| 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. |
CATGTGAACGCGAGACAAGACTCACAACTCACAACAACTTAACTGATCAA
CTCTTCAAGCTCACGTGTCCTCTTGTTTCTCTGCGAATGCACCCACTCTT
CCTTTTATACACACACAACATAGAATTAAGACTGTTTGGTTTACTCCACC
TCTTCAACATCTCTCTCTTCCCCTCAGGCATTTCGTCATCAGAACTTGCA
GACAAGAGACATTAGATGGCCTGGGGAAACATATATACTCGGCGCGTGAA
AGTTTTCACGTTGGCTCTTGTAATGTACTTGGACTATAAGGCTTTGCAAA
AGAGAGAGAAATGGGTGAGTAAATCTAAACGAGATGCCTTGTGGGAAAAG
CTTCATGAGCGCAATGCAAAGCGAGTCCTGAAGGTTATAATTGAATTGGA
AGGAATGTGGGTGAAACTTGGACAGTACATGTCCACACGTGCCGATGTCC
TCCCGGATGCATATATACGCGTGCTTACGCAGTTGCAAGATTCTCTTCCC
CCTCGCCCTTTAAAAGTGGTTTGTGAGACCATACAGAAAGAATTGGGAAA
ATCAATGGGGGATCTGTTTCTAAATTTTGTTCAAGTTCCTCTGGCAACCG
CATCAATAGCCCAAGTTCATCGTGCGACCCTAACTGATGGACGGGAAGTG
GTTGTTAAAGTTCAGCATGAAGGCATCAAGGCAATTATCTTGGAGGACCT
GAAGAATGCAAAATCCATTGTTGACTGGATTGCGTGGGCAGAGCCGCAGT
ATGACTTTAACCCAGTTATCGATGAATGGTGCAAAGAAGCACCTAAAGAA
CTGGATTTTAATCGTGAAGCTGAGAATACGAGTTTAATATCCAGAAACCT
TGGTTGCAATGATCAACATGATGAGAAAGTGCCTGCTAATCACGTGGATG
TCTTAATTCCCGAAGTTATTCAGTCAACTGAAAGGGTCCTCATCCTCGAG
TATATGGATGGGGTTCGTTTAAATGACTTGGTATCACTTGAAAATTTGGG
TGTTGATAAGCAAAAACTTGTTGAAGAAATTACGCGTGCATATGCGCACC
AAATTTATGTGGGTGGTATATTCAATGGTGATCCTCATCCAGGGAATTTT
CTTGTCAGCAAAGAGCCTCCACATCGTCCAATTTTGCTTGATTTTGGTCT
TACTAAAGTTTTGACGAGTTCTATGAAACAAGGTTTAGCAAAAATGTTTC
TGTCATCTGTTGAGGGTGATCATGTGGCACTTCTGTCTGCTCTTGCGGAA
ATGGGATTTAGATTTCGAATGGACTTGCCAGATGAGGCAATGGATCTAAC
AGCTTTAATATTCCGTAATTCAGCACCTACCAGAGAAGAAGATGAACACT
TGAAATCTTACAAGGAGAAAGCAAAACTTAAGAAGGAAAGCTTGAAGCTC
AGTCAGAAAGAATCTCGTCGCTTTAATCCTGTTGATGCTTTTCCGGGTGA
TATTGTGATCTTCAGTCGGGTTCTCAATCTACTAAGAGGGCTTTCATCTA
TAATGAAGGTTCGCATAAATTATGTGGATATCATGAGGCCGTTTGCTGAA
TCTGTTTTACAATGCAATATTGATAATGGCCCGAGATTAAATGCGCAATG
GATATACAACACTCCTGTTCATTCTGATGTGGAGGCAAAATTGAGGAATT
TATTAGTTGAGCTGGGGAATGCTAATAAAATTCTTGGAATACAGGTATGT
GCCTACAAAGATGGGCGAGTGATTATTGACACTGCTGCTGGTGTGCTCGG
AAGATATGATCCTCGTCCTGTTCAACCTGATACCCTATTTAATGTGTTCT
CTGCAACAAAGGGTATCACAGCCGGAATGGTACATTGGCTTGTTGATAAT
AGAAAATTGAAGCTGGATGAAAATGTTGCAGATGTATGGCCAGAATTCCG
ATCAAACGGAAAAGATGGAATAAAGGTGCACCATGTCCTCAACCATACAT
CTGGTCTGCACAATGCTCTCTCTGATCTTAGTCGGGAAGATCCCTTATTA
CTGTGCAACTGGGATGAGTGCCTGAATCGCATTGCAGAGGCTGTCCCTGA
GGGCTCACCTGGACAACAGCAGCTATATCATTATCTCTCTTTTGGTTGGT
TATGTGGGGGAGTTGTTGAGCATGCATCCGGAAGAAAGTTTCAGGAGATT
CTGGAAGAAGCTTTTGTTCGGCCTCTTGGCATTGAAGGCGAGCTATATGT
TGGAATTCCTCCAGGTCTGGAAACTCGACTTGCGACACTTACAGTAGATA
CTGAGGATCTCAGCAAACTCTCTGGAATCGCTAGCCGTAACGACCTTCCT
TCAAGCTTTCAGCCAGGCGATATTCTTCAGATGCTTACTACCCTTCCAGC
CACATTCAATACACTTAATGTTCGCCGTGCCATCTTACCTGCTGCTAATG
GACACTGCTCTGCCCGTGCACTTGCTCGTTACTATGCAGCTCTTGCTGAT
GGTGGTGTCATCCCTCCACCACATTCCACTTCTTCCAAGCCACTGCTTGG
CAGCCACCCCCATATTCCAAAATTCAGTGCCAAGAAAATTGATAAGAAGT
CTAAAGGTCGCAAGAGCAAGGGAGCCTATGAAGCCTTGAGCACATCTGAT
AAGTCTGAACCGGTCACGACTGATGAACATACCATTAATCTTAATGGTAG
AGATGAAAGCCACATATCCATTGATTCTGTACCTACTGCTGGCAGTAGTC
GCAGCAGTAACAATAATAATATTACTAACACCAGTGCCACTGACCATCAT
GAATATGGTTCCAAGATATTTAATGATGAATCAATTCATGATGCATTCTT
AGGTGCTGGACAATACGAAAACATGATATTTCCAAACGGAAGTTTTGGAC
TTGGATTCAAGAGAATCAAGTCGAAGGATGGCTTCCTTATCGGCTTTGGG
CACTCGGGCATGGGAGGATCAACCGGCTTCTGCGACATGAACAACAGATT
TGCTGTCTCGGTTACAGTAAACAAGATGTCATTTGGGAGTGTTACTGCTG
CTATCATCAAGTTTATTTGTTCAGAACTAAACCTTCCAGTTCCTGTAGAA
TATTCTGGATCAGGAGGACCTGATATCTCAGCAAGTTTGGAGAAGCCGAT
TATAAATTAAGGAAAATTTTCTTCTCTTAGGCTACTGTAACGATATGTAT
ACACATGGGCATGACCCTAAATTCATCATAGAGGAGCTTTAAGCTTGATA
CTCTATACACAGGTACATAGGAATACTACACAATCCAGATTACTTCTTGT
AGCACATTGTAGAATGTTGTTAACGTTGTAACGATGTGCATAAAATTTCA
TAGGCTTGATATTTCATCTGTTTCCTGATGATTTGCTCA
MAWGNIYTRRVKVFTLALVMYLDYKALQKREKWVSKSKRDALWEKLHERN
AKRVLKVIIELEGMWVKLGQYMSTRADVLPDAYIRVLTQLQDSLPPRPLK
VVCETIQKELGKSMGDLFLNFVQVPLATASIAQVHRATLTDGREVVVKVQ
HEGIKAIILEDLKNAKSIVDWIAWAEPQYDFNPVIDEWCKEAPKELDFNR
EAENTSLISRNLGCNDQHDEKVPANHVDVLIPEVIQSTERVLILEYMDGV
RLNDLVSLENLGVDKQKLVEEITRAYAHQIYVGGIFNGDPHPGNFLVSKE
PPHRPILLDFGLTKVLTSSMKQGLAKMFLSSVEGDHVALLSALAEMGFRF
RMDLPDEAMDLTALIFRNSAPTREEDEHLKSYKEKAKLKKESLKLSQKES
RRFNPVDAFPGDIVIFSRVLNLLRGLSSIMKVRINYVDIMRPFAESVLQC
NIDNGPRLNAQWIYNTPVHSDVEAKLRNLLVELGNANKILGIQVCAYKDG
RVIIDTAAGVLGRYDPRPVQPDTLFNVFSATKGITAGMVHWLVDNRKLKL
DENVADVWPEFRSNGKDGIKVHHVLNHTSGLHNALSDLSREDPLLLCNWD
ECLNRIAEAVPEGSPGQQQLYHYLSFGWLCGGVVEHASGRKFQEILEEAF
VRPLGIEGELYVGIPPGLETRLATLTVDTEDLSKLSGIASRNDLPSSFQP
GDILQMLTTLPATFNTLNVRRAILPAANGHCSARALARYYAALADGGVIP
PPHSTSSKPLLGSHPHIPKFSAKKIDKKSKGRKSKGAYEALSTSDKSEPV
TTDEHTINLNGRDESHISIDSVPTAGSSRSSNNNNITNTSATDHHEYGSK
IFNDESIHDAFLGAGQYENMIFPNGSFGLGFKRIKSKDGFLIGFGHSGMG
GSTGFCDMNNRFAVSVTVNKMSFGSVTAAIIKFICSELNLPVPVEYSGSG
GPDISASLEKPIIN
| Relationships |
|---|
| The mRNA, XM_017373544.1, is a part of gene, LOC108204211. |
| The polypeptide, XM_017373544.1, derives from mRNA, XM_017373544.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |