| 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. |
TATCATTTGAGAGATCTAAAAGAGGCAACCCGATTCCTCAACCCGTTTGG
TGGCAAAGTCCATAGCATATAATCCCAAATTCATTCCCCTTCTTCTCCTC
GTTCTCTCTCTAATACTAATATATATAGGTTTTTATGCTCTTCGTATACT
CTGTGTGTTGATATTTATTAATTCTATTCAATCGAGGGCTAGGGTTTAGA
AAGCTTCTATCTCTTTAATTTGATGGAGGAAAACGATGATAATCTATCCA
ATAAATCTCGGCTTATTGATATTGATGATACAGTAGATACGCTAGAGCCC
AAAGAATGCGATGTGGCTGGTGAAAAAAGCAGCGATTTTGAGTGTGTTGG
TCGTGAAATTGAAGAAGCTGAGGCTTCGATTCCTGTGACCGAATCGGAAA
ATCTGTCTGAGAATTGTGTGGAGCTGGAAATTGATGGTAAGTTTAGTGAC
GGCGTGGAGGTGGAAGCCGGGGAATTGGAAAGGAAGGATGAGTTGAGTGG
TGAAATAGAGGTTAGTGGGGTCGGTGTGGATGCGAGTGGAATTGAGGTAA
GAGATGATAAGGATGATGAAATTGAGGGAGAAGTTTTGTATGATACTGTG
CGAGGAGATGATAAGAATGATGAATTAGAGGGAGAAGTTGTGGCGGAGAA
GAAAGATGAATTACAGGGTAATTATGGGTGTCAGGTTGCGAAAGAGGGGG
AGGTAGAAGGTAATGGTGTCGACGAGGGAGAGATATTGGGGGATAATGAT
CAGGTGGAAGATAAAGATGTTTGTGAGGATGGTTTTGACGATAAGCAAAA
TGTTTGCGTGCAGGTAGTGGCGGAAAAGAAAGATGAATTGGAGGTTGAAG
GTGGTATGAATGTGGGAGAAGAAGCGGGGGATAAAGTTGTGCCCGAGAGT
GAGATAAAAGATGAGGCTGGGGTTGAATTACAGGCAGGGGCTGTATGTGA
GGAAGTGAAAGCGGAGGAGCTTAAAGGTGATTGCGGAACTGAGGTAGTCG
GGGAAGCTCTGTGTGAGGTTGGCAATGAGGCTGAGAACAAAAGTGAGATT
GAGACTGAGATGAAAGTGAGTCGGGAGCCTGTTAAGAATGTTGATGATAT
GGTGGAGGAGGAGAAAGTGGAAATGGGATATGTCTCGAGTCAGTCTCTGA
ATGAAGTGGAGGAAAGGGCTGCTAATATTGAGGATAATGCAGAACATAGT
TCCGGTTTAATTGGTCTTGCCGAAGATACAGTCATGGAGGAAAAGAATTT
GGTAATGGAAAGTGTAAACAAGAAAAGAGATGATGAGTTGGATTCTGCTC
CAGAGTCTGATGATGAAGAAGATATAATGGAAACTGGAAGAGAATACGAT
GAGGATAAATTTGAAGGAGAGGTTCCTCAACCAGATGGTGATTCACAGTT
GGCTGAAGATGAAGAAGATATAATGGAAACTGAAAGAGAATTTGATGAGG
ATAAATTTGAAGGAGAGGTTCCTCAACCAGATGGCGATTCACAGTTGGCT
GAAGATGAAGAAGATGAAAGATTGGTGGGGGACGAGGAGATTCCCGCTGC
CGATGTTGAAATGGAAACAGAAACTGATGCAGGTGAATTAGTGAAGATCA
GTGGAGGGAAGCGGAAGAGAGGAAAGAATACAAAAGCTGCAGGAAAAGCT
CAACCACTCAATATGGTCGGACTTCCGGTTGAGGAGGAGGATGTTTGTTT
TGTTTGCTTTGATGGTGGAGACCTCGTGCTGTGCGACCGAAAGAACTGCC
CTAAAGCATACCATGCTTCTTGTGTTAATCGTAATGAGAAATTCTTTCAA
GCCAAGGGTCGTTGGAATTGTGGTTGGCATCAGTGCAGCCATACAAACTG
TCAGAAAAATGCATACTATATGTGCTATACATGTACTTTTTCCTTGTGCA
AAGGATGTATTAAGGATGCAGTCATATTATGTGTTAGAGGAAACAAAGGC
TTTTGCGAAGCTTGCATTAAAATTGTGATGATGATTGAAGATAATGCACA
AGGAAGTCAGGCACAAATTGATTTTGATGACAAGTCTAGCTGGGAGTACC
TCTTCAAGGATTACTGGATAGATCTTAAAGAAAGTCTGTCTATTTCTCCA
GTTGAAATTGCTAAGGCTAAAAACCCATGGAAAGGATCTGCTTTAGGGGC
TAGCAAAAATGAGTCTCCTGGGGAGCAGCTTGACACAAAGGATGATGTTG
GTGTTGGAACTGATAATGCCTCTGATAATCCTGAAGCGAGTAAGCCTAAA
AAAAGAAAGTACAGTAAACGTCTAAAGTCTCGTGCTACTAAGCAAGATGA
GTCGACAAGTGAAGCAATAACAGCTGGCGCGGAAAGAAAGTCTACACCTA
AAAGCACCGAATGGGCATCAAAAGAGCTTTTAGAATTTGTTATGCACATG
AGAGATGGGGATAGAACTGTTCTATCTCAGTTTGATGTTCAGGCCCTATT
GCTTGAATACATAAAAACAAATAAACTTCGTGATCCTCGTCGAAAAAGTC
AAATCATTTGTGATGCTAGGCTTGAAAATATATTTGGAAAAGCTCGTGTG
GGACATTTTGAAATGTTAAAACTTCTTGAATCTCACTTTTTAATGAAGGA
GGATACACAGATAGATGATGTTCAAGGTAGTGTTGTTGATACTGAAACCA
ACCATGTTGATGCTGATGGGAACATTGAATGTGTGATAAAAAGTGGGAAG
GATAGGAAACGTAAAACACGGAAGAAAGATGGCCGGGAACGTCAATCTAA
TCTTGATGATTATGCTGCCATTGATATTCATAACATTAGCTTAATATACC
TAAGAAGGAAGTTGATGGAGGATCTACTGGAAGATATTGAAACCTTTAGT
GACAAGGTGGTTGATACTTTTGTGAGGATAAGAATTTCTGGTAGTAATCA
GAAGCAAGACATATATAGGCTAGTCCAAGTCAAAGGTACGACCAAAGTAG
ACGACTTCTATAAAGTTGGCAAGCGGACAACTAATCTGATGATAGAAATT
TTAAATCTTAACAAGAAGGAGGTTATATCGATTGATAGCATTTCAAATCA
GGAGTTCACGGAGGACGAATGCAAACGTTTACGCCAGAGTATAAAGTGTG
GGTTCATCGCGCCCATGACGGTGGGTGCCATTCAAGACAAGGCCATGGAA
GTCCAGGTTGCAAGAGTAAATGATTGGCTTGAATCAGAAGTACAGCGGCT
TACTCATCTTCGTGATAGAGCAAGCGATTTAGGCAAAAAGAAGCAACTCA
GAGAGTGTGTAGAGAGTTTACAGCTTCTGAGGACCCCTGAAGAGCGTAGG
CGTAGACTAGAAGATATTCCTGAGATACATGCAGACCCAAAGATGGACCC
TGAATTTGTGTCGGAAGATAATGATAGTGAAATTGACAGTAGTAAACAAG
AAATATATACGAGGCCCAGAGGTTCTGGGTTTAGCAGGAGAGGAAGGGAG
CCCATATCTCCTGGAAGTGGTGATGCGAAAGAATCCTGGACTGGTAGCAG
GAGAAGTTCTGGTAAAGGTTGGGAACTTAACAGAAATTTGTCGGATAAGA
ATCTTGCAAATACAGTTGAAGATGCTCCTCTTAGTATTGGAGTATCTGCT
GATAACTCATGGAATAATGGTAGAGGCAGCGAGACAGAAAAACCTATTAT
ATTGGAGAAGCCAAATTCAGTTACAAGTTCTGAAGCTTTTGGATTTAATA
GAAATTCTGCTGCTAGATCTGATTCATCCTCTCATGTACAATCACAAAAG
TCTCCTGCATCTTTGCTTGCTCCAGTTGCTACAGCTCCATTGAACATCAG
TGAAATAGACAAGATATGGCATTACCAGGATCCACATGGAAAAGTTCAAG
GCCCGTTTTCTATGGCTCAGTTACGTAAATGGAGCAATACCGGATACTTT
CCCTCTGATCTCAGAATATGGAGTAGTTCTGGAAATAAAGATGATTCTTT
GCTTTTGACTGATGCATTGGCTGGGAAGTTTCAAAAGCTGCTCCCAGACA
ATGGGATTCCAAATAGTAATAACCTGCATAATCCTCATCTCCCACCCTTG
CACTCTTTACATCAAGGGCGGGAGGTTCAAGATGCCGAGAAATTGAACTC
TGATCAGAACCATTTTACCATGGATTCAAATATTAATTCAGCATCAAGGA
ATTGGGCTGCTCATTCAGTTGAGATCCCACTACTTTCTGCAGACGGGACA
AATTCTAATCATAATGGCAGAAACAATTTGGTAAATCTCCCTTCCCCTAC
CCCAAAACAAAGGTCTTCTGGGGAAGCGGGCCGTCCTATTGGTGGCGTCT
CTCTACCTGGTAGCATTGAAGCCTTGCAGTCACCTGCGGCAGCTACCCCA
GATAGTACCAGGAACTTGATGCTGGCATCTGAGAAAACTCCTTCAATTTC
TCATCCTGCTTTTGGGGCATCACCTAACCCTGAACAGGGTAATCTTCTAG
GCTCAACTATATCTCTTCCAAATCCTCAGTCAACTGTGGCTTCATTGCAT
GGAGGGCAGAATGTCAGCCATCCGTTTATTGCACCTGAAACTAATGCTAA
TATCGTGCAGTCTGTCACTGCTAACAACCCTGCACTTGGAACGCAGAATT
GGGCTGGTGCCCCTACCCAGAGTTTGGAAGCAAATTCTTCGATTCAAGCA
TCCACCCAACAGCCGGTGTACGCTCAGTGGAGTGGGGTTCAATCAACTCC
TGTGCAGAATCCATCTATAAATTTTCCAGTGCAAGGTGTCCCGCAGGTAC
CAAACTCCTGGAGGCCTCCAATGCAAACTAATCAAACTAACATGCAGCCT
AATGTCCAGTGGGGAACGGGAATTGCAGACAACAGTGCTTCTCAGAACTT
GCAACCTGATAATCCAAATTCTGGTTGGGCTTCAATGCAAGTAAGTCCGA
ATATAGGATGGTCAGGACCTAATCCAAACATGAACTGGATGGCTAGTGTT
CAAGGGGCACAACCTGGGAATCTGAATGCCGGCTGGGTTATACCCGGTGG
AAGTTCAGGAGTTGGTTTTCAAGGGGCAGTTCCTGGAAACATAAATTCAG
GTTGGGTTCCTCAACCTGGCAATGCCGTTGGCGTTGTACAAATGCTTGGT
CCGATGAATGCAAATCAAGGCTGGTATTCAAATATGGCAGCCAGCACTCA
AGGTGCAGCCCCTGGAAACGGAAATGCAGGTTTGGCGGCACCCATCTCGA
ATCTAGGATCTAATGTTCAGGGACAAATGCCAGGAAATGCAAATACAGGC
TGGTCAGCACCATCAGGAAATGCAAATCAGGGTTGGGGCCCGCTAGCAGG
GAATCAAGGGAACAACAGAAGCCAGCACCATCGCATTGGTGATAAGTTCT
CTAGTCAAAAGGATCAGGGTTCTCAACCAGGTAGAAATTGGAACAAGCCG
TCATCATTTGGAGGTGGAGGTGGAGGTCCTAGACATGGCGGCTCTAGAGG
AATATGCTATATGTTCCAGGACACAGGGCATTGCAAGAGAGGAGATTCTT
GCAGTTTCCGGCACTCATTATGAAATTTCATAGTATATGTGATAGGGATC
ATGTACATTAAATTTCAGTTTAGTGGGGCTTCCAACTCTGTTTCTGATAG
GTTTTTTGTTTTACAAAACTAGAACTTTGTGTGCTATAGCAGCAAATATC
AACGCCCCCTCGTTTTGTAGTAGCTTAGTTTTAAGTTGACCGGTCTTTAG
TACATTGGATTTTAAAAGATGCAATAACCAGTTGATTACTGCTAGGTAGT
TTTGTCTAA
MEENDDNLSNKSRLIDIDDTVDTLEPKECDVAGEKSSDFECVGREIEEAE
ASIPVTESENLSENCVELEIDGKFSDGVEVEAGELERKDELSGEIEVSGV
GVDASGIEVRDDKDDEIEGEVLYDTVRGDDKNDELEGEVVAEKKDELQGN
YGCQVAKEGEVEGNGVDEGEILGDNDQVEDKDVCEDGFDDKQNVCVQVVA
EKKDELEVEGGMNVGEEAGDKVVPESEIKDEAGVELQAGAVCEEVKAEEL
KGDCGTEVVGEALCEVGNEAENKSEIETEMKVSREPVKNVDDMVEEEKVE
MGYVSSQSLNEVEERAANIEDNAEHSSGLIGLAEDTVMEEKNLVMESVNK
KRDDELDSAPESDDEEDIMETGREYDEDKFEGEVPQPDGDSQLAEDEEDI
METEREFDEDKFEGEVPQPDGDSQLAEDEEDERLVGDEEIPAADVEMETE
TDAGELVKISGGKRKRGKNTKAAGKAQPLNMVGLPVEEEDVCFVCFDGGD
LVLCDRKNCPKAYHASCVNRNEKFFQAKGRWNCGWHQCSHTNCQKNAYYM
CYTCTFSLCKGCIKDAVILCVRGNKGFCEACIKIVMMIEDNAQGSQAQID
FDDKSSWEYLFKDYWIDLKESLSISPVEIAKAKNPWKGSALGASKNESPG
EQLDTKDDVGVGTDNASDNPEASKPKKRKYSKRLKSRATKQDESTSEAIT
AGAERKSTPKSTEWASKELLEFVMHMRDGDRTVLSQFDVQALLLEYIKTN
KLRDPRRKSQIICDARLENIFGKARVGHFEMLKLLESHFLMKEDTQIDDV
QGSVVDTETNHVDADGNIECVIKSGKDRKRKTRKKDGRERQSNLDDYAAI
DIHNISLIYLRRKLMEDLLEDIETFSDKVVDTFVRIRISGSNQKQDIYRL
VQVKGTTKVDDFYKVGKRTTNLMIEILNLNKKEVISIDSISNQEFTEDEC
KRLRQSIKCGFIAPMTVGAIQDKAMEVQVARVNDWLESEVQRLTHLRDRA
SDLGKKKQLRECVESLQLLRTPEERRRRLEDIPEIHADPKMDPEFVSEDN
DSEIDSSKQEIYTRPRGSGFSRRGREPISPGSGDAKESWTGSRRSSGKGW
ELNRNLSDKNLANTVEDAPLSIGVSADNSWNNGRGSETEKPIILEKPNSV
TSSEAFGFNRNSAARSDSSSHVQSQKSPASLLAPVATAPLNISEIDKIWH
YQDPHGKVQGPFSMAQLRKWSNTGYFPSDLRIWSSSGNKDDSLLLTDALA
GKFQKLLPDNGIPNSNNLHNPHLPPLHSLHQGREVQDAEKLNSDQNHFTM
DSNINSASRNWAAHSVEIPLLSADGTNSNHNGRNNLVNLPSPTPKQRSSG
EAGRPIGGVSLPGSIEALQSPAAATPDSTRNLMLASEKTPSISHPAFGAS
PNPEQGNLLGSTISLPNPQSTVASLHGGQNVSHPFIAPETNANIVQSVTA
NNPALGTQNWAGAPTQSLEANSSIQASTQQPVYAQWSGVQSTPVQNPSIN
FPVQGVPQVPNSWRPPMQTNQTNMQPNVQWGTGIADNSASQNLQPDNPNS
GWASMQVSPNIGWSGPNPNMNWMASVQGAQPGNLNAGWVIPGGSSGVGFQ
GAVPGNINSGWVPQPGNAVGVVQMLGPMNANQGWYSNMAASTQGAAPGNG
NAGLAAPISNLGSNVQGQMPGNANTGWSAPSGNANQGWGPLAGNQGNNRS
QHHRIGDKFSSQKDQGSQPGRNWNKPSSFGGGGGGPRHGGSRGICYMFQD
TGHCKRGDSCSFRHSL
| Relationships |
|---|
| The mRNA, XM_017402255.1, is a part of gene, LOC108227217. |
| The polypeptide, XM_017402255.1, derives from mRNA, XM_017402255.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |