| 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. |
CTAAACAAACATCAAAACACTATCTCTTTATTTTTTCCAGAGAGACAGAG
AGAGAGAGAGAGTTGAAAAATCCAATCTTTTTGTGCTCGAGTATTCAGAT
TCGCCGGAAAATACTCAACTTTCTCCATTTCCGGCGATTTCTAGCCGGCG
TGTTCAGCTCAATTCACGAAATTGTTACTTGCGCTGATGAGATTTATTTA
CATATAGATCGAGAGAGTAATGGATAGGATTCGAGATGGTAGACGAGCTG
CTGCTTCCAATATTCCGAACGGATTATCGCGACGGCGTCATCGAACTAGC
TCTTTCAGAGATTCACCTGAGGACGAAGCGGAGATGCATGAACCGGCGAG
ATTGCGAGAGAGAGGAGTGAAGAAAGATCGAGAGAGAGATCGAGATCGAG
AGAGGGAGCGGTCGAGGAGTAGTAAAAGGAGAAGAGCTGATAGATTGATG
AACGCCGCCGATGAGAGCTCTGAGGAAGACGAGAGTGTGAATGATGAAGA
GGATGAAGATGATGACGTCTCCGCTAATTTCTCCAGGATGTTGCCGCCTC
TGCCTACTCCGATCTTATCGCAGCCGTCGATTTCGAGTAATTATAATAAT
CATAACAATTCGCATAGTTATAGTCATAGTCATCATCAGAATCTGAACCG
GAAGAGTTTGTTATCGGACGGTGGTAAGATGTATAAAGCGGCTGTTCCGG
CGTGGAAAGCTGCCGCTGATGAAATGATTGGTGTCTCTGTTCCTAGGAAG
GCCAGAACTGCATCAACGAAGAGGTCGCATGATTGGGTTTCTAGTGGTGG
TGGAGGAGGAGAGCAGATGAATCACCGGCAAGCTTCAAGTTCGCCGGTTA
GAGGAGGAATTGCTATGTCAACGCAGTCTGGGGCGGTTGTGAGGGAGGCT
GTTCCTTTGTCGCCTCCTTCGTCTTCAAATGTTTCGATTAAGAAGAAAAT
TAAATCTAGTGGAGGAATGAAGCCTAGACCACAACCAAGGTCTACGACAA
CTTCAAAGTCTTCGTCTTCCAATAATAATCCGGAGGAGCTGGAAATTGAG
ATTGCTGAGGTTTTGTATGGACTCATGACTCAATCTCAAGCTCCTCCAAA
AAATGATTTATTGTCGAAGAATGAATTTAATAACAAATCTAGTAGTGAAG
CTAAATCTCGAGCTTCTTCCCCAGTATCTAATTCTTCTTCAGCGGCTCCA
ATAACTGCTGTTGCTCCGAAGAGGAAGAAGCCGCGACAATTGTTAGATAA
TAATTTTGTGGGTAGTTCAAGTACGCGAAGCAGTCCATCAATGAAGTTAG
AAATTGATCAGACGGCAAGGTCTGAACTAAGTCCCCCTAATCTGGAAAGG
AATTTTGGATCTGCAGCTGAGAATGGCGAATCTGCAAATTCAGGTAAATC
TGGTGCGGAAAATAACCAACATCTATCAAAGTCTATGAAGCTGGAAGCGG
GCACGTTGTGTGAATCGGCTTTAATGGAAGAAGCTGGGGAAAGCCGAGAT
GTGGTGTCAACAACCAAGGAAGAGGTTAATTCTATCAAGAAGGATGTACC
TGTGGTTAAATTAAAAGATGATCCCAAGGAGATGATAGTGACATCGATGG
CAACATCATCTAATGTGAAAACAGCAGCTCCAGCAATTGAGAAGAATAGG
GAGGAAAAATATCAGATAGATCTGATGGCCCCACCTCCTCAATCAAGATC
ATCACCTGAAAGGGACAGAGCTGTTAATTTTATGGGTGATCAAAATATGA
TGGTTTTTGATATGGAAAAGAAAAAAGAGATGAGCAATGCTAAAGAAACT
GATAAAGTGGGAAGTAGCAAGGAAGATATAGTGATTCATTCTGCTGAGAA
AGTTGCAAAGACGGTAATTGAAGAAGTTGAATTCCAGAAATCATTTGTTA
GCAAGGAGCGGAACATTGATCTCCAGTTAGATTTGGAAAAAACGGGTATG
GACACTGTTAGCAACCCTCAAAATGATCATGTTGTGAAATCACAAGTACA
GTTCTCTAAAGCTGCATTCAAAGAAGAGCAGCAAAATACGGACAAAAGTG
CTCAATCCATCTCTTTGCCTTTGCCTATGTCTGTTGCTAGCTGGCCTGGC
GGAATTCGTCCTCCAATTGGGTACATAGCACCACTACAAGGAGTTGTATC
AGTTGAGGGGGGTACCATGCCTACAGCACCAGTTCAGCCTCTTTTCTCTC
AACCACGGCCTAAGAGGTGTGCCACACATTGTCATATTGCAAGAAATATT
CACTATTACCAGCAACTCATGAAGATGAATCCTTTCTGGCCAGCGCCTTC
TGGCACTACTGCTTCTATGTTTGGAGCCAAATCCTCCAATCTCAATGTTA
TCCCCCCTACAGAACTACACGGTAACAGTTCTGGAAGGAGTCTGAACTCC
ATGCAAGACAAGGGTCATAGTCTTGCTATCTTCCCAGGGAGTGCTGTAAA
AGAAAATTTTGCCCAACCTGCTAGCATTGCGGATGCTGGGCATGCGAAGC
AACAAATTTTGCTTCAGCAAGCTATGCCTCCAGTACCTCCCACTAATATG
ATGCATGGCCCTGCTTTTATATTCCCCTTCAATCAGCAACAGGCGGCTGT
TGTAGCTACTTCTGGAAGGCCTGCTTCGGTAAAATCACCAACCACCACAG
GGGGTCTACCTTCTACTGGTGCGCCAAACTCAGCTACTGTGGCTGCCTCG
GCACCGACACCTGCAAGTGCACTAGGCTTTAACTACCCAAATATGGCTGC
GAATGAAACCCAGTACTTGGTGTTACAGAACAGTCCATACCCATTCCCAA
TTCCAGCTGTTGGGGCACCACCAAATTTTAGAGGCCATGCTCAGCCAATG
CCAATGTTCAATGGATCTTTTTATCCTTCTCAGATGATACATCCGTTGCA
ACTCCAGCAACAGCAAGTACCAACAACTCAGCAACAACAGCAAATCCAAC
AGACTCATCAGAACACAGGTGGCGGCTCCATGTCTTCACAGAAGCATTTG
CAGTCCCAACAGCACCGTCCGCAAGGCATTGCGATCAATGGTGGTGAAAC
TGGAAATGGAGTCTTGCAGAACTTTGCTGCCCCTAAAAGTCGTTCCTCTC
AGCAATCACAGCAGCATCATAATCAGCATTTACCCCCTTCACAAGCAAGG
CAGCATGAAAGTGACGTAGGCGGTGAAGACAGCCCATCAACTGCTGATAG
TCGAGGATCTCGCGCACCAGTGAATGTGTACAATCAAAACTTTTCCATGC
CCATTCATCCCCAGAATTTTGCTTTGATGAACTCATCTGCTGCTTCAGCT
GGTGCTACGGTTGGCAGTGGTGGGAATCAAAGTGAGAAGAAGCAAACACA
ACATCTTCAGGGTTTCAAATCAGGTGTTGAATCCCTTTCATCTCAAGCAT
ATGCTATGTCATTTGGTCCCATGATTGGTTCCACTTCGGCTTCTGGAATT
GACTTGTCTTCCATGTCACAAAATCATGCCATCCTTCAGAGCTTACCAGA
GGCTACTACAAGGCACAGCTATCATCAGATTATGCAGGCAGCAGCAACTG
CCCAAGCTGTTCAGCAAAAGAAGAATACTAGATTGTCAGAAGATGGTAAA
ATTGGCGGTGCTGTTGCATCCAGTGCAGATGAAGAGAGGAAGGTGCTAAC
GGGCAAGGGTCCAGCTTCTAGTGGAGTACAGTCCATTAGTTTCTCTAGAC
CAGACTTTGTTGATGCATCTGAATCTGCAACCCCTAAAGATAGTGCTTCC
AACAGCATGGCTCGAATGCTGAACCTTGCACCTGGTGCTGCTCGAATGCC
TAATGTTATGAATTTGGTTGGCCCTTCCAATTCTCAGTTGCATGCTCAGT
TGCAACACCAACAACACCAACAGTTGATTCAGATGCACAACCAGCAGCAA
CATCAACAGCAGCAACAACTAGCAGCTAACATGACAGCTCGTAGCAAGAC
ACCATCAAGTAATGGAATTGCGTCGTCGGAGCACTTAACTTCATCATCAG
TAGCTTCCAAGTTTCCAAATTCAATATCCGGCTTTCCACCAAATTTTGTT
CAAAGCAGCAATAACAGTAGTCCGACCCAATCTTCGCAATGGAAAAATTC
TAACAGAACTCCCACCTCCCAAGTTCAATCATCACTGGTCTCATCAACGT
CATCCCCCAAAAATCATCAACAGCAGCAGACAAGAACCCTTCAAAACCAC
ACTCAAATATCCTTTGGGACAAATCAGAAACCATCAGCATCTCCAGGGCA
ACAGCATCCTAATAGCAGCCAGTCCCCATCCCCACCAGTCGTAGTCGGAT
CTCCTACCCATTCTTCCCTTTCTAAAGGTGCTAACTCTAGCCCAAGAATA
AATACTGCTTCGGCAAACAAGACTGGTCAAGCATCTACATTGTCTTCTCA
GCAGACAAAGAATTCGACATCTGTTCCGAGCCAAAAGGCCTCTCCGGCGG
GTGGGAGAAATGTTCCATCAGTTCTTGGGAACCCTCACAGTGCTTCTCTG
AGTGCTACAACTAAAACACAAATTCAGATGCAGCAGCTGCAACAACAACA
GCGACAGCAACAACAGTTTCAGCAGCAGTTATCAAAGCAAACACTGCAGC
AGGCAATGTTTTTTTCAAATCCTTATTTTCAAGGCCAACCACCGAATTCT
GCTAGTTCTAATACTTCAGCTGCCAGTGGTTATAATCTTCAAAGGAGGCA
GCCTGAGCAACCACAGCACTCTCAGCAATCTCAAGGATCCTCTCCAAGTT
CTTCCGGGATGTTGTCTATGGGTCCTCCACCAACACAATCTAGTACCAGC
ACAACTGATCCTGCAAAAGCCGCTGCTGCGGCTGCGGCCGTGGCAGCAGC
CACGGCAGCTGCTAGCAGTATGAAAGGAGGTGGTTTTTCCTCGCAGGGTA
TTCTCCATTCTCCCCAGTTTGGGGTACAGTCATCAGGAAATTCTCATCAG
TCACTGCCGGTTGGATTCTCCTATGGTCACAACGTACCAGCTGCGGTCCA
AGTGAAGCCAGCAGAGCCAAAACAGCCAACTGAGCAGAAACAACCAGCTG
CCTGACAAGGAATAAAAGAAGATACCGCATTGTCGGAGCTTAGACTGTTC
TTTGAAGGGAATGGATTGCCCTTTTGAACTGGCGACCCACAATTTTGAGG
AAGTTGAGTGAAGGAGAAGATCTGCAGGGGCTGGACATAAATTATAGCCT
GTTATGTGCCCTTGTGTGCGTAAGATCTTCTTTAATCTGCTAAGTTTGAT
CACACATTAATCGATAGTGATGAAGTAAAGTAGCAGGGGAAGACCCAGAG
CAGCGATATGCATGGCAGATAATTTAACCAAGCTGAGTGGCAGAATTGAT
GAAGAAGTTCTGTTCCATTCATCCCTACTCTGCAAATTATACCTCTGGAG
TAACTGTTATAACCATGAAAATAGAAGAACGTTTAGATTTGGCACATATA
TATGTAATGGAGGGCTGTCCATGTATATATATGTCTGGCACATATGATAG
TTAACCCCCTCTCAAATTTTTTAATTTAATGGGTCCCCTTGTCTCTTTGT
TTGAATATTTGTGATTTGTGATGATAATCTTGGAGAAAAATGAGTTGTTT
CTTTTGCCAGTA
MDRIRDGRRAAASNIPNGLSRRRHRTSSFRDSPEDEAEMHEPARLRERGV
KKDRERDRDRERERSRSSKRRRADRLMNAADESSEEDESVNDEEDEDDDV
SANFSRMLPPLPTPILSQPSISSNYNNHNNSHSYSHSHHQNLNRKSLLSD
GGKMYKAAVPAWKAAADEMIGVSVPRKARTASTKRSHDWVSSGGGGGEQM
NHRQASSSPVRGGIAMSTQSGAVVREAVPLSPPSSSNVSIKKKIKSSGGM
KPRPQPRSTTTSKSSSSNNNPEELEIEIAEVLYGLMTQSQAPPKNDLLSK
NEFNNKSSSEAKSRASSPVSNSSSAAPITAVAPKRKKPRQLLDNNFVGSS
STRSSPSMKLEIDQTARSELSPPNLERNFGSAAENGESANSGKSGAENNQ
HLSKSMKLEAGTLCESALMEEAGESRDVVSTTKEEVNSIKKDVPVVKLKD
DPKEMIVTSMATSSNVKTAAPAIEKNREEKYQIDLMAPPPQSRSSPERDR
AVNFMGDQNMMVFDMEKKKEMSNAKETDKVGSSKEDIVIHSAEKVAKTVI
EEVEFQKSFVSKERNIDLQLDLEKTGMDTVSNPQNDHVVKSQVQFSKAAF
KEEQQNTDKSAQSISLPLPMSVASWPGGIRPPIGYIAPLQGVVSVEGGTM
PTAPVQPLFSQPRPKRCATHCHIARNIHYYQQLMKMNPFWPAPSGTTASM
FGAKSSNLNVIPPTELHGNSSGRSLNSMQDKGHSLAIFPGSAVKENFAQP
ASIADAGHAKQQILLQQAMPPVPPTNMMHGPAFIFPFNQQQAAVVATSGR
PASVKSPTTTGGLPSTGAPNSATVAASAPTPASALGFNYPNMAANETQYL
VLQNSPYPFPIPAVGAPPNFRGHAQPMPMFNGSFYPSQMIHPLQLQQQQV
PTTQQQQQIQQTHQNTGGGSMSSQKHLQSQQHRPQGIAINGGETGNGVLQ
NFAAPKSRSSQQSQQHHNQHLPPSQARQHESDVGGEDSPSTADSRGSRAP
VNVYNQNFSMPIHPQNFALMNSSAASAGATVGSGGNQSEKKQTQHLQGFK
SGVESLSSQAYAMSFGPMIGSTSASGIDLSSMSQNHAILQSLPEATTRHS
YHQIMQAAATAQAVQQKKNTRLSEDGKIGGAVASSADEERKVLTGKGPAS
SGVQSISFSRPDFVDASESATPKDSASNSMARMLNLAPGAARMPNVMNLV
GPSNSQLHAQLQHQQHQQLIQMHNQQQHQQQQQLAANMTARSKTPSSNGI
ASSEHLTSSSVASKFPNSISGFPPNFVQSSNNSSPTQSSQWKNSNRTPTS
QVQSSLVSSTSSPKNHQQQQTRTLQNHTQISFGTNQKPSASPGQQHPNSS
QSPSPPVVVGSPTHSSLSKGANSSPRINTASANKTGQASTLSSQQTKNST
SVPSQKASPAGGRNVPSVLGNPHSASLSATTKTQIQMQQLQQQQRQQQQF
QQQLSKQTLQQAMFFSNPYFQGQPPNSASSNTSAASGYNLQRRQPEQPQH
SQQSQGSSPSSSGMLSMGPPPTQSSTSTTDPAKAAAAAAAVAAATAAASS
MKGGGFSSQGILHSPQFGVQSSGNSHQSLPVGFSYGHNVPAAVQVKPAEP
KQPTEQKQPAA
| Relationships |
|---|
| The mRNA, XM_017367025.1, is a part of gene, LOC108199275. |
| The polypeptide, XM_017367025.1, derives from mRNA, XM_017367025.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |