
GCTCGAGAAAGAAAGGATAGAAGTAACAGGTTAAAAGAAAGCAGATGTTC
GTAAAATTACATTGAAATCAAACTTGTAACCGCATGGTCCGGGGAGGATA
AGATGTACGCAACCATGCCCTGGCTTCACAGTAAGGAGCTCTAATTTTAA
TACAAATACGATATTGGTTCGATTTAGATTGACTTTGACAAAA
MSSVCVSLPLPAKTPLKPININPNFKPPNFDDNLIHLANTAQIHKAMHLI
TTHQHKLTPDLNTYSTLLKSCIRTRNFDLGKLLHNNLISSGLVFDDHVIM
LNSLITLYSKSGDLVTAKCLFDSVGDRRDLVSWSAIISGFAHNGMERESV
CMFVDMIKSGERPNQFCFSGVIHACCSRGNVDVGLGIFGFVIKTGYFEAD
LCVGCALIDLFAKGLSDMKLARVVFDRMPERNAVTWTLMITRYAQMGFSG
DALELFLSMVENGFVADRFTFSSVISGCAELGWLDVGKQLHSLVVKSGLS
TDVCVGCSLLDMYAKSGGSLIDSRNVFNRMSEQNIMSWTAMITGYVLSGG
FDREAIEMYIKMIESRVLPNEITFSSLLKACGNLADTKAGEQIYSNAVKL
GFSSVNCVGNSLVSMYARSGSIEDAQKAFEILFEKNLISYNILVDAYAKN
LNSDEAFDIFNQIEDTEIGVDAFTYASLLSGAASVGAVGKGEQLHARLLK
SGFESNQFIRNALISMYSKCGNIVAAYQVFDDMEDRNVISWTSIITGFAK
HGLAKRAREMFEQMLLAGVKPNDVTYVAVLSACSHAGLMDEGWKHFNNMY
KEHGINPKMEHYACIVDLLGRLGYLESAVQFIESMPYTADPLVWRTLLGA
CHVHRNTEIGKYAAEMILKQDPSDPAAHVLLSNLYASKSQWDHVTEIRKG
MKQRNVVKEVGCSWIETGNTVHKFYVGDTSHPQARDIYGQLDQLAVKIKK
LGYIPDTNFVLHNVVEEQKEQYLFQHSEKIAVAFGLISTAKPKPIRIFKN
LRICGDCHTAMKYISLATGRDIVVRDSNRFHHFVDGSCSCNEYW
| Relationships |
|---|
| The mRNA, XM_017403430.1, is a part of gene, LOC108227988. |
| The polypeptide, XM_017403430.1, derives from mRNA, XM_017403430.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |