| 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. |
TGTTGATGGGTCAGTGTAGAAATAGCTATAACTAGGGTTATTATACTGGC
AGCGCTGCTTATTTTTCCCCTCACAAAACTCATCATCCATCTATAAAGTT
TCGATCTTTACATCTGATTCTACTATTTACATTCGGATTCATCTTCTGCC
CAATATAGTTTTGTAATTTTTGCCGTTCCAGATTTGAAGTACTCTAGAAG
GAGGCAGATCTCAGAGCAGATATGGGTTTTGACAATGAGTGCATTGTCAA
CATACAATCTCTAGCGGGCGAGTACTTCTGTCCAGTTTGTCGCACACTTG
TTTACCCAAATGAAGCACTCCAGTCACAGTGCACTCATTTATATTGCAAA
CTCTGTCTAACATATATTGTTGGAACTACAAAGGCCTGCCCCTATGATGG
ATACCTTGTGACAGAAAAGGATTCCAAGCCACTTGTTGAATCAGACAAAG
CACTAGCAGAAAGGATAGGCAAAACTCCTGTGCATTGTCTGTTTCACAGG
AGTGGATGTTCTTGGCAGGGACCGTTATCTGAGTGCACATCTCATTGTTC
TGGCTGTTCTTTTGGAAATTCCCCTGTTGTGTGCAACAGATGTGGTGTGC
AAATTATACATCGCCAAGTACAGGAGCATGCACAAAATTGTGCTGGTGCA
AATCCTCATGTGCAGCAGACCGCTGAAAATCCAAAAGATGCTGCTACTGC
TGTTGCAGTTACTACCACAAACTCCAGCCAGGCAACTTCTCAACCTGTAG
TTAGCGCCTCACAGGCACTGGTACCACAGACTGTCACGGCTCCTCCAGCC
ACACAAGATTCGAATCCTCATGTCCACACAATCGCTACTAGTGCTGCGAT
GAGTACAGAGCAGTGGTATCCTCAACATTTTCAACAGTATCAACAGCAGT
ATCCTGGATATGATCCATACCAGCAGTACTACCCATATCAACAACCTGCA
CAACAGGTGCAACAGCATGTACCATATGCAGGACAACCTCAGGTCTATGC
TCAGCCCCCAACTGGAATGCAGGGTCATCATCAGCCATTACCTCAGGTCC
AAGGGCAAGGGCCAGCACAGACTCAGCCACAACCCCAAGGACCACCTCAA
GCACAGTCCTTTGTGCAGAATCAAGTCAACTCACAACAACAACAATCTCA
TATCCAAGTTCACACTCAAACAGCTGCCCCGGGTCAAATCCCTCCGCAGC
AGCCTTACCCCCAAGCACAACCTCATCCGCCACCCAATTCTATGCAGCCT
CCTGCACAACAGAATATTCAAGCACCCTATCAGCAGACACAGTTTCAGGG
ACATTCAGTGCAGCTTCAAATACAGCCCCAGCCTCACTCTAACCCCCAAC
CTGTTTTACAATCTCAGCCCCAAAGTCATCCTTATCCACCAAGTCAGCAA
CCTGCTCCCAGTGTTGTACCAGGTTATCAGTCACATCACCCAGTTCAGCC
TCAGCAGCAAATCCTGCCTGCCCCCCAACACTATCCTATGCCCATGCATC
CGTCTAGTGGGTCTTTTCCTCCAGCTGCTCAGTTCCCTCAGCAACCCCCA
CATTTACGACCACCTCCGACTAATCCTTCACTACCTAATCAACAACAGGC
AAACCTTATGCAGAGTCAAAGCCAAATCCAGGGCGTCCCTCCTGCCCAGC
ATCCTCATATATATCCTCAAACTCCTCAGCAGGGGTACATTGGTCACCAA
CGTCCTGCCGGACAACCGATGCAGCAGCCATATCAGCAATATGGACAGCC
ACCTTTTCCGTCACAGGCATCTGGTTCAGTTCAAGGTCCATTTCACCAGA
TTCCTTTCGGTCAGCAGCCAATGCAGACCCAGTCTCAAGCTCAGGGCCCA
ACTCAGTTGCAACAGAGTGCTGTTGCCCGTCCTCCGCCACAAATGCATGG
CAGTGTGCAAGCACATGGCATGCCACCCCAGCAACCTCCATCCTATGGCG
GTAGACCCATTGCACCAAATCAAACGGCAACATCTCACCCTTTTGCACAA
TCTGGTGGCGCGTTTGGTGGCGCTCCTCACTCCAGACCATTGCCGTCAAG
TTCAGTTCAACAATCTGAGCATCAGATATTCGAGGGTGGCATTGCCAACC
AACAGCAAGTGCCTTCGGGGCAACAGTTTTCTCAGTCTGATCGAGAAATT
AAGCATATAATGGGTGAAGGAAATGCTGCCCCGCAAGGTGGATCAGCTTT
AAACAAAACTGTGGGAAATGATATTAGCGGTCCTGAAGAGGATTCTGTTA
GGGCTAAAGCGCAGGACTCTGAAATTAGAGGTAAAAGTGGGGATGAGGAA
CATAATATCACAACTGAAGGTGAAAAGAAAGGAACTAGGAGCCAGGTCGC
AGAAGCTGAGGTTGATGCATTGAAAACAGGTTCTTCTGAGCCATCACTGG
AGAAAACTGGTAAGGAAAAAACTGGAACACTTAATGAGATGGATGGCAGT
GTGTTTGCTGTCAAGGATTCTACTTCACGACAAACAGAAGCTTTTGTCGG
ACATAAGAAAGATAATACAAATGTGTTGGCAAATGAAAACAAATCGAGTC
ACGGCCAAGTCTCACAACAAGGCCTGGCCATTGGTGAATATGCTGGGTTC
CATGACAAGGGTCTCCCGAACTCCTCTAATCAAGCTCAACTAACGGATCA
AGGCAGATATCAGATGCCTTCAGGGACCTATGGGCCTCCATCTCAGCAAC
AAAGACATACTATGCCTTCAAATTCACAGTCGGGTCCTTATGTAGGAGCT
CCACCTAATGCACTACCAGGTCAAGGACCTGCTCACTTAAAACCTCAGGG
ACCGGGACTTTCGGGTCCACTCCATCAATCTCTTCATCCATCTGAACATT
TCCATCAATCTGGTTCTTCTCAATCACATGAAAGCTTCCAAGGTGTACAG
AGGGGGCAATATTATCAGAATAACCCTCCTCAGCCTCCGTTCTCCAGAAC
TAATAAAGCCGAACCAACAGGACCGCTACATGGCTCTGATAATGCTGGTC
CTCTGCAGAATCAGAGGCTTCACCACTTAGAGGGTAGATATCCGGACCCC
AATGTATCAGGATCCTTTGATAGAGGTCTATATGAGCAGACTTTAGCAAA
TGAAAACCGTGTGCCTGGAGCTGCGCTTGGGCTGCATGCTAAAAATGTTA
ATGATGATCACATGAAACAATTTAGAACTGGACCAGCTGGACGTAATAGT
CAGGGTGAGTATGAGCAAGCACTGAAACAGTTCCCTAAGCCTGCAAATAT
TGGGAATGGCTCAATAAGAGCAGGTGAATATCCTCATGAACATAAATCTG
AGCTTCCTTCAAAGTTCTTGCCCCCATATAATTCTGATTCTCAGCCAGGA
TTTCATGGTTCAGGGCCTGGATTTGGTGTGGATCATCTGCCTCCTAGAAG
TCCTGGAAGAGAATTCCACGGCATTCCATCCCGTGGGTTTGGAGCCCAAT
CAGGTGGGCCACACAATCAGCCTGGTCTTGATAATGTTCATGGCTGGGGC
TCCCATGCAGTTAATGAAGGGCCAAGATCTTTTGACATATCTTCAGATCC
AGTTGGCAAGACTTTTCGTGATCATTTTAGGAGTGGTGATATGGCTGGTC
AAGATTTTATTCCTAATCATATGCGCCGGGGTGAACTTTTTGGTCCTAGA
AATGTACCAAGTCATATTCGTGCTGTAGAGGGTTTTGGAACATTTTCGGA
TCCTCGTATGGGGGAATTGAATGGGCATGGGGGTTTCCCATATGGAGAAT
CATTTGCAGGAAATAAGTTAAATCATCCGCGTCTTGGTGAGCCTGGATTT
AGGAGTAGCTTTTCTCTGCATGAATTTCCACGTCCTGGTGGTTTTTATGA
AGGGAACTTGGAGTCTATTGATAGGTTCAGAAAGAGAATGCCCGCTAGTA
TGGGATGGTGCCGGATTTGCAAAGTTAATTGTGATACTGTGGATGGCCTT
GACCTACACTCACAAACACCGGAGCACCAGCAGAGGACAATGGAAATGGT
TATGAGCATCAAGCAGAATGCAAAGAGACAGAAGACTTCAAAAGATCAAT
CTTTTGTGGAAGAGGGAATCCGGTCAAGAAATGCTGGCAACAGGGGACGA
GGAAAGAAAGTTTAAGTGGCGCAGATCTGCTGTGTCAAGTTTCAAGGTGG
TGTCTTATCTAGTGTTGAAGCTTCAATCTTCGTACAATTAGCATTAGGTG
ATACACCCTTCCGTGTTTCACTATTTTATCAGGATGATTTATGCTATTCC
TGTCATTTCAGATTGCTCTCTTGATGATTATGCTTACTTTTGGATTGAAG
TATTAGTATAAATCTGTTTGACAGAAATTTTCACATTGGGATGCTTATAT
GTTTACATTTTATCAAAAGAATATTAGTAGTAGTAT
MGFDNECIVNIQSLAGEYFCPVCRTLVYPNEALQSQCTHLYCKLCLTYIV
GTTKACPYDGYLVTEKDSKPLVESDKALAERIGKTPVHCLFHRSGCSWQG
PLSECTSHCSGCSFGNSPVVCNRCGVQIIHRQVQEHAQNCAGANPHVQQT
AENPKDAATAVAVTTTNSSQATSQPVVSASQALVPQTVTAPPATQDSNPH
VHTIATSAAMSTEQWYPQHFQQYQQQYPGYDPYQQYYPYQQPAQQVQQHV
PYAGQPQVYAQPPTGMQGHHQPLPQVQGQGPAQTQPQPQGPPQAQSFVQN
QVNSQQQQSHIQVHTQTAAPGQIPPQQPYPQAQPHPPPNSMQPPAQQNIQ
APYQQTQFQGHSVQLQIQPQPHSNPQPVLQSQPQSHPYPPSQQPAPSVVP
GYQSHHPVQPQQQILPAPQHYPMPMHPSSGSFPPAAQFPQQPPHLRPPPT
NPSLPNQQQANLMQSQSQIQGVPPAQHPHIYPQTPQQGYIGHQRPAGQPM
QQPYQQYGQPPFPSQASGSVQGPFHQIPFGQQPMQTQSQAQGPTQLQQSA
VARPPPQMHGSVQAHGMPPQQPPSYGGRPIAPNQTATSHPFAQSGGAFGG
APHSRPLPSSSVQQSEHQIFEGGIANQQQVPSGQQFSQSDREIKHIMGEG
NAAPQGGSALNKTVGNDISGPEEDSVRAKAQDSEIRGKSGDEEHNITTEG
EKKGTRSQVAEAEVDALKTGSSEPSLEKTGKEKTGTLNEMDGSVFAVKDS
TSRQTEAFVGHKKDNTNVLANENKSSHGQVSQQGLAIGEYAGFHDKGLPN
SSNQAQLTDQGRYQMPSGTYGPPSQQQRHTMPSNSQSGPYVGAPPNALPG
QGPAHLKPQGPGLSGPLHQSLHPSEHFHQSGSSQSHESFQGVQRGQYYQN
NPPQPPFSRTNKAEPTGPLHGSDNAGPLQNQRLHHLEGRYPDPNVSGSFD
RGLYEQTLANENRVPGAALGLHAKNVNDDHMKQFRTGPAGRNSQGEYEQA
LKQFPKPANIGNGSIRAGEYPHEHKSELPSKFLPPYNSDSQPGFHGSGPG
FGVDHLPPRSPGREFHGIPSRGFGAQSGGPHNQPGLDNVHGWGSHAVNEG
PRSFDISSDPVGKTFRDHFRSGDMAGQDFIPNHMRRGELFGPRNVPSHIR
AVEGFGTFSDPRMGELNGHGGFPYGESFAGNKLNHPRLGEPGFRSSFSLH
EFPRPGGFYEGNLESIDRFRKRMPASMGWCRICKVNCDTVDGLDLHSQTP
EHQQRTMEMVMSIKQNAKRQKTSKDQSFVEEGIRSRNAGNRGRGKKV
| Relationships |
|---|
| The mRNA, XM_017366974.1, is a part of gene, LOC108199243. |
| The polypeptide, XM_017366974.1, derives from mRNA, XM_017366974.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |