| 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. |
CGAAATAGGGGAATTGAAGGCAAGTCCATACTAGTTCTTCTTCTTCTTGT
TGATAATCGAATACTGCGCATCACTGAGCGGGTGTCAATGGACTCCTACA
CTCCATTACTGGAGAGAACTCGAGTTCCCCAACCCTCTATTCAATCCTAC
GCCGTTATATCCATTTTCGACAAGTTCCGATCCTCTCCGCCCCACCTGAT
TGACGCCGGAAGAGAAGCAATCGCTCAATGTCTTCTCTCCTCTTCCCCCG
CCGTCGTCGATCAGTCCGTACGCCAATTGTGTCGTCTCGTGATCCAGGAG
AAATTCAAATTGTCTGATGCTTTGATGGAGCTCCAATCAGCCTTAGAAGC
CTCCCAATCACGTTTTGTTGATGTGTTTGTCAAGGCTTTAGGCTTTCTCG
TTCGCTTAGGCTTCCGGAATCATCCTCATTCGTTTCGCTTTTCGTCTTCC
AATGCTCATCCTTTTGTCAAGATACTTTGTTGCAGGCCAGAGGTTCAATC
GGAACTTGTCAAACAAGTTGTTTTGTTTATGGTGTCCAACAAGAGTATTG
GAATGCTTAAAGTTTGTGATTTTTTAAGCTCCTTTTTCAACTTTATGACC
ATAAGAATGTCCGATTTTAATTCCTGTTGTCGAAGTCTGGTTTCGTCTGT
GGCATCTCTTTGCTGTTCATATCCTCTGGACGCTCTGCCTGTTATGAAGC
TGCTAGTTAAATGTCTCAGATTTTGTCCTAGCAAAAATGAAGAAGAAAAT
GTTTCTTACGTTTTGGAACACATGGTGAATATGTTTATTGTGGTTTTGCG
GCAGCTGGTTGAGATAGGATTGCTTGTTCATGAGACCCAGCTACAATGTG
TGGAACTTCTCGAAACCATCTTTTCACTGAATATATATCTTGACAAGGGT
TCCTGTAGGAGTGAAGCTGTGATTGAAATGTCAAGGCGTCTAGAAGAGTT
TGAGCACAAACAACTCTCCATACTCCGAATGCTTTTGCTTCTCTTGAAAT
GGAAAGGTGAAAAGGGTAATCTTGTTACTGAATGTGTGGTTGAAGAACTT
CTTTTCATATTTCCTCTCATGAACCTCATGTCCTCCCCTTCAATATCTGT
TAAACAAGCAGCAACAAATTTGCTTTCCATGTTGTATAAGTCCGCAACAA
ACTTGTTGGTTACACAAGCCAAAGATCAAGGCATTAGAAGGAAAAAACCA
CCCATTAGCAGACCTGAGCATATCTTTTACAGGCTTCTGCTGCATATATG
GTATCAGGATCAATTTTTGTCATATGCTTCATCCAACTTAGTTATGACGA
ATGGTGAAATTAATATGAAAGGAACATATCAGTTACCAAAGAGATGGACT
GACATGATGGCAGAGTATGCACTTGGGGTCATTGAAAAACAGAAGTCTTC
CGTACCCATCTCCCAGTCTGAGAGCATCTTGCTCAAGGAGATGGCACCAT
ATCTTAGTGCTATAATGAGTGTTCTTGTCCTGCATCGTGCCATGGGTGCT
TCAGCTGTAGATCTATTGGCTGTTTCTGGCGACATGAACCCTAAACTTGG
TGTACCACTGCTACTAGTCATCTTATTCTATAATAACATAAACTGTGCTA
AAGATCGAGACTTCCATCAGATACTGCTAAAGCTTTTGGGGATACTTCCA
TCGCTTGCTTCGCATCCTGCAATGGTTCCACTTGTTGTTCAGACTATATT
GCCGATGCTTCAGAATGACACGAAACCTGTGCTGTATGCTACTGCCACAC
GTGTACTTTGCAAGACATGGGAGATCAATGATCGTGTATTTGGGAGTTTG
CAGAGCGTATTACTCCCGAATCGATTTATCCAGTATGCATCTCAAAGAGA
TATATGTATAAGCATGGCAATTTCTATACGAGATGTTTGCAAGAGAGATC
CTGATAGAGGCGTGGACCTTATTCTCTCTGTATCGGCTTGCATTGAGAGC
CGTGATTCTTCAATTCACACTATTGGCCTTTTAAGTCTTGCCCATCTTTG
TGAAGCTGATGTAATCGATTTCTATACTGCTTGGGGTGTTATAAGAAAGC
ATTTGCTCAATTACTTGGAAAATCCTATTATATGTCACGGCGTTTCTCTT
CTTCTACGATGTGGTGCAATGGATGCTGCTGTATTCCCAGAAGCAGCAAA
TGATATATTGCATATATTGTGGGAGATTGGAACCACCCTCCATCCTGCTA
GTGAATTAATGTGGACAAAGGCTCGAGCAGCTGCCTTTGAATCATTGACT
TATTATGAGGTATTACATGTTCAGAACAGCACTCCAGAATTTAGAGAGAG
AACCATGGAGTTGCTTACTGCTGAGACCGATACCGAAGTGCTTTGGGCTA
TGGAAAAATTTGTCATAAATATTATCAAATTTGAGCACCAGACAAGGCAA
AGATTAGTGAAGGAGAAACGGGTACCTCGAAATAAAATCGAGAAGTTGGT
AAATATATCTCCACAGCTAAATTTCAAGCAAGGAGATGATAGAAAAATTA
GAGATTTACCTGGTGCAGCTCTTTTTTCCCTTACCTTTACTCATGATGTG
AACAAGCCCGGGGCTGCAAAAGATCTGCATGCTAAATTTAGGACTGCATT
ATTGGACATAGCAGCATCACTCCATCTATCAAGAAATATTTCGGTTGCGG
TTCTTTCCTTCCAGTCATGGAAAATTTTCATGCAACGCTGGATAAAGGAG
CAGATCATGCTAAATGACGTGAAGGGATTATCCACATCATTAAATAATAC
TAATAAACCTGCTAATGATATCTTGAAGAGTATAATACAGATTGCAGAGG
AGTCTATTCCCAGATTGGCTGAAAATATTGCACTAGCTGTTGGTGCATTT
TGTATGGTTCTTCCTGCATCGGCTCATGCTGTCAAATCTACTGCCTTAAA
TTTCCTGCTGAAATGGCTATATCAGTATGAACATGAATATCGCCAGTGGT
CTGCTGCAATATCTATTGGAGCAATCTCAAGTAATTTGCATGCAACTGAC
TATAAACAAAAGTTTCAAAATATCAATGCACTTCTTGAGGTTGCATCAAT
CTGCAAAAGCACATTGGTAAAAGGGGCTTGTGGACTTGGATTGGGGTTAT
CTTCTCAAGATCTCATTACCAGGGTAAAAGTTGATGATGAATCTGACTCG
CATAAAGAAACATACATGATGCAGGAAACATATCTGCTTGGACGGATTGT
GAGGGCTTTATGCCAAATGTTAAGCAAAATTACTCGACTATCATCTGATG
CACTAGAATTACAAAGCATATGTGCATACTTTGGTCAAGCAACAGATGCT
GGTGATTCAGAGAGCTTTCTCATTATCCATGATAACTTGGAGGAAGATGT
ATGGGGTATTGCTGGAGTTGTTCTTGGTTTAGGAAATACTGTTGCAGCAG
TGTATCGGACCGGAAATCATGACGCTGTGTGTAAAATAAATGGCTTGATA
AGTTCATGGATGCGACATGTCAATCCTTTAATTATTAACTCAACTACCAG
CGAGAAAATTGAATTAGCATTGTTAGTAGGATCTTGTCTTGCTCTTCCTA
ATTTAGTAGATTTCTTCCAGAGAGTGGATGATCTTGATGATTCTGAACTG
GATAATCTGATAAGTAGCTTTAAGGATCTTATTTCTGAACTTGTCTCAGT
TAACAAATCAGGCGTACTTTATCAAAGTTTGTTGTTTGCATCCTGTACTG
GAGTAGGAAACCTTTTGGCATGCATCTTGAATGAAGGGGTGCATTTAGTT
CGAGTTGAATATGTTACTGACTTGCTAATGTTGTTCAAAAAATGCTATAC
AGCCTCTTATCCCCCTCTTGTCCATTTGGGTGGGATGCTTGGAATTGTAA
ACATATTAGGTGCTGGTGCTGGTTTTCTGTTCCAACGTGATTGTTCAACC
TTTCTGCACCCTGTTCATGATCTCAAGAATTCTTCTTATATTACGGGGTC
TTTGCTTTCAAGTTCTGCTATGGAGCCAAATCTGGTGTCATTAGTTCAGG
ACATCTTTCTTGTTTCTCAAAATCCTGATGACCAACAACTACAATCATAT
GCCGCATGGGCCATTTCTTTTCTTAGACATTATTTGTGGTACAGAAATGT
TAGAAATGAAGATGATAACTCCCAGCGCGATGCAGTTGGTTCAAAATTTG
TTTCTTCAAATCCTCCAGACGACAGTTTAGTCATGAAGCTCTCTTTGTGG
TTAATGAATCACAGCTTCCCTGGGACAGGTACTGCTCATGTTAACACAGT
TTTGACTGCTTTACGATGTCTTACTAGTGCTCCAAGATTACCACTATTAG
ATTGGGGAGCAATCATCAGACGGTGTATGAGACTCAATTCTGTAGATCAT
GTATTATTACCCTCGGATTCAGCTTCTTCAAGGAGAGTATTTGTACGGGA
GGAGTGCCTGTTATTCTCTTTAGCCCATGCAAAGGAATTTGATCCTCTTC
TCAGCTTACTAGATGAGTTGTCTGACTTGCCCAGGTTTAGGATGCTCGAG
CTAAATATGCAGTCTTTTCTGCTCTCTCGTCTTGCAGACATGAGTAAGGT
TTTTTCAGGTTCTAGGATCGAAAAGCTATTTGATGATGTGGCAAACTTTG
TAAAACTGTTAGTTCCTTCACATCAGCTATATAATTCGGAACAGAAAAGT
TTATTAAGGATTTCTTGCTGGAAGGGTCTTTCTTTATGTTTAATGGGAGC
TACAGCTGACGGAGAAGATCATGTTTCTTATATGGAAAACTGCTTGAAGG
TTCTGTTTTGTTCAACATCTTCTAGTGCAGTAGTTGGTCAGGATCATTTA
TCAGAGGAGTGGTCTGCTGCAATTAAGTGCTTGGCACAGGCTCGGCAGCC
TTGGTTACTTGACTTTTTTAAGGTCTCAGAGGTGGATTTCAGATCTGGAG
ACATGTACTTTCTTGAAGTAAAGAAAAAAATTCAAGCAACATGCATGCTA
GCGCGGACCGGTTCCATTCCATTGTCTCATATTGGAAGCCTGAAAGCATA
CATGCTAAACACCAGATCACAAGATATCTGGGAGGTGCTAGTAGAAGTTG
CAGCCACCCTTCAAAATGCTGATGGAAGCATTAAAAGACAGTGGGTTCTT
GATGCTGCTGAAATTAGCTGTGTAACCAGACATCCGTTGACGGCGATGCA
GTTCCTTGGCCTGCTATGTGGCAGCTTCAGCAAGTATATGCCTTTTCTGA
TTGTTGACCGGATGACTGTGTTATGTGACTTTCCAGTTGCTCTTGCTTCT
CTTCTATCAGAAACTAGCTGGGGCAATGTAGCAGAATCTGTAGTTTCACT
TCTGTGGTCAACAACAGAACGGTTACATGATTGGGTTACAAACACGGAAA
TAGTTCTCAGTGATTCCCCAATTTCCCAGTCTATTGACCAAAGTGAGGAT
TCTATGGCTGATTTTCTCTTGAAGTTGCTGCATCATACATGCGTTTCTCT
GAAAGACTATCTGCCGATGGAGAAGCAGCTTAGTCTTGCTAACATGGTTA
TTCCTTAACCCTTCAACTCTCAGAGGACCAAATTTACGAAATTTAGATAG
AAAATAGTTTACTAATTTCTGTAGCTATCATTAAATATGATCAGATGTTA
TTTTGTTGTAAAACTAGAAGTATATAAAAGATGTGGCAAAAAAAAAAAAG
AAGTATATAAAAGAGATTAGTGTGATACAGTACAAAAGAGGGAGATGTTA
TCAATCTGAGACTAGCCATTATTCGGTTGAAA
MDSYTPLLERTRVPQPSIQSYAVISIFDKFRSSPPHLIDAGREAIAQCLL
SSSPAVVDQSVRQLCRLVIQEKFKLSDALMELQSALEASQSRFVDVFVKA
LGFLVRLGFRNHPHSFRFSSSNAHPFVKILCCRPEVQSELVKQVVLFMVS
NKSIGMLKVCDFLSSFFNFMTIRMSDFNSCCRSLVSSVASLCCSYPLDAL
PVMKLLVKCLRFCPSKNEEENVSYVLEHMVNMFIVVLRQLVEIGLLVHET
QLQCVELLETIFSLNIYLDKGSCRSEAVIEMSRRLEEFEHKQLSILRMLL
LLLKWKGEKGNLVTECVVEELLFIFPLMNLMSSPSISVKQAATNLLSMLY
KSATNLLVTQAKDQGIRRKKPPISRPEHIFYRLLLHIWYQDQFLSYASSN
LVMTNGEINMKGTYQLPKRWTDMMAEYALGVIEKQKSSVPISQSESILLK
EMAPYLSAIMSVLVLHRAMGASAVDLLAVSGDMNPKLGVPLLLVILFYNN
INCAKDRDFHQILLKLLGILPSLASHPAMVPLVVQTILPMLQNDTKPVLY
ATATRVLCKTWEINDRVFGSLQSVLLPNRFIQYASQRDICISMAISIRDV
CKRDPDRGVDLILSVSACIESRDSSIHTIGLLSLAHLCEADVIDFYTAWG
VIRKHLLNYLENPIICHGVSLLLRCGAMDAAVFPEAANDILHILWEIGTT
LHPASELMWTKARAAAFESLTYYEVLHVQNSTPEFRERTMELLTAETDTE
VLWAMEKFVINIIKFEHQTRQRLVKEKRVPRNKIEKLVNISPQLNFKQGD
DRKIRDLPGAALFSLTFTHDVNKPGAAKDLHAKFRTALLDIAASLHLSRN
ISVAVLSFQSWKIFMQRWIKEQIMLNDVKGLSTSLNNTNKPANDILKSII
QIAEESIPRLAENIALAVGAFCMVLPASAHAVKSTALNFLLKWLYQYEHE
YRQWSAAISIGAISSNLHATDYKQKFQNINALLEVASICKSTLVKGACGL
GLGLSSQDLITRVKVDDESDSHKETYMMQETYLLGRIVRALCQMLSKITR
LSSDALELQSICAYFGQATDAGDSESFLIIHDNLEEDVWGIAGVVLGLGN
TVAAVYRTGNHDAVCKINGLISSWMRHVNPLIINSTTSEKIELALLVGSC
LALPNLVDFFQRVDDLDDSELDNLISSFKDLISELVSVNKSGVLYQSLLF
ASCTGVGNLLACILNEGVHLVRVEYVTDLLMLFKKCYTASYPPLVHLGGM
LGIVNILGAGAGFLFQRDCSTFLHPVHDLKNSSYITGSLLSSSAMEPNLV
SLVQDIFLVSQNPDDQQLQSYAAWAISFLRHYLWYRNVRNEDDNSQRDAV
GSKFVSSNPPDDSLVMKLSLWLMNHSFPGTGTAHVNTVLTALRCLTSAPR
LPLLDWGAIIRRCMRLNSVDHVLLPSDSASSRRVFVREECLLFSLAHAKE
FDPLLSLLDELSDLPRFRMLELNMQSFLLSRLADMSKVFSGSRIEKLFDD
VANFVKLLVPSHQLYNSEQKSLLRISCWKGLSLCLMGATADGEDHVSYME
NCLKVLFCSTSSSAVVGQDHLSEEWSAAIKCLAQARQPWLLDFFKVSEVD
FRSGDMYFLEVKKKIQATCMLARTGSIPLSHIGSLKAYMLNTRSQDIWEV
LVEVAATLQNADGSIKRQWVLDAAEISCVTRHPLTAMQFLGLLCGSFSKY
MPFLIVDRMTVLCDFPVALASLLSETSWGNVAESVVSLLWSTTERLHDWV
TNTEIVLSDSPISQSIDQSEDSMADFLLKLLHHTCVSLKDYLPMEKQLSL
ANMVIP
| Relationships |
|---|
| The mRNA, XM_017373680.1, is a part of gene, LOC108204308. |
| The polypeptide, XM_017373680.1, derives from mRNA, XM_017373680.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |