| 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. |
CTTGGAAGGTTTTTATACCTTTGATAATTTAACAATCTTTCCTCTTCTTG
TTCGGCTATCATTTCTCTTTCTTAGGGTTTTTTTTCAGATCGTCAATCAC
CCCTCTTTTCTAATCTCCCTAAAAATTAGGGCTTTTTTCATAACCCACCA
ATCTCAACCCTCAGAAATTCAATTCACCATGTGAAATCATCTCAAACACC
CCCAATTTGTTGATTTTCGAACAATTGAATCATGAATTTACAACCCAATT
TACCGAATGAAATGATGATGGGGCAAGTGCCCCAGATGGCTAATTCATCG
TTTAATGCGCAGGCACAGAATGTACAGAGTGGTGGTGATCATCGAAACCA
CCCGGATACGGAGAAAGTTCGGAGATTTGTGCAGAAGAAGATTTATGATT
ATTTGATTCTGAGAGGGCAACAGCAATCGAGTGATCTTTCGGCCAAAAGA
ATGATTGATTTGACAAGGTTGTTGGAGAAGGCTTTGTTTAATGCGGCTGC
GACTTTGGATGAGTATATGAATCAGGATTCTTTGGAGACTCGGTTGCTTT
TTTATTTGAAGCAGTTGCGGAATACGCAGAATCAGAGGTTGTTGCAACAG
CAGCAGATGAATTCTGGGTTGGCGAATCAGAATCAGCAGGTGATGCAGCA
ACAGCAAGTTAATTCGGGCTTCGGGAATATGAATCAGAATCAGCAGTTTG
TGCAGCATGGGAATTCCTCCGGGAATTTGAGTACTATGATCCCGACTCCC
GGTGGCTTTTTGCCACTTACTAGTAGCATGGGTAGTGCATCTTCTTTTTC
TAATGGTTATCAACAGCCAACTTCAGTCTTTCCCACAACTTCGGGTAGCA
ACAACATGGTTTCATCAGTGGGTGGTGGTGAGAGAATTCTTAGCCAGATG
ATGCCTACTCCGGGATTTGTTAATTCCAATAATACTGAGGCTTACAGGAG
TTTGGAGTCTAGTAATAGTGGTGTGGTCCCAACTGTTGAATCTATGATGG
TATCACAGCCCCTGCAACAAAAGCAGCACATCAGTGGTCAAAACAGACGT
ATATTGCACAATGTTGGTAGTCATATTGGTGGTGGGATCAGAAATGGGAC
CTTCAGTGGTGGTTTGGGAATGATGACTAACTATGCACAGCCTGTGAATG
GTACAGGTAGTTTTGAAAACCAACTGCCAATGTCACAAGTTCTGCATCAT
GATGGGTACGGGAGTGGTAGTGCTGATTTTTCTGGCTCTGGTACGGGTAA
TGTGTATGCTTCTTTGAATGCTCCTGGGCTTATGGCGAATAATCAGGGCA
ACCAATCAGAATTTCTCACTGCTCAACAGGATGTGCATGTAAAGCCTTTG
ATTGAACAGTCCGTAAAGATTAATTCTCAATCGACACAGTCATTAACTGA
GAATGTTGTGCAGTCTCATCAGCAACAACTTCTCCAGCAACCTAATCAGA
TTTCCCAACCAAGGCTGCAAAATCAGCCAAACCAGCTAGTCCAGCAAAAT
CAGCTTATCCAGCAAAACCAGCACATCCAACAAAACCAGCACATCCAGCA
AAATCAAAGTTTACCAAATGGCGAATTACAAATGCGCAAAAACCAGCTGA
GGTGGTTATTGTTCTTGGGTCATGCCAAATCTTGTCGTGCTGCTGAATCT
TGTGCAGAAAAGCATTGCATAACTGTTCAGAAACTGTATAAGCATATTGA
AACATGCACACTAACTCAATGCCCATATCCTCGTTGCCATGGTACAAGGT
CATTACTTAATCATTACAAGATATGCAGGAGGACAGACTGCCCTGTTTGT
GTTCCGGCTAGAACTTTTGTGAACAAGTGTAAAGAATCTAGGACTAATGA
TCCCTCTGTCAATGGATCTTTTAGTACCTATGATAATAGGAATGCCTCAG
GCAGGTTGATTAATCAGTCTGTTATAGATACAGAAGATGTAAATCCTCCT
ACAAAACGCACAAAGATCGAGCAGCCTCTGCAGTCTCCAGTGCCTGACCC
TGAAACTTCTGCTCAGCCACTTCCTGCTTTTCGTGATTCTTGTACTCTGC
CGGATGTACAGTATTTGGAACATAGACCTGATGAAACTTGTAGACCAGTG
AAATCAAATGTTACAGGGGTGAAGTTGGAAACTTATGCACAAGATGTTCC
TCATGTTGAGCTGAAAAAAGATATGAATGAGAACTCTATGCGATTGTCTG
ATGGCGTTTCTTCTGTACCCAGTGGTGCTAGTGGCATCCCTAAGGACGAA
AGTTTTAATGCTGGTAAAGAAGTTTACCAGACTAAGCCTGAGAGCGTTAC
ATTGCCTGCTGAAAACGTGAGTACAACCAAGTCTGGGAAGCCAGAAATTA
AGGGAGTATCATTGACAGAATTGTTTACTCCAGATCAAGTTCGGGAGCAT
ATCACAGGTCTCAAGCAGTGGGTTGGCCAAAGTAAAGCGAAGGCAGAAAA
AAATCAAGCCATGGAACACTCAATGAGTGAGAACTCTTGCCAGTTATGTG
CAGTTGAGAAGCTAAATTTTGAACCTCCACCAATTTATTGCACACCTTGT
GGTGCTCGCATCAAACGAAATGCGATGTATTACACCATAGGAGCAGGTGA
TTCACGCCAATACTTTTGCATTCCTTGCTATAATGAAACTCGTGGAGAGA
CTATTTCTGTTGATGGAACTCCTTGTCTAAAGTCAAAACTTGAGAAGAAG
AGAAATGATCTAGAGACGGAAGAAGGGTGGGTTCAGTGCGACAAGTGTGA
AGCTTGGCAACATCAAATATGTGCATTATTTAACAGTCGGAGGAATGAAG
GTGGACAAGCTGAGTTCACTTGTCCAAACTGCTATATTGCTGAAGTTGAA
AGAGGAGAACGTACGCCCTTACCACAGAGTGCAGTACTTGGAGCAAAAGA
TCTGCCGAGAACAATTCTAAGTGATCACTTGGAGCAACGACTCTTTAAAC
AATTGAAGCAGGAGAGAATAGACAGGGCAAGAGTCCAGGGGAAAACTTAT
GATGAGGTTCCAGGAGCGGATTATCTTGTTATTAGGGTCGTGTCTTCGGT
GGATAAGAAGTTGGAAGTGAAGCCACGATTTCTTGATATTTTTCGTGAAG
TGAATTACCCCAACGAGTATGCATATAAGTCGAAGGTAGTGTTATTGTTT
CAGAAAATAGAAGGCGTAGAGGTATGCCTATTTGCTATGTACGTTCAGGA
ATTTGGAGCAGACTGTCAACAGCCAAATCATCGCCGTGTTTATCTGTCCT
ACCTGGATTCTGTGAAGTATTTCAGGCCAGAGATTAAAGCAGTAACGGGA
GAGGCACTCCGTACATTTGTATACCATGAAATTCTGATTGGCTACCTTGA
ATATTGCAAGAAACGTGGCTTTACGAGTTGCTACATATGGGCTTGTCCTC
CACTAAAGGGTGAAGACTATATTTTATATTGCCATCCAGAAATTCAAAAG
ACCCCAAAATCTGATAAGCTCCGGGAGTGGTATTTATCAATGTTGAAAAA
AGCTTCAAAGGAGAAAGTTGTGGTTGAGTTGACTAATTTATATGACCATT
TCTTTGTATCTGGTGTTGGTGAATGTAAGGCTAAGGTGACTGCAGCTCGA
CTCCCATATTTTGATGGTGACTATTGGCCTGGTGCTGCTGAAGATATTAT
CAATAAGCTTCAACAAGAAGAGGATGGTGGGAAGCTGCATAAGAAAGGGA
CAACCAAAAAAACATTCACTAAAAGAGCTTTAAGAGCATCTGGTCAAGTT
GATCTGTCTGGAAATGCCTCAAAGGATCTCATGCTAATGCATAAACTTGG
TGAAACAATTAGTCCAATGAAGGAAGACTTTATCATGGTCCACTTGCAGC
ATTCATGCAGTCATTGTTGTATTCTGATGACTTCAGGAAACTGTTGGTTT
TGCAGCCAGTGCAAAAGTTTTAAGTTGTGCGATAAGTGTCATGAAGAAGA
ACTAAAACTTGAAGAAAGAGACAGGCATCCCATCAATCAGAGGGGTATGC
ATATGCTCTATCCTGTTGAAGTCACTGGCGTGCCTGCAGATACACAAGAT
ACAGATGAGATTCTTGAAAGCGAGTTCTTTGATACGCGGCAGGCGTTTCT
TGGTCTTTGTCAAGGTAATCATTATCAGTACGATACCTTACGCCGCGCTA
AACATTCTTCAATGATGGTCCTTTACCATCTTCACAATCCGACGGCTCCT
GCTTTTGTGACTACATGCTATGTATGTCATCTTGACATAGAAACTGGTCA
AGGTTGGCGCTGTGAGATATGCCCAGATTATGATGTATGCAATGCTTGTT
ATGAAAAGGATGGAGGAGTTGATCATCCTCACAAGTTGACTAATCATCCA
TCAATTGCGGATCGTGATGCACAGAACAAAGAAGCTAGGCAACAAAGAGT
GATTCAGCTGAGGAAAATGCTCGATCTGCTGGTACATGCATCTCAATGTC
GTGTTCCGGAGTGCCAGTATCCTAATTGTCGCAAGGTGAAAAGGCTTTTC
CGCCATGGCATGTCCTGCAAAATTCGTTCGGGTGGAGGCTGCCTTCTATG
TAGAAGGATGTGGAATCTTCTTCAACTTCATGCTAGATCATGCAAAATAT
CTGAATGTCATGTGCCTCGGTGCAGAGATTTAAGAGAACATTTCCGTAGG
CATCAACAGCAGGCTGATAGTCGTCGACGTGCTGCTGTTACAGAGATGAT
GAGGCAGCGGGCTGCTGAGGTTGCTGGTGGTAATTCCTGATATCAAGCTG
TGGAGATGTGTCAATCAACCAAGATAGTAGTTTTGCTGTTTCTTGTCTTC
GTTGCTGATACCTACAATCAGGACAGTAAACAACACAAGCAGCTTTCCGT
TGGTGCTTGGGGTGGCAAGGTTGCTGCGAAGTTGGTTGACTATGAAGCGA
CTTGATCAATTTTTTCATTCTTAGCAGGGGGAGTGAGTAATTTTTTGATT
CTTAAAGTTAAAATCTTTCCTTCCCTTCTAATAATTAGTAGTTTGTTTAA
GCTGTACACAAGTCAGAAATACATGTAGCAGCAGGAGAAAGGAGTTAATA
TGAATTATGGATTTTGTTTTGGCAAAATATGGCCAGTTATACTTTTGCAG
TTGGCAATATGGCCAGTTATACTTTTGCAGTTCTTTACATATCATTGACT
TCACTCACATTTGGTTTGTGTTGTGAATCATTTCTATGAAATCTTTATGG
GAATATTACTCCTTTGAACCCCAAA
MNLQPNLPNEMMMGQVPQMANSSFNAQAQNVQSGGDHRNHPDTEKVRRFV
QKKIYDYLILRGQQQSSDLSAKRMIDLTRLLEKALFNAAATLDEYMNQDS
LETRLLFYLKQLRNTQNQRLLQQQQMNSGLANQNQQVMQQQQVNSGFGNM
NQNQQFVQHGNSSGNLSTMIPTPGGFLPLTSSMGSASSFSNGYQQPTSVF
PTTSGSNNMVSSVGGGERILSQMMPTPGFVNSNNTEAYRSLESSNSGVVP
TVESMMVSQPLQQKQHISGQNRRILHNVGSHIGGGIRNGTFSGGLGMMTN
YAQPVNGTGSFENQLPMSQVLHHDGYGSGSADFSGSGTGNVYASLNAPGL
MANNQGNQSEFLTAQQDVHVKPLIEQSVKINSQSTQSLTENVVQSHQQQL
LQQPNQISQPRLQNQPNQLVQQNQLIQQNQHIQQNQHIQQNQSLPNGELQ
MRKNQLRWLLFLGHAKSCRAAESCAEKHCITVQKLYKHIETCTLTQCPYP
RCHGTRSLLNHYKICRRTDCPVCVPARTFVNKCKESRTNDPSVNGSFSTY
DNRNASGRLINQSVIDTEDVNPPTKRTKIEQPLQSPVPDPETSAQPLPAF
RDSCTLPDVQYLEHRPDETCRPVKSNVTGVKLETYAQDVPHVELKKDMNE
NSMRLSDGVSSVPSGASGIPKDESFNAGKEVYQTKPESVTLPAENVSTTK
SGKPEIKGVSLTELFTPDQVREHITGLKQWVGQSKAKAEKNQAMEHSMSE
NSCQLCAVEKLNFEPPPIYCTPCGARIKRNAMYYTIGAGDSRQYFCIPCY
NETRGETISVDGTPCLKSKLEKKRNDLETEEGWVQCDKCEAWQHQICALF
NSRRNEGGQAEFTCPNCYIAEVERGERTPLPQSAVLGAKDLPRTILSDHL
EQRLFKQLKQERIDRARVQGKTYDEVPGADYLVIRVVSSVDKKLEVKPRF
LDIFREVNYPNEYAYKSKVVLLFQKIEGVEVCLFAMYVQEFGADCQQPNH
RRVYLSYLDSVKYFRPEIKAVTGEALRTFVYHEILIGYLEYCKKRGFTSC
YIWACPPLKGEDYILYCHPEIQKTPKSDKLREWYLSMLKKASKEKVVVEL
TNLYDHFFVSGVGECKAKVTAARLPYFDGDYWPGAAEDIINKLQQEEDGG
KLHKKGTTKKTFTKRALRASGQVDLSGNASKDLMLMHKLGETISPMKEDF
IMVHLQHSCSHCCILMTSGNCWFCSQCKSFKLCDKCHEEELKLEERDRHP
INQRGMHMLYPVEVTGVPADTQDTDEILESEFFDTRQAFLGLCQGNHYQY
DTLRRAKHSSMMVLYHLHNPTAPAFVTTCYVCHLDIETGQGWRCEICPDY
DVCNACYEKDGGVDHPHKLTNHPSIADRDAQNKEARQQRVIQLRKMLDLL
VHASQCRVPECQYPNCRKVKRLFRHGMSCKIRSGGGCLLCRRMWNLLQLH
ARSCKISECHVPRCRDLREHFRRHQQQADSRRRAAVTEMMRQRAAEVAGG
NS
| Relationships |
|---|
| The mRNA, XM_017386368.1, is a part of gene, LOC108214388. |
| The polypeptide, XM_017386368.1, derives from mRNA, XM_017386368.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |