| 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. |
TTAAGACCCAAATAGGGAAGCTGCTGGAGTTGCTCTTAGCGGGGATGCTC
TGAGCCCTCGCCTTTCTTTTTCTTTTCGGGTTGTCGAGAATAAACACGAG
CACGAGCGTAACAACTCCTACAAGAATTACCCTCTCCTGTAATTAAAAAG
ACAGAAAAATCTTTGAAAAACGCCAAGTACAGTGCAAAACAATAGATTTG
AATACTTGGTGCGTGTTGCTGACAAAGGAAGGGGGGTTTACACAATTACA
CTTTGCAGGGTTTAGCAATTTGGTACATGTGAACGAAATACACACACTTC
TGCATATATGCGTCTCTCAACTTTGGGGCGTATGGAACTAGCCTTGTTGT
TGATCTGAATTTCGATCCGAACAGGCATGGCGCAGGACGCGGTTGTGCGG
CATGTGCCTCTTAATCCTTGCTGTGAATTGTTACAAAAGAAAGAGTACAA
GTTGTCGCAGAAACTTGCCAAGTCGGAAGAGGGTCGCAATTTTCTCAAGA
AGGCTATAGAGATTCTCCAGGATAAAATCGCCAATTTTGAAGCTGAAAAT
GTCAAGCTGAAGGAAGAACTAGAGCTGGCAAGTACAAAACCAAAAGATGA
TGGAGAGAAGATAATCGAAGAATCAGCTAGCCGAGATACTTTGGAGAATG
AAATATCTGTATTGAGGTCTGAGATATCCTGTTTGAAGCAAAAGGGATGT
TCAGGATCTAAAGACATGGATGAGCAAGTTGCAGGTCTTCAGACACGCGT
CTCTGAAAGGGAAGAGGAGATATCTATTCTCAAGGAACACCTTGAGAAGG
AGAGAACGAGAGCTGAGAATGAGAAGAAGAGGGCTGAGAGGGAATTGAAG
ATAGCAAATGAAGCACTGCAATCAGCCAAGGCAGATAAGGCCAGGGCTGA
AAAACTTCAGGCAGACAATGAAAGAGAGCTGAAAATGAATGAATCCACTA
TTCGAAGTTCTTTGGAGAATGAGATTTCCTCACTAAAATCTGAGATAGCA
GTGTTGCAGCAACAAACTGTCTCAGGCTCTCAAAATGCAAACAAAGAAGC
AGCTCTTCTTCAAGAAAGTGTCTCTGAACATAAAGCAGAAATACATCGGC
TCAAAGAACTTCTTCAGATTGAAAAAAATTGTGCAGATTTTGAGAAAAAG
AAAGCTGAGGAAATGAGGAAGAAACTTGATGATGAAAAATGTCGGGCAGA
AAAAGTGATTTCTGAGAGTAAAACAGATTTGAGAGTAGAAGAATCAGCTG
TCCGAGTTTCTTTAGAAGATGAAATCTCTTCACTGAAGTCACAGATAACA
CCTCTGCAGAAACAGACTGTTTTGGGAACTCAGGATGTAAACAAGGATAT
GGTTCTTCTTCAAGACTGCATTTCCGATAAGGATAAAGAAGTTAACAGGC
TCCAGGAGCTTCTTCAGATAGAGAAACATAGAGCAGATTCCGAAAAAAAT
AAAGCTGAAGAGGAAAGGAAGAAAGTTGATGAGAAGAAGGTTTGGGCAGA
AACAATGATTGCTGAGAAAGAAAGTGAGATAATATTGAAAGAATCAGCTG
TACGACTTCCTCTAGAGATTGAAATTTCTTCCCTGAAATCTCAGCTAGAG
CTATTGCAGCAACAAATTGTCTCACAAGCTCAAGATGTGAGCAAGAACTC
GGGAGCTCAAGATGTGAACAAGGAAACAGAAAGGCTTATATCTGATAAGG
AAACAGAGATAAGTCAGCTCAAGAAGCTTTTGCAGAAAGAGAAAAAAAGA
GCAGATTCTGAGAAGAAAAATGCCGAGACTGAGAAATGTAGGGCTCAAAA
AGTGCTTGCAGATAGGGAGAGAGATTTGAAAGAAAAAGAGCAGGCTGTTC
GGCTTTCTCTGGGTATTGAAATCTCTGCTCTAGAGTCTCAAATACATTTG
TTGCAGAAAGAAATTGCAGTTCGAGATGAAAAGAAGGAAGTAAATCTTTA
TCAATCACTTGTCTCTAAAAAGGAGGCTGAAATTAATAAGCTCAAGAAAC
TTGTTGAGAAAGAGAGAAAGAGAGCAGAATGTGAGAAGAAAAAATCCGAG
GCAGGAAAGAAGAAAGTCAATGAATTCCAGAAGATTGCGGACACAGAAAA
AACTAGGGCTGATGAAGAAAAGAGGCTTGCGGATATTGAAAGAAAAAATG
TTGAGGAGGCTAGACTGCAGTTGGAGATTTCAAGGGCTGAAATTCACGAT
TTAAGAGCAAATTTGAAGTCGGAGTCATTGAAAGTTTTACAGGCAAATGA
TAATCTTGAGATAGAAAAACAAAAGGTGGTCAAAGAAAGACAACGGGCAG
ATATGGAGATGGCTAAAGCTGAAGAGCAAAGTAAAACTTTAGAAACCACG
AGGAGGGAGATTGTAGAGGAACGTACTCGTGCTGATTGTTTATCTCTGCA
GTTGGAAGAAGATAGGGGAAGGCTTACTAAATTACGGGAAGAAATAGGTG
AACAAGTGTCCTCCCAAGATACAGGGAAGGATGCTGGCGACCTTTCTGTT
GATATAACTAGCATAAAGCTTCTGAAAAAAACATTAGAGCTTGAAAGAAT
GCAAGCAAAGCATGCAAAAGAAGTTGCTAGTTTCGAAAAGGATCGTAATA
TTTTACTACAACAGGAAATTCGTCGAATAAAGGAGGCGTTTTCCGGTATT
GTTGATCATCTGGACATACTAGATAAGTGTTCCTCACACCGGGATGTAGG
TATAAATGACCTTGAAAAGAATTCCAATGTTTCAAGGAGTCGAGGTTTAA
AAAGAAAATTCATGGATGAAGAATTATGTCAGGTACAACACCATAATGGA
AATGAACTTATGAAGTCTAGTTCACCCTTGGATGCTTATGTTACCCACAA
GCATCACAAGCAATGTAGTGCACCTTTACTTTCATCTAAAGACTGTACTG
AACCCCTATCAGGTATTGGCTCTAAAGCGATGCCTCTGCTTGGAGGTACC
AAACAAGCATTGTTAAGAACGGCAAATTCCAATATGGCATCTTTTTCTGA
TAAAGCGTTACTGGGATCACAGGAAGGATGGGCCTTATCTGTTGGTGAAT
CAGATAAGTTGGCAGAGGGGGGAATAAACATGCAACTTACTGTCCCAGGG
TCGTCTAATAATATGAGCAAGCCTATGCACAATAAAATATTTGCGCCGTT
GGATGAGAATAGCGTTAGATGTCCTCTTAGAATCAATGCTGTTGTGGATG
AGGTTGAACTTGATAGAGATAGAAATAGGAGTCTCGATGCTGTTGAATCG
TTTGAATATATGTATTATGAGGGTAAGAAGTGGTGTCGACAAATAACCGA
AAACGTATCTGTGCAGCAGGATATGCTGGAATGTAGCGTAGAAGGCGTGC
CATCTAATATAAATTACGCTAATCAAGAAAGGGAACATTCAGTTTTTGTA
AAAGAAATAGCCATGTCCAACAATTTGAAGACATATTCGCACCCCACTGA
TTCTCGATCAATGTGTGATGCAACAGGGACGACTCATGCATGCAATGAAG
AAACTGGGGATGCTAGCAGGAATTATTTGTGTAGTATTGATGAAGTGGAA
GATGGTGACTATCTTAAATTGCTTTCCTTAGATAATCCTCTCGATGAAGA
AACTTATCGCATGGCGAGGGAGAGGCCCTTGTCGCCAACTCTTCCTGAGA
TAGGCTCTTTAAGTGTGGGAGCACATGAAACAGATGACAATGACTCCATT
AATGCTGCATCACCACATAATGATACCATGGTGCCATTTTGCAGTGCTGA
TGAGGAGATTGATTCAAGTAAATTAAATGCCTATACCTCCGGGACTTGCC
ATGTTCTGCCATTTCCAGAGAAGGTTGGTGTCACTGGTTTGAATGTGACT
TCGGAAAATAATGACACGTTTCTTACAAGTGATCCAGGCAATTTAGGCCA
GTCATTTTGTGGTCATAAAGGGCTCAATGCTGCAAGTGGAAGTAAACCTA
AGCCTGCTTGCAGTCCTTGCTATATTGTTATATTTTCAGATATCACCAGT
AATAACAGCATTTCTAAGATATCATCTGCCACAAGAACGTGTCTGGCCCA
GTGCTCTATGCTGCCTCAAACAGATCATGTGGTTCAGGTGATGTCTACTC
TTTTGAAGGTTGAAGGTCTTCTATCCAGGGAAATGGTATGCGTGTTCTTT
TCAATGTTATTGCGAAGCATTCCTGAGTGTGCATTGGAAGACTTCAAGAA
CCTCGCTGATGGGAGCTTGGTCCGCTCCTTTGAAATATTTGCTCAGAAAG
TGCACTCAGTGATGGATGATTTAGAGACAAAAAGTGTTGATGAATTATTG
AACTTGGACGAGCTTCTTAGCCTCATTGAAGATTTTCTAATTCATAGAAG
AGTTGTACATTGTGATGTATTGTCTGAGTCGTTGGCTGTAAATGATCCTA
AACTTGACAATAATGCAAGTGGAAGGAATATGCTATCCTTTCAAGCTGCT
TCAGATCAACAGTTGATTAGTGCATCCTTAGTACTAGCTTCTATATGTTT
AGCATTTGATCATATTGGTGTTGTATGTGAGACCTCATACAACATGTTGA
AAATGCGAAGAATTGACTCATCGACACTCGCTATTCTTCATGTTTTTGCA
TATATCTCTGGAGACAAGTACTTCAACAATTGTGACTACAGCTTATCCAT
GACAGTAGTAAAATCTTTAGTTAATTTTTTAGAGAGGGAAATGTCATCGA
TTAGCGCGCCACAAGTTGGGTTTCCTCGGTGCAAAAATTGCCCATATTCT
GGGAATGCAATTCCCATGGATATAGTAGTTTCACTGCTCATAAAAAAACT
TCATAGCTATGTCTTATCGAATGTCTCATATGAAGATCTGAGGGAAGCAA
CTGTTTACATGAATTATGAAGCTCCGATTGGCAGTGAAAACAGAGAACCA
AGTTCAGGTGATGGAGAAAACCCGCAAGTCCAATGTCATAAGTTTGATGT
CCCCTGTTCCCAGAAAACAAGAATGTCTACTTCCTGCAGGACCCTGTTAT
ATTTGGGCGATGTCCTGTCATTACTTGAGCTGGTAGCATCTATCATGAAC
TGGAGTTGGTCGTTCACAAATATTGTTCGGAAACTTCTGGAGATACTTGA
TTCCTGTGGCATTGAGAAGCTTGTGCCTGCTATCGTTGTTCTACTGGGCC
AGTTGGGGAGGTTTGGTGTTGATGCAAGTGGGTATGATGATGGTGGAGTT
GAAACCCTTCGAGGTCGATTGTCTTCATTCCTGCACCAAAAGGCCTCGGC
TGTGACAGGATTACCATTTCAAATAGCAACTGTGACTGCTTTACTTGGAC
TTGTTCCCATCAGGTTTGAAGAACTTTTTAAGAGTAATAGCGGGCTTTCG
GAAGTAGTTAAAGATCCTGGTCCTGCTGATTGTATAAGGAACTGGTTTTC
TTCACTGAGCAAGGAACAGCAGTCCTTATCAATCAGACTTTTGCTTAATA
ATGTAGCTAGTTTGAGAATGGATTGTGCTCTGCTACAAGCGTAAATTTTG
CAAAGCTAAAGTTGTTTGTTTTTGTACACCTGGTTTAATTACTCATATGT
TGTGCCTCTGTATGTGTTGGGAATTTAGTTTTTGTTGCCTCTTTGATTTG
CAGTATTATAGAAATCATGTAGTTAGGATCAAGGAGAAAGAAATTTTAAT
TTTCCTTTGCCTA
MAQDAVVRHVPLNPCCELLQKKEYKLSQKLAKSEEGRNFLKKAIEILQDK
IANFEAENVKLKEELELASTKPKDDGEKIIEESASRDTLENEISVLRSEI
SCLKQKGCSGSKDMDEQVAGLQTRVSEREEEISILKEHLEKERTRAENEK
KRAERELKIANEALQSAKADKARAEKLQADNERELKMNESTIRSSLENEI
SSLKSEIAVLQQQTVSGSQNANKEAALLQESVSEHKAEIHRLKELLQIEK
NCADFEKKKAEEMRKKLDDEKCRAEKVISESKTDLRVEESAVRVSLEDEI
SSLKSQITPLQKQTVLGTQDVNKDMVLLQDCISDKDKEVNRLQELLQIEK
HRADSEKNKAEEERKKVDEKKVWAETMIAEKESEIILKESAVRLPLEIEI
SSLKSQLELLQQQIVSQAQDVSKNSGAQDVNKETERLISDKETEISQLKK
LLQKEKKRADSEKKNAETEKCRAQKVLADRERDLKEKEQAVRLSLGIEIS
ALESQIHLLQKEIAVRDEKKEVNLYQSLVSKKEAEINKLKKLVEKERKRA
ECEKKKSEAGKKKVNEFQKIADTEKTRADEEKRLADIERKNVEEARLQLE
ISRAEIHDLRANLKSESLKVLQANDNLEIEKQKVVKERQRADMEMAKAEE
QSKTLETTRREIVEERTRADCLSLQLEEDRGRLTKLREEIGEQVSSQDTG
KDAGDLSVDITSIKLLKKTLELERMQAKHAKEVASFEKDRNILLQQEIRR
IKEAFSGIVDHLDILDKCSSHRDVGINDLEKNSNVSRSRGLKRKFMDEEL
CQVQHHNGNELMKSSSPLDAYVTHKHHKQCSAPLLSSKDCTEPLSGIGSK
AMPLLGGTKQALLRTANSNMASFSDKALLGSQEGWALSVGESDKLAEGGI
NMQLTVPGSSNNMSKPMHNKIFAPLDENSVRCPLRINAVVDEVELDRDRN
RSLDAVESFEYMYYEGKKWCRQITENVSVQQDMLECSVEGVPSNINYANQ
EREHSVFVKEIAMSNNLKTYSHPTDSRSMCDATGTTHACNEETGDASRNY
LCSIDEVEDGDYLKLLSLDNPLDEETYRMARERPLSPTLPEIGSLSVGAH
ETDDNDSINAASPHNDTMVPFCSADEEIDSSKLNAYTSGTCHVLPFPEKV
GVTGLNVTSENNDTFLTSDPGNLGQSFCGHKGLNAASGSKPKPACSPCYI
VIFSDITSNNSISKISSATRTCLAQCSMLPQTDHVVQVMSTLLKVEGLLS
REMVCVFFSMLLRSIPECALEDFKNLADGSLVRSFEIFAQKVHSVMDDLE
TKSVDELLNLDELLSLIEDFLIHRRVVHCDVLSESLAVNDPKLDNNASGR
NMLSFQAASDQQLISASLVLASICLAFDHIGVVCETSYNMLKMRRIDSST
LAILHVFAYISGDKYFNNCDYSLSMTVVKSLVNFLEREMSSISAPQVGFP
RCKNCPYSGNAIPMDIVVSLLIKKLHSYVLSNVSYEDLREATVYMNYEAP
IGSENREPSSGDGENPQVQCHKFDVPCSQKTRMSTSCRTLLYLGDVLSLL
ELVASIMNWSWSFTNIVRKLLEILDSCGIEKLVPAIVVLLGQLGRFGVDA
SGYDDGGVETLRGRLSSFLHQKASAVTGLPFQIATVTALLGLVPIRFEEL
FKSNSGLSEVVKDPGPADCIRNWFSSLSKEQQSLSIRLLLNNVASLRMDC
ALLQA
| Relationships |
|---|
| The mRNA, XM_017373018.1, is a part of gene, LOC108203823. |
| The polypeptide, XM_017373018.1, derives from mRNA, XM_017373018.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |