| 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. |
CTTGGGGGAGGGGATCCAAATTTCGCAAAGCTGGCGGCTACACTAGCTTG
GAGAGGAGTTGCTGCCAGTAATGGCACCAACCTCTCTGCTAATGATGTGG
AAAGAAACGGGGATGCTAAGTCTCATGATCAAGAGCCTTTAACTCCAGTT
CCATTCATCAAGAAGGGTTCGAGAGAGCGCAGTAGCATGGAGGATCCAGA
TGGGACATTAGCTAGTGTTGCTCAGTGCATTGAGCAATTGCGCCAGAGTT
CCCCATCTTTACAAGAAAAAGAGTTATCCTTGAAGAAATTATTGGAGCTT
ATTGATACACGTGAAAATGCTTTCAGTGCTGTTGGATCACATTCGCAGGC
AGTTCCAGTACTGGTATCTCTTCTTAGATCAGGATCACTTGGGGTAAAAA
TACAGTCTGCTACAGTTTTAGGATCACTGTGCAAAGAGAATGAACTACGG
ATTAAGGTATTGCTGGGGGGTTGCATTCCACCACTTCTTGGTCTTCTCAG
GTCCAGCTCAGCAGAAGGTCAGGTCGCTGCAGCGAAGACTATATTTGCTG
TTTCTCAAGGTGGCGCCAAGGATCATGTTGGCTCAAAGATATTTTCAACT
GAAGGCGTTGTGCCAGTTCTATGGGGGCAACTTGAGAAGGGACTTAAGGC
TGGAAATGTTGTTGATAACTTGCTGACCGGAGCTTTGAAAAACCTCTGCA
GCAGCACTGAGGGTTTTTGGCCTGCAACAATACAAGCTGGGGGGCTAGAT
ACACTTGTAAAGTTGCTTGCAGATGGACAGTCTAGCACCCAAGCAAATGT
TTGCTTTCTCCTTGCATGTATGATGATGGAGGATGCATCTGTTTGTCCCA
AAATCTTGGCTGCTGATACTACAAAGAAACTCCTTAAGCTACTGAGTCCT
GGAAACGAAGCTTCAGTTAGAGCCGAAGCTGCTGGTGCTTTAAAATCTCT
CTCAGCTCAGTGCAAAGAAGCAAGGCGGGATATCACCAGTTCTAATGGTA
TACCTGCTTTGATAAATGCTACAATCGCTCCTTCAAAAGAATATATGCAA
GGTGAGTATGCACAAGCTTTGCAGGAGAATGCAATGTGTGCCCTTGCAAA
CATATCTGGTGGCTTGTCATATGTTATCTCAAGCCTTGGTCAAAGCCTTG
AATCGTGCACGTCACCTGCACAAGTAGCTGACACATTAGGGGCATTAGCT
TCTGCACTAATGATTTATGACAGCAAAGCAGAAACTACAAGAGCTTCGGA
TCCTGATGATATTGAGCAGACTCTGGTGAAGCAGTTCAAACCTAGTTTGC
CATTTCTTCTGCAAGAGCGTACCATAGAAGCTCTTGCCAGTTTATATGGA
AATGCCACGCTCTCTGGAAAGCTTGCAAATTCAGATGCAAAACGCTTGCT
AGTTGGTTTGATCACCATGGCAAGTGACGAAATTCAGGATGAGTTGGTGA
GATCTCTTCTCATATTGTGCAACAATGAAGGCACACTATGGCATGCCCTT
CAGGGACGCGAGGGAATTCAGCTTTTGATATCTCTTCTTGGGCTGTCATC
AGAGCAACAGCAGGAATGTGCTGTTGCATTACTCTCCCTTTTATCGAATG
AGAATGATGAAAGCAAGTGGGCAATTACAGCTGCAGGAGGTATTCCTCCG
CTTGTTCAAATATTAGAGACAGGATCCCCAAGAGCGAAGGAAGATTCCGC
AACAATCCTTGGAAACCTCTGTAATCACAGTGAAGATATAAGAGCATGTG
TTGAAAGTGCTGATGCTGTTCCTGCTTTGCTTTGGCTACTGAAAAATGGG
AGCTCCAATGGTAAAGAAATTGCTGCAAAGACATTAAATCACTTGATCCA
CAAATCAGATACAGCAACCATTAGTCAGCTTACTGCATTACTTACAAGCG
ATCTACCAGAATCTAAAGTTTATGTTTTAGATGCGTTAAAAAGTTTACTT
TCTGTGGCCCCCCTCAGTGACATGGTGCGTGATGGCAGTGCTTCCAATGA
TGCTATTGAGACAATGATTAGAATATTAAATTCTACCAGAGATGAAACAC
AGTCTAAGTCTGCGTCAGCCCTTGCTGGTATATTTTCTTTTAGAAAGGAC
TTGCGTGAAAGTAGCATTGCAGTTCAGACTGCCTGGGCAGTCATGAAACT
TTTACATGTAGACTCCGAGAACATTTTAGTGGAGTCCCTTCGTTGCCTTG
CTGCAATATTTCTATCAATTAAGCAGAATCGCAATATGGCTGTAGTTGCA
AGAGATGCATTGCCTGCATTACAGGTTCTTGCGGCCTCGTCTGTTCTGCA
AGTTGCAGAGCAGGCCATATGTGCACTTGCAAACCTTCTCTTGGATAGTG
AAGTTTCAAAGAACGCCACGCCTGAAGAGATTATCTTGCCTGCTACTCGG
GTATTGCATGAAGGCACAACTGCTGGAAGGAGCCATGCAGCAGCAGCAAT
TGCTCGGCTTCTCAATTCTCGCAAGATCGATAATGAGATTACTGATTGTG
TGAACCGCACCGGAACAGTTCTTGCATTGGTTTCTTTCCTAGAATCAGAA
AAGACAGGGTCTGCAGCCTTATTGGAGGGATTAGAAGCACTAGTTATTAT
ATCAAAATTTGAAGGTGATAAAGGAAAGATCAAACCTGCATGGGCAGCTC
TAGCTGAATACCCAGATAGCATAAGCCCTATTGTGTCGTGCATTACTGAT
GCAAATCCCTTGTTGCTTGATAAGGCTATAGAGATATTGTCACGGCTATC
TTTGGCTCAACCGGTTGTTTTGGGGAAGGAAATTGTTAATGCCTCGGAAT
GTATATCATCTATTGCTAGGAGGGTAGTTAGTTCTTCAAAGGAAACAGTC
AAGATTGGAGGAACTACGCTTCTTGTTTGTGCTGCCAAAGTGAATCTTCA
GAGAGTTGTGGATTATTTAAATGAATCAAATTCGTGTGCATATCTCATTC
AGTCTCTTGTAGGAATGCTGATCTGTACAGAAAATTCTCAGGTTGAAGGC
CAAGTCAATAAGGAAGGGGTAAATATTCTTAGGTATGCTGAAGAACTAAG
AAGCAGTGGGAATGAGACAAGTACATATGTCATCTATGGTTCAAACACCG
CCATTTGGCTTCTCTCTGCTCTTGCTAGTAACAGTGAAAAGAGTAGAACT
CTGATAATGGAAGCAGGCGCCATTGAAGTTCTCACTGATAGAATCTCACA
GTGTTTGTCAGAATATACTCAGGATTCTGAAGAGGAAAGTAGCATATGGA
TCTGTGCTTTATTGCTAGCAATTTTATTTCAGGACAGAGATATCATACGT
GCACATGCAACAATGAAAGCTGTACCTGTACTAGCTAACTTGTTGAAGTT
AGAGGAGTCAGCAAACAGATATTTTGCTGCACAAGCCATTGCCAGTTTAG
TATGTAATGGCAGCAGGGGGACTCTACTATCAGTCGCAAATTCAGGGGCA
GCAGGTGGACTCATTTCCTTGCTTGGGTGTGCTGATGCTGATATATGTGA
TTTGCTTGACCTGGCAGAGGAATTTTCCTTGGTCCGTTATCCGGAACAAG
TTTCTCTTGAGCGGTTGTTTAGGGTCGATGACATTAAAGTTGGTGCAACC
TCGAGAAAAGCTATACCGGCACTAGTTGATTTACTTAAGCCAATTCCTGA
TCGTCCAGGGGCACCATTCTTATCATTAGGGCTTCTTCTTCAGCTTGGAA
AAGATTGCCCTTCAAATAAAATTCTTATGGTAGAAGCTGGAGCTCTGGAA
GCACTGACCAAATATCTGTCACTTGGCTTGCAAGATGCAATTGAAGAAGC
AGCTACGGATTTGTTAGGTATGTTATTTAGTACTGCTGAGATATGTAGAC
ATGAAGCTGCATCTAGTGCTGTGGGCCAACTTGTTGCAGTATTGCGTTTG
GGTGGGAGAGGAGCAAGGTATAGTGCTGCTAAAGCATTGGAAAGCCTGTT
TTCTGCTGACCATATTAGGAATGCAGAATCTGCCAGGCAGGCTGTGCAAC
CTTTAGTGGAAATTCTTAATAAGGGTTTGGAGAAAGAGCAACATGCTGCT
ATTGCTGCATTAGCTAGGTTACTGGGTGACAACCCATCAAGAGCCTTGGC
AGTTGTAGATGTTGAAATGAATGCGGTGGATGTTCTTTGCAGGATTCTTT
CGTCTAACTGTTCGATGGAGCTGAAAGGGGACTCTGCTGAGTTATGCTGT
GTACTTTTTGGAAATACAAAAATTAGATCCACAATGGCTGCAGCTCGCTG
TGTGGAACCTCTGGTTTCTTTGCTTGTGGCTGAGTTTGGTCCTGCTCAGC
ATTCTGTTGTTCGTGCATTGGATAAGTTATTGGATGATGATCAATTGGCC
GAGCTAGTAGCTGTGCATGGAGCAGTTATACCTCTGGTAGGCCTAATGTA
TGGCCGCAATTATGTACTCCATGAGGCTATTTCCAGAGCTCTTGTGAAGT
TAGGAAAGGATAGGCCTTCTTGTAAGATGGAAATGGTAAAAGCTGGGGTG
ATTGAGAGTGTTCTTGATATTCTTCTTGATGCACCAGATTTTCTATGTGC
AGCTTTTGCAGAGTTGCTCCGAATATTAACCAATAATGCCACCATTGCCA
AGGGTCCATCTGCGGCAAAAGTGGTTGAGCCTTTCTTTCTGTTGTTGACA
AGAGCCGAGTTCGGACCTGATGGACAGCATAGTGCTTTACAGGTTCTAGT
GAATATCTTAGAACATCCTCAGTGTCGTGCTGATTATACCTTGACGTCCC
ACCAAGTGATCGAACCAATTATTCCATTACTTGAATCTCCTGCACCACCA
GTGCAGCAGCTAGCAGCTGAACTTTTAACTCACTTGCTCCTAGAGGAACA
TCTTCAGAAGGATCCAGCAACACAGCAAGTTATTGGCCCACTTATGCGTG
TTCTTGGCTCTGGTTTACAAATACTTCAGCAGAGAGCTGTTAAAGCTCTT
GTTAATATTGCACTGATTTGGCCTAATGATATCGCTAAAGAGGGTGGTGT
CAGCGAGCTGTCCAAAGTAATATTGCTATCTGACCCTTCTTTGCCTCAAG
TCCTGTGGGAATCTGCTGCTGCTGTTTTGTCCAGTATTCTTCAGTTCAGT
TCTGAATATTATTTGGAAGTACCTATTGCCGTTTTGGTAAGATTACTTCG
TTCTGGAACAGAAACTACAATAGTTGGTGCACTAAATGCTCTCCTAGTTT
TGGAAAGCGATGATGCCACCACTGCTGTAGCAATGGCTGAAAGTGGAGCC
ATTGAGGCTCTTTTGGAACTTCTTCGATGTCATCAATGCGAGGAAACTGC
TGCAAGACTTCTGGAGGTATTGCTGAACAATGTAAAAATCAGAGAAACAA
AAGCTATAAAGTCTGCAATCGTACCACTATCACAGTATCTCTTGGATCCC
CAAAGCCAAGCTCAACAAGCAAGATTATTGGCAACTCTTGCTCTTGGAGA
TCTATTTCAGAATGAGGCTCTTGCTCGATCTGCAGATGCTGTTTCAGCCT
GTCGTGCTTTAGTAAACCTGCTTGAAGACCAACCTTCAGAAGAAATGAAA
GTGGTTGCAATATGTGCATTGCAAAACCTTGTAATGTACAGTAGATCAAA
TAAAAGAGCGGTTGCAGAAGCTGGAGGCGTGCAGGTTGTACTGGACCTGA
TTGGTTCAAGTGACCCAGATACATCAGTTCAGGCTGCAATGTTTGTTAAA
CTTCTCTTCTCTAACAATACTATTCAGGAATATGCTTCCAGTGAAACTGT
CAGAGCTATAACAGCTGCAGTTGAAAAAGATTTGTGGGCTACTGGATCAG
TAAATGAGGAGTACCTAAAAGCTCTTAATGCACTTCTTGGAAACTTCCCT
CGTTTACGAGCCACAGAGCCCGCAACACTTAGCATTCCACATCTAGTGAC
AGCCCTCAGGACTGGCTCAGAGACGACTCAAGAAGCAGCTTTGGATTCAC
TCTCTCTTCTTCGGCAAGCTTGGACGGCATGCCCTGCTGAGGTGTCCAGA
GCACAATCAACCGCTGCTTCTGAGGGGATTCCTGTGTTGCAGTACTTAAT
TATGTCTGCCCCACCTCGAGTTCAAGATAAGGCAGACCATCTTTTGCAGT
GTCTGCCTGGGACGCTGACGGTGACTGTTAAACGTGGAAAGAATATGAAA
CAGTCAGTTGGAAATCCAAGTGTGTATTGCAAGCTAACACTAGGAAACAC
TCCATCCAGGGAGACCAAGGTTGTGTCAACTGGTCCAAATCCAGATTGGG
ATGAACCATTTCAGTGGCAATTCGAAAGTCCTCCAAAAGGCCAGAAGCTT
CATATTTCCTGCAAGAATAAAAGCAAGATGGGGAAGAAATCATTTGGAAA
AGTTACAGTCCAAATTGATCGTGTTGTGACACAAGGGGAAGCTGCTGGGG
AGTACTTTCTGCTGCCTGAAAGCAAAAGCGGTAGTAAGAGAAGCCTTGAA
ATAGAGTTCCAATGGACTAATAGCAATAATATGCCCCAGTCCGAAGCTTA
GGATAGAATTATACATGTTTTAAATATTTTTTGTCTCAAGTATATCTCGT
GTTGGTGTATATAGTATCCTTGAGAGTTGAGGGTTTATATTTGCAGTTAA
TAATGTCTTGTGCATCCTGAAGCTGCAGTTGAGAATTCTTTGCAAGTGGT
AGCTTATGTCCTATTTCATTTTGTTTCAGCTGTATTTGTTACAATGTTAT
AGTCATTGTTGATATGTAGAATTTTTCCCCCCTACATAAATATTAATGCA
AATGTTGAGTTCTATTACTGTA
LGGGDPNFAKLAATLAWRGVAASNGTNLSANDVERNGDAKSHDQEPLTPV
PFIKKGSRERSSMEDPDGTLASVAQCIEQLRQSSPSLQEKELSLKKLLEL
IDTRENAFSAVGSHSQAVPVLVSLLRSGSLGVKIQSATVLGSLCKENELR
IKVLLGGCIPPLLGLLRSSSAEGQVAAAKTIFAVSQGGAKDHVGSKIFST
EGVVPVLWGQLEKGLKAGNVVDNLLTGALKNLCSSTEGFWPATIQAGGLD
TLVKLLADGQSSTQANVCFLLACMMMEDASVCPKILAADTTKKLLKLLSP
GNEASVRAEAAGALKSLSAQCKEARRDITSSNGIPALINATIAPSKEYMQ
GEYAQALQENAMCALANISGGLSYVISSLGQSLESCTSPAQVADTLGALA
SALMIYDSKAETTRASDPDDIEQTLVKQFKPSLPFLLQERTIEALASLYG
NATLSGKLANSDAKRLLVGLITMASDEIQDELVRSLLILCNNEGTLWHAL
QGREGIQLLISLLGLSSEQQQECAVALLSLLSNENDESKWAITAAGGIPP
LVQILETGSPRAKEDSATILGNLCNHSEDIRACVESADAVPALLWLLKNG
SSNGKEIAAKTLNHLIHKSDTATISQLTALLTSDLPESKVYVLDALKSLL
SVAPLSDMVRDGSASNDAIETMIRILNSTRDETQSKSASALAGIFSFRKD
LRESSIAVQTAWAVMKLLHVDSENILVESLRCLAAIFLSIKQNRNMAVVA
RDALPALQVLAASSVLQVAEQAICALANLLLDSEVSKNATPEEIILPATR
VLHEGTTAGRSHAAAAIARLLNSRKIDNEITDCVNRTGTVLALVSFLESE
KTGSAALLEGLEALVIISKFEGDKGKIKPAWAALAEYPDSISPIVSCITD
ANPLLLDKAIEILSRLSLAQPVVLGKEIVNASECISSIARRVVSSSKETV
KIGGTTLLVCAAKVNLQRVVDYLNESNSCAYLIQSLVGMLICTENSQVEG
QVNKEGVNILRYAEELRSSGNETSTYVIYGSNTAIWLLSALASNSEKSRT
LIMEAGAIEVLTDRISQCLSEYTQDSEEESSIWICALLLAILFQDRDIIR
AHATMKAVPVLANLLKLEESANRYFAAQAIASLVCNGSRGTLLSVANSGA
AGGLISLLGCADADICDLLDLAEEFSLVRYPEQVSLERLFRVDDIKVGAT
SRKAIPALVDLLKPIPDRPGAPFLSLGLLLQLGKDCPSNKILMVEAGALE
ALTKYLSLGLQDAIEEAATDLLGMLFSTAEICRHEAASSAVGQLVAVLRL
GGRGARYSAAKALESLFSADHIRNAESARQAVQPLVEILNKGLEKEQHAA
IAALARLLGDNPSRALAVVDVEMNAVDVLCRILSSNCSMELKGDSAELCC
VLFGNTKIRSTMAAARCVEPLVSLLVAEFGPAQHSVVRALDKLLDDDQLA
ELVAVHGAVIPLVGLMYGRNYVLHEAISRALVKLGKDRPSCKMEMVKAGV
IESVLDILLDAPDFLCAAFAELLRILTNNATIAKGPSAAKVVEPFFLLLT
RAEFGPDGQHSALQVLVNILEHPQCRADYTLTSHQVIEPIIPLLESPAPP
VQQLAAELLTHLLLEEHLQKDPATQQVIGPLMRVLGSGLQILQQRAVKAL
VNIALIWPNDIAKEGGVSELSKVILLSDPSLPQVLWESAAAVLSSILQFS
SEYYLEVPIAVLVRLLRSGTETTIVGALNALLVLESDDATTAVAMAESGA
IEALLELLRCHQCEETAARLLEVLLNNVKIRETKAIKSAIVPLSQYLLDP
QSQAQQARLLATLALGDLFQNEALARSADAVSACRALVNLLEDQPSEEMK
VVAICALQNLVMYSRSNKRAVAEAGGVQVVLDLIGSSDPDTSVQAAMFVK
LLFSNNTIQEYASSETVRAITAAVEKDLWATGSVNEEYLKALNALLGNFP
RLRATEPATLSIPHLVTALRTGSETTQEAALDSLSLLRQAWTACPAEVSR
AQSTAASEGIPVLQYLIMSAPPRVQDKADHLLQCLPGTLTVTVKRGKNMK
QSVGNPSVYCKLTLGNTPSRETKVVSTGPNPDWDEPFQWQFESPPKGQKL
HISCKNKSKMGKKSFGKVTVQIDRVVTQGEAAGEYFLLPESKSGSKRSLE
IEFQWTNSNNMPQSEA
| Relationships |
|---|
| The mRNA, XM_017384371.1, is a part of gene, LOC108212649. |
| The polypeptide, XM_017384371.1, derives from mRNA, XM_017384371.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |
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- 36814402