| 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. |
AAAATTCAAGAGAAGCAGAAAAACGAGGAGAGAAGTTCTAGTGAGAGAAA
CTAACAAAACATCGAAACAACACACTATCCTCTCTCCTTTTCCTAGAGAG
AGAAACTTGAAAAATCTCATCTTTTTGTGCTCCAGTATTCAGATTCGCCG
GAAAATACTCCGTTTCTTCATTTCCGGCCGGCGAGTTCAGCTCAATTCAC
GAAATTATTACTTACTCTGATGATATATATTTGTATATAGATCGAGAGAG
TAATGGATAGGATTAGAGATGGGAGACGAGCTGCTGCTTCGAATATTCTT
AACGGATTATCGCGACGGCGTCATCGAACTAGCTCTTTTAGAGATTCACC
TGAGGACGAAACGGAGATGCATGAACCAGCGAGATTGAGGGAGAGAGGAG
TGAAGAAAGATCGAGAGAGAGATCGAGATCGAGAGAGGGAGCGGTCGAGG
AGTAGTAAGCGGAGAAGAGCTGACAGATTGATGAACGCCGCCGATGAGAG
CTCGGAGGAAGACGAGAGTGTAAATGATGAAGAGGATGAAGATGATGATG
TGTCCGCTAATTTCTCCAGGATGTTACCGCCTCTGCCTACTCCGATCTTA
TCGCAGCCGTCGATTTCGAGTAATTATAATAATCATAACAATTCGCATAG
TTATAGTCATAGTCATCATCAGAATCTGAACCGGAAGAGTTTGTTATCGG
ACGGTGGTAAGATGTATAAAGCGGCTGTTCCGGCGTGGAAAGCTGCCGCT
GATGAAATGATTGGTGTCTCTGTTCCGAGGAAGGCCAGAACTGCATCAAC
GAAGAGGTCGCATGATTGGGTTTCTAGTGGTGGTGGAGGAGAGCAGATGA
ATCACCGGCAAGCTTCAAGTTCACCGGTTAGAGGAGGAATTGCTATGTCA
ACGCAGTCTGGGGCGGTTTTGAGGGAGGCTGCTCCTTTGTCGCCTCCTTC
ATCTTCTAATGTTTCAATTAAGAAGAAAATTAAGCCTAGTGGTGGAGTAA
AGCCCAGACCACAGCCACGGTCCACCACAACTTCAAAGTCTTCGTCTTCA
AATAATAATCCGGAGGAGCTGGAAATTGAGATTGCTGAGGTTTTGTATGG
ACTCATGACTCAATCTCAAGCTCCTTCGAAAACTGATTTATCGTCCAAGA
ATGAATTTAACAACATATCTAGCAGTGAAGCTAAATCTAGAGCCTCTTCT
CCGGTTTCTAATTCTTCTTCAGCAGCTCCGGTGACCACTGCTGCTCCGAA
GAGGAAGAAGCCACGACAATTGGTAGATAATAATTTAGTGGGTCTTTCCG
GCACACGGAGCTGTCCAGCAATGAAGGTAGAAATTGATCAGATGCCGAGG
TCTGAACTTTGTCCTCCGAATCTGGAAAGAAATCCCGGATCTGTAGCTGA
GAACGGCGAATCTGCAAATTCAGGTAAATCTGGTGCTGAAGCTTCAAAAT
CTATGAAGCTGGAAGCTAGCACGTTGTCTGAATCGAAGGTGGTTTTGATG
GAAGATGCCGGGGAAAGCCGTGATGCGGTGTCAACAACCAAGGAAGAGGT
AAATTCTATCAAGAAGGATTCATCCGTGGTTAAGTTGAAAGATGTTCCCA
AGGAGATGATGGTGACATCGATGGCGACATCAACTAATGTGAAAACAACA
GCTCCAACAATTGAGAAGAAACGGGAGGATAAATTAAATATAGATCTAAT
GGCTCCACCTCCTCAATTAAGATCATCACCTGAAAGGGACAGAACTGTTA
CTTTTATGGGTGAACCAAATAGGATGGTTTTTGATATGGAAAAGAAGGGA
GAGATAAGTAAATCTAAAGAAACTGACAAAGTGAGAATTAGCAAGGAAGA
GACAGTGATCCAATCTGATGAAAAAGGTGCAAAAAAGACAGTAATCGAAG
AAACTGAATTCCCAAAATCATTTGTTAGCAAGGAGAGGAACATTGATCTC
AGCTTTGATTTGGAAAAGCCGGGTATTGATACTGTAAACAATACTCAAAA
TGATCTTGCTGCGAAATCACAAGTGCAATACTCTAAGGCCACATTTAAAG
AAGAGCAAGAGCAACAAAACACGGACAAAAGTGTTCAATCCATCTCTTTG
CCTCTACCCATGCCTGTGTCTAGTTGGCCTGGTGGAATTCCTCCTCCAAT
GGGGTACATGGCACCACTACAAGGAGTTGTATCAGTTGAGGGGGGTAACA
TGCCTTCAGCAACAGTTCAGCCACGGCCAAAGAGGTGTGCCACACATTGT
CATATTGCGAGAAATATTCACTATTATCAACAACTCATGAAGATGAATCC
TTTCTGGCCAGCACCTTCTGGCACTGCTTCTATGTTTGGAGGGAAACCCT
CCAATGTGAATGTTATGCCCCCTACAGAGCTACATGGTAACAGTTCCGGA
AGGAATCTCAACTCCGTGCAAGACAAGGGGCATAGTCTTGCCATCTTCCC
AGGCAATGCTGGAAAAGAAAATTTTGTCCAACCTTCTGGTGTTGCAGATG
CTGGACATGGAAAACAACAGATTTTACTTCACCAAGCTATGCCTCCACCT
CCCAATAATATGATGCATGGACCTGCTTTCATATTCCCTTTCAACCAGCA
ACAGGCGGCTGTGGTAGCTACTTCAGGCAGGCCTGCATCTGCAAAATCTC
CAGCTACCACAGGAAGCCTACCTTCTACCGGTGCACCAAATTCAGCTACC
GTGACTGCCTCAGCACCAGCACCTGCAAGTGCACTGGGTTTCAACTACCC
GAATATGTCTGGAAATGAAACACAGTACTTGGTGTTACAAAACAGTCCAT
ACCCATTCCCGATTCCAGCCGTAGGGGCACCACCAAATTTTAGAGGCCAT
ACTCAGGCAATGCCAATGTTCAATGGATCTTTTTATCCTTCTCAAATGAT
CCATCCGTTGCAACTCCAGCAACAGCAAGCACCAACTTCTCAGCAACAAC
AAATCCAACAAACTCATCAGAACACAAGTGGTGGCTCCACGTCATCACAG
AAGCATTTGCAGTCCCAACAGCACCGTCCACAAGGCATTCCTATCAATGG
TGGCGGAACCGGAAATGGAGTCTTGCAGAACTTTGCTGCCCCCAAAAGTC
GTTCATCTCAACATCCACAACAACATCATAATCAGCATATACCCCCGTCA
CAAGCAAGGCAGCTTGAAAGTGAGGTGGCTGGTGAAGACAGCCCATCAAC
TGCTGATAGTCGAGGATCTCGGGCTCCCGTGAATGTATACAATCAGAACT
TTGCCATGCCCATTCATCCTCATAATTTTGCTTTGATGAGCTCATCTGCT
GCTTCAGCTGGTAATCCCGGTGGCAGTGGTGGAAATCAGAATGATAAGAA
GCAAACACACCAACAACATCCAGGGTTCAAATCAGGAGTTGAGTCCCTTC
CATCTCAAGCGTTTGCTATGTCATTTGGTCCCATGATTGGTTCCACTTCT
GCTTCTGGAATTGACCTGTCTTCCATGTCCCATAATCATGCCATCCTTCA
AAGCTTACCAGAGTCTACAAGGCAAAGCTATCATCAGATGATGCAGGCCG
CAGCAACTGCCCAATCTGTTCAGCAAAAGAAAAATTCTAGAATATCAGAT
GATGGTAAAATTGGGGGTTCTGCTTCATCCAATGTAGATGAAGAGAGGAA
GGTTATAACCAGGAAGGGTCCAGCTTCTAGTGGTGGACAGTCCATTAGTT
TCTCTAGATCAGACTTTAATGAGGCATCCGAGTCTGCAACTCCAAAAGAT
AGTGCTTCTAACAGCATAGCTCGAATGCTGAACCTTGCACCTGGTGCTAC
TCGCATGCCTAATGTAATGAATAATTCTCAGTTACATGCTCAGTTGCAAC
ATCAGCAACAGTTGTTCCAGATGCACACTCAGCAGCAACAGCAACAACTA
GCAGCTAATGTGACAGCTCGTAGTAAGACACCAACAAGTAATGGGATTTC
ATCCTCCGAGCACTTAACTTCATCATCAGCATCTGCGAAGTTTCCAAATT
CAATATCTGGCTTCCCACCAAATTTTGTTCAGAGCAGCAATAACAATTGC
CCAACACAATCTTCACAATGGAAAAACTCTAACAGAACTCCCACCTCAGT
TCAGTCATCACTGGTCTCATCAACATCATCCCCCAAAAGTCAACAGCAGC
AGTCAAGAACTTTACAAAACCACACTCAGATATCCTTCGGGACAAATCAG
AAATCATCAGCATCTCAGATGCAGCAGCATCCTAATTGCAGTCAGTCTCC
ATCCCCTCCTGTTGCAGTAGGATCTCCTACTCATTCTTCCCTCTCTAAAG
GTGCTAGCTCTAGCCCCAGGACAAATACTACTTCCACAAACAAGACTGGC
CAAGCATCTACATTGTCATCGCAACAGGCCAAGAATTCACCATCTGCTCC
GGGCCAAAAGTCTTCTCCGGCAGGTGGAAGGAATGTTCCCTCAGTTCTTG
GAAACCCTCACAGTGCACCTCTGAGTGGTACAACTAAAACCCAAATTCAG
ATGCAGCAGCTGCAACAACAACAGCGACAACAGTTTCAACAGCAATTATC
AAAGCAAACACTGCAGCAGGCACTAGTTTTTTCGAATCCTTATTTTCAAG
GGCAACCACCTAATTCTGCTAGTTCTAATACTTCAGCTGCTACTGGGTAT
AATCTTCAAAGAAGGCACTCTGAGCAACCGTCGCAGCAACCTCAAGGGTC
CTCTCCAAGTTCTCCTGGAATGTTTATGTGTCCTCCAGCCACACAATCTA
ATACCAGCACAACTGATCCTGCAAAAGCGGCAGCTGCAGCTGCAGCTGTG
GCAGCAGCTGCTAGCAATATAAAAGGAGGTGGCTTCCCCTCGCAAGGAAT
TCTCCATTCTGCCCAGTTTGGTGTACAGTCGTTGCCTGTTGGATTTTCCC
ATGGTCACAGCGTGCCAGCTGCGGTCCAAGTAAAAGCGGAGCAGAAACAG
CCAGCTGAGCAAAAGCAACCAGCCGCCTGACAAGAAATAATTGAAGATAC
ACTGAATCCTTGAAGCTTAGACTGACCGTCCGTGAAGACGGGGTGCCCTT
TTTGAAGTAGCAACCCACAATTTTGGGGAAGTTGAGTGGGAGGAATGAAC
TGCATGTGGATTTGGGCTAGACATGAATTATAGTTTGTTGAGTATGTGCC
CTTTTGTGCATAAGCTCTTCTTTAGTCTGACAATGTTGATCATGCATTAA
TGGTACTAATTGATCGTGACTAAGTAAGTTAACTGGGTAGCGATTCACGA
TTAGAGAGGAATGCTAGAGGCATGGCATTTTTTAAAGGAAGCTGCAGAGT
TGATGAAGAAGTCTTCTTCCTTCCATCTCGATTTTGTGCAATGTTCTGTT
TATATACTTCTGGCGTAATGTTTATTACCATGAAAATAGAAAAAAAGTTT
AGATTTGGCATATATATATGTGTAATGGAGGGCAGTCCATGTATATATGT
CTGGCACATATGATAGTAAACCCCTCTATATTTTTTTAATTTAATGGTTC
TCCTTGTCTC
MDRIRDGRRAAASNILNGLSRRRHRTSSFRDSPEDETEMHEPARLRERGV
KKDRERDRDRERERSRSSKRRRADRLMNAADESSEEDESVNDEEDEDDDV
SANFSRMLPPLPTPILSQPSISSNYNNHNNSHSYSHSHHQNLNRKSLLSD
GGKMYKAAVPAWKAAADEMIGVSVPRKARTASTKRSHDWVSSGGGGEQMN
HRQASSSPVRGGIAMSTQSGAVLREAAPLSPPSSSNVSIKKKIKPSGGVK
PRPQPRSTTTSKSSSSNNNPEELEIEIAEVLYGLMTQSQAPSKTDLSSKN
EFNNISSSEAKSRASSPVSNSSSAAPVTTAAPKRKKPRQLVDNNLVGLSG
TRSCPAMKVEIDQMPRSELCPPNLERNPGSVAENGESANSGKSGAEASKS
MKLEASTLSESKVVLMEDAGESRDAVSTTKEEVNSIKKDSSVVKLKDVPK
EMMVTSMATSTNVKTTAPTIEKKREDKLNIDLMAPPPQLRSSPERDRTVT
FMGEPNRMVFDMEKKGEISKSKETDKVRISKEETVIQSDEKGAKKTVIEE
TEFPKSFVSKERNIDLSFDLEKPGIDTVNNTQNDLAAKSQVQYSKATFKE
EQEQQNTDKSVQSISLPLPMPVSSWPGGIPPPMGYMAPLQGVVSVEGGNM
PSATVQPRPKRCATHCHIARNIHYYQQLMKMNPFWPAPSGTASMFGGKPS
NVNVMPPTELHGNSSGRNLNSVQDKGHSLAIFPGNAGKENFVQPSGVADA
GHGKQQILLHQAMPPPPNNMMHGPAFIFPFNQQQAAVVATSGRPASAKSP
ATTGSLPSTGAPNSATVTASAPAPASALGFNYPNMSGNETQYLVLQNSPY
PFPIPAVGAPPNFRGHTQAMPMFNGSFYPSQMIHPLQLQQQQAPTSQQQQ
IQQTHQNTSGGSTSSQKHLQSQQHRPQGIPINGGGTGNGVLQNFAAPKSR
SSQHPQQHHNQHIPPSQARQLESEVAGEDSPSTADSRGSRAPVNVYNQNF
AMPIHPHNFALMSSSAASAGNPGGSGGNQNDKKQTHQQHPGFKSGVESLP
SQAFAMSFGPMIGSTSASGIDLSSMSHNHAILQSLPESTRQSYHQMMQAA
ATAQSVQQKKNSRISDDGKIGGSASSNVDEERKVITRKGPASSGGQSISF
SRSDFNEASESATPKDSASNSIARMLNLAPGATRMPNVMNNSQLHAQLQH
QQQLFQMHTQQQQQQLAANVTARSKTPTSNGISSSEHLTSSSASAKFPNS
ISGFPPNFVQSSNNNCPTQSSQWKNSNRTPTSVQSSLVSSTSSPKSQQQQ
SRTLQNHTQISFGTNQKSSASQMQQHPNCSQSPSPPVAVGSPTHSSLSKG
ASSSPRTNTTSTNKTGQASTLSSQQAKNSPSAPGQKSSPAGGRNVPSVLG
NPHSAPLSGTTKTQIQMQQLQQQQRQQFQQQLSKQTLQQALVFSNPYFQG
QPPNSASSNTSAATGYNLQRRHSEQPSQQPQGSSPSSPGMFMCPPATQSN
TSTTDPAKAAAAAAAVAAAASNIKGGGFPSQGILHSAQFGVQSLPVGFSH
GHSVPAAVQVKAEQKQPAEQKQPAA
| Relationships |
|---|
| The mRNA, XM_017367013.1, is a part of gene, LOC108199265. |
| The polypeptide, XM_017367013.1, derives from mRNA, XM_017367013.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |