| 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. |
CCACTGCAAGGACCCAACTAAAGCTTAAAGGCCTGCTTCGTACAAAGTAG
TTATCCATATTACTTCTTCCCTTTCTTAGCCCGATCCGACCCACCCAGTT
CATCTCTCGCTCTTTTCCTCCAAAGTATTCCGGTGAAAGATCGGAGCCCC
GTTCGTCACTTCAGGGACATGGAACATCCAGAAAACGAGTCTCGTTCTGG
TGGTGAACAAAGCCAAGGCAAGCCAGATGATGAGGAAGCTGGGGCTCGCC
TCGAAGAATTTAAGAAATCAGTGGAGTTTAAAATGACTCTTCGTCAGAGT
AACCTAAATCCTGAAAGTCCTGAGCCAAGTTTCCTCAGGACACTAGATTC
CAGCATTAAGCGCAACACTGCAGTTATTAAGAAACTGAAGCAGATTAATG
AAGAACAGCGTGAAAGTTTAATGGATGAATTGCGAAGTGTCAACTTAAGC
AAATTTGTTAGTGAAGCAGTGACCGCTATCTGTGAAGCGAAGCTTAGAAC
ATCAGACATCCAAGCAGCAGTCCAGATCTGTTCTCTGCTCCATCAGAGGT
ATAAAGATTTCTCCCCAAGTTTGGTTCAAGGGCTCCTAAAAATCTTTTTT
CCTGGAAAAACCCTGGAGGACCCAGATGCTGATAAGAATTCAAGGGCCAT
GAAGAAGCGCAGCTCGCTCAAACTCCTTTTGGAACTATATTTCGTTGGTG
TGGTTGATGATTGTAGTGTTTTCGTCAATATTATTAAGGATCTTACGAGC
ATGGAGCACCTAAAGGATCGTGATGCAGCTCAGACCAATTTGTCCCTTCT
TTCTAGTTTTGCTCGGCAAGCTAGATTCTTTCTTGGACTTCCGCTGTCTG
GACAAGAAATTCTTGAAGAGTTTTACAAAGGACTTAACATTACACCAGAG
CAGAAGAAATTTTTCAAAAAGGCTTTTCATGTATACTATGATGCAGCGGC
AGAGCTTCTTCAGTCAGAGCATACGTCACTGCGCCAAATGGAGCACGAAA
ATTCAAAAATATTAAATGCAAAAGGCGAGCTAAGTGAGGAGACTGCAACT
GCATATGAAAAGCTCCGGAAGTCGTATGACCATCTATATCGTGGTGTTTC
TGCTTTAGCTGAAGCCCTTGACATGCAACCTCCCGTGATGCCAGAGGATG
CCCACACAACTAGGGTCACTACAGGGGAGGATGCATCATCTCCTGGTCCT
GGGAAAGATTCTTCTACCCTTGAAGCAATATGGGATGATGAAGATACAAG
AGCTTTCTATGAATGCTTACCAGACCTCAGAGCATTTGTTCCTGCAGTAT
TATTGGGAGAATCAGAGTCCAAGGTGAATGATCAATCTGCAAAGACACAT
GAGCAATCAAGTGATTTGACTACTGAATCGGACCAGCAGATTGTTACACA
AGATATTGCAGAGGTTTCTATAGGTTCTGAAGTTTCACAGGATTGCAAAA
ATGAAAAAGGAAAGGAAAAGGATGATAGTAATGATAAAGAAAAAGCCAAA
GAATTAGAGAAAGGAAAAGAGAAGGAAGCTGATCGAAAAGGTGATGCTGA
AAAAGAGAAACTTAAAAATCCTGAAGGAACCAATCTGGACGGTTTGTTGC
AGAGGCTCCCAGGTTGTGTTAGCCGAGACCTAATTGATCAATTGACGGTG
GAGTTTTGCTACGTGAATTCAAAATCTAGTCGCAAAAAGCTCGTGAGGGC
TTTATTTAGTGTCCCCAGGACATCTCTAGAGTTGCTCCCGTATTATTCGC
GCATGGTGGCTACTCTGTCGACTTGTATGAAGGATGTGTCTTCTATGCTC
ATACAGTTGTTGGAAGAAGAATTTAACTTTTTGCTGAATAAGAAGGATCA
AATGAATATAGAAACTAAGATCCGCAATATTCGGTTTATCGGAGAACTCT
GCAAATTTAAAATTGCACCTGCGGGCCTTGTTTTTAGCTGTCTAAAGGCA
TGTTTGGATGATTTTACTCATCATAATATTGATGTTGCTTGTAATCTCCT
TGAGACCTGTGGCCGTTTTCTTTACCGTTCACCTGAAACTGCTGTACGCA
TGGCTAACATGCTGGAGATATTGATGCGCTTAAAGAATGTGAAAAATCTT
GATCCTCGTCACAGCACTCTTGTAGAGAATGCTTATTACTTGTGCAAGCC
ACCAGAAAGATCTGCACGAGTCTCTAAAGTTCGTCCTCCATTACATCAGT
ATATTAGAAAACTTCTATTCTCGGATCTTGACAAGTCATCAATTGAACAC
GTGCTGAGACAACTTCGTAAACTACCATGGAGTGAATGTGAGCCCTATCT
TTTGAAATGTTTCATGAAGGTTCACAGGGGGAAGTATGGTCAGATACACT
TGATTGCTTCACTTACTGCTGGCTTGAGTAGATATCATGATGAATTTGCT
GTTTCTGTTGTTGATGAGGTCTTGGAAGAAATTAGGGTTGGCTTGGAGTT
GAATGATTATGGAATGCAGCAACGGCGCATTGCACACATGCGTTTCTTGG
GGGAATTATACAACTATGAACATGTGGATTCCTCTGTCATTTTTGACACA
CTTTACTTGATTCTCGTTTTTGGCCACGGAACAGCTGAGGAAGATGTATT
GGATCCACCAGAAGATTGTTTCCGTATCAGGATGGTTATAACGCTTCTTG
AAACATGTGGACATTATTTTGATCGAGGTTCCTCAAAGAGAAAGCTTGAT
AGATTCCTTATTCACTTTCAGAGATACATATTAAGCAAAGGAGCAGTGCC
ACTGGATATTGAGTTTGACTTGCAGGACTTATTTGCAGACTTGCGTCCCA
ACATGACCAGATATTCATCTGTTGAAGAGTTAGATGCAGCTCTCGCTGTA
CTTGAAGAGCATGAACGTAAAAATTTAAGTGAAAAAAATAATACTGAGAA
ACACTTGGACACAGAAAAAGTATCTAGTGGACAATTGGGGCGTAGTTCAG
TTAATGGACAAATGCTTTCGGATGGTGTCAAGGCAAATGGCGAGGCACAC
GAAGAGGCAACAGAGGACACTGACACAGACTCTGGAAGTGACACAATTGG
TCCAGCTGGACACTATGATGAGGAAGAGCTGGATGAAGAGAATCACGATG
AGACTCATGACAGTGAAGAGGACTACTCAGATGGGGGTGATAATGCTTCT
GATGAAGATGATGAAGTCCGGGTTCGGCAGAAGATTACGAAAGTGGATCC
TTTAGAAGAAGCTGACTTCGATAGAGAATTCAGAGCTCTGATGCAGGAGA
GCTTGGAGTCCCGTAAATTGGAATTGCGGGCTCGGCCAACTTTGAATATG
ATGATACCGATGAACATATTTGAAGGACCTACGAAAGATCATCATGGAAG
AGGAGTGGAAGGTGAAAGTGGTGATGATACTTTGGATGAAGAGGCAGGAG
GAAGTAAGGAGGTTCGGGTTAAAGTTCTTGTAAAGCGTGGCAGCAAGCAG
CAAACAAAAGAGATGTTTATACCCCGAGATTCCACACTTGTGCAAAGTAC
CAAACAGAAAGAAGCTGCTGAGCTTGAGGAGAAGCAAGACATCAAAAGGT
TGGTTCTGGAGTATAATGATAGAGAGGAGGAGGAGCTGAATGGATTAGGC
AACCAACCAAATAGCTGGATTCAAAGTGGTGGTGGTAGAGCTTCTAGCCG
AGGCCACGCATGGGATGGGCATGGTGGGAGGGGTGCTGGATCACGTCATC
GGTATCATCACCATTCTGGGGGTGGGATATTTTATAGCAGAAGAAGATAA
GGTTGACCAACACTTGGAAAGTAAAGAGACCAAAGAAGCTTGGGGAAGAA
CATATTCCCCCCGCCCCAAAGAAACCCTTCAACATACTAAACCAGTACAT
TCAGTTTAATCCTTGTGGGATGCTTGCCGTTGTTTGCGGAGGTATCATAC
AGGTCCTAAATTAACTTTTGGTTCCTTCGATGCATATTTTTAAGTCGGTG
GTTCTAGCTTATTAGTACAGGCAGGGTTGCAGAGTAATAGATATAGGAGT
TTGCAGATTGGGATCTGTCTGCTAAAAGCTTCACAAGAGTGAGCTGTCAG
TGTTTATCTATGTATATAAGTTGTCAACAAGAAAGGAAATTGATCAGTGT
GTAACAGTGTGTTATGTTTGTGCATGCAAATTTCAGCTTTGTACTTGGAT
CTTTCAGTAGTAAATGGTACAGGATTTCCAAGAAAAAGATGGCCAAATTA
CAAGAAGTCGTCAAAATTACACCAGTACAGGACAAGGACATCAAATATTA
CATGCATTGCAATCTACTTTTTTGTTTGGATTCGTAATTTTGTCGATGAA
CTAGTCTTTTCATTTTTATGGAATGTGAACAAATTGCTTCAGAGTTCAAT
TTGAAGGGCGCTGAGTCATAAACTTGTGTTTTGTTTGGCTGGGAGGAACC
AAAGTTGTTATTTTTAGA
MEHPENESRSGGEQSQGKPDDEEAGARLEEFKKSVEFKMTLRQSNLNPES
PEPSFLRTLDSSIKRNTAVIKKLKQINEEQRESLMDELRSVNLSKFVSEA
VTAICEAKLRTSDIQAAVQICSLLHQRYKDFSPSLVQGLLKIFFPGKTLE
DPDADKNSRAMKKRSSLKLLLELYFVGVVDDCSVFVNIIKDLTSMEHLKD
RDAAQTNLSLLSSFARQARFFLGLPLSGQEILEEFYKGLNITPEQKKFFK
KAFHVYYDAAAELLQSEHTSLRQMEHENSKILNAKGELSEETATAYEKLR
KSYDHLYRGVSALAEALDMQPPVMPEDAHTTRVTTGEDASSPGPGKDSST
LEAIWDDEDTRAFYECLPDLRAFVPAVLLGESESKVNDQSAKTHEQSSDL
TTESDQQIVTQDIAEVSIGSEVSQDCKNEKGKEKDDSNDKEKAKELEKGK
EKEADRKGDAEKEKLKNPEGTNLDGLLQRLPGCVSRDLIDQLTVEFCYVN
SKSSRKKLVRALFSVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQLLEE
EFNFLLNKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFT
HHNIDVACNLLETCGRFLYRSPETAVRMANMLEILMRLKNVKNLDPRHST
LVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSIEHVLRQLR
KLPWSECEPYLLKCFMKVHRGKYGQIHLIASLTAGLSRYHDEFAVSVVDE
VLEEIRVGLELNDYGMQQRRIAHMRFLGELYNYEHVDSSVIFDTLYLILV
FGHGTAEEDVLDPPEDCFRIRMVITLLETCGHYFDRGSSKRKLDRFLIHF
QRYILSKGAVPLDIEFDLQDLFADLRPNMTRYSSVEELDAALAVLEEHER
KNLSEKNNTEKHLDTEKVSSGQLGRSSVNGQMLSDGVKANGEAHEEATED
TDTDSGSDTIGPAGHYDEEELDEENHDETHDSEEDYSDGGDNASDEDDEV
RVRQKITKVDPLEEADFDREFRALMQESLESRKLELRARPTLNMMIPMNI
FEGPTKDHHGRGVEGESGDDTLDEEAGGSKEVRVKVLVKRGSKQQTKEMF
IPRDSTLVQSTKQKEAAELEEKQDIKRLVLEYNDREEEELNGLGNQPNSW
IQSGGGRASSRGHAWDGHGGRGAGSRHRYHHHSGGGIFYSRRR
| Relationships |
|---|
| The mRNA, XM_017367186.1, is a part of gene, LOC108199391. |
| The polypeptide, XM_017367186.1, derives from mRNA, XM_017367186.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |