| 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. |
GATGCCATAAACCCTCTCTGAGAAAAAAAAATCTCTAATTTGATTGGTAA
AATACTTGACACACTGCAGAGTGCAGTCTGCACTACAAATCTACATTATT
GTAATCTTATACACACACACACACACAAACACAAACACACTTGCTTACAC
ACATTGATGCGGAGTTGAACTTTTTCACTCCTTTCAGATCTGTTTAGCTA
GCAGATCACTGTTATTTAACATGACGATTCTGCATCATCTGCTCCTCATC
GCTTGCATATTCATCTCTCTCAATCCAATCATTCCTGCGATTGCTGATTC
TATTCTAGGTTGCGGCGGATTCGTCGAGGCGAGTTCGGCTTTGATTAAGT
CACGGAAGGCAACTGATGCGAAATTGGATTACTCACATATCACGGTTGAG
CTTCGGACTGTTGATGGATTGATGAAGGATAGAACACAGTGTGCTCCAAA
TGGCTACTACTTCATTCCGGTTTACGACAAGGGCTCCTTTGTGATTAAAA
TAAAGGGACCTCAAGGGTGGTCATGGGATCCTATTCAAGTCCCTGTTGTT
GTTGACCACAATGGTTGCAACGCCAATGAAGATATAAATTTTCAATTCAC
AGGGTTCACTGTATCAGGTAGAGTTGTTGGAGCTGTTGGTGGAGAGAGCT
GCTCGCACAAAACTGGTGGTCCATCAAGTGTAACAGTTGAGCTTTTGCAT
CATCCCTCGGGTGCTGTTGCTTCATCTGTTTTGACATCCACTGATGGAAG
TTACTCCTTTTCAAATATTATTCCAGGGAATTACAATGTACGTGCTGCAC
ATAATGATTTGCCCATTGAAGTCAAAGGTTCCACAGAGGTGGAACTGGGC
TTTGGAAACGCTGTAATTGATGACATTTTTTATGTCCCTGGCTATGATAT
TCATGGACTGGTTGTTGCGCAGGGAAATCCTTTATTGGGTGTTCATATAT
ATTTATATTCAGATGATGTCTTGGAGGTAAATTGTCCTCAGGGTTTTGGT
GATCCTCCAGGCGAGAGCAAAGCTCTCTGTCATGCTATATCTGATGCTGA
TGGAGTGTTTAAATTCAAATCTATCCCCTGCGGGTTATACAAGCTGATTC
CATACTACAAGGGAGAGAATACAGTGTTTGATGTTTCACCTCCATTCTTG
TTTGTGTCAGTTCAGCATGAGCATGCAACCGTCCCTCAAAAATTTCAGGT
TACTGGATTTTCTGTTGGTGGTCGTGTAGTCGATGGAAATAACAAGGGAG
TGGATGGTGTAAAGATTATAGTAGATGGCCAAGAAAAGTCTATTACCGAT
AAAGAAGGATTTTACAAGCTTGACCAGGTGACATCTAAACGTTATACAAT
AGAAGCAAAGAAAGAGCATTACAAGTTTGACAAACTGCATGATTTCATGG
TTTTGCCAAACATGGCTTTGGTTGATGATATTAAAGCAATCTCCTATGAT
GTCTGTGGCCTAGTAGAGACGGTCTCTCCTGGGTATAAAGCGAAGGTTGC
TTTAACTCATGGACCAGAGAATGTTAAGCCTCAAGTAAAACAAACTGATA
ATAATGGCAATTTTTGCTTTGAGGTTCTGCCGGGTGAGTACCGCTTGTCA
TCTTTTGCAGCCAAGCCTGAGAGTTCTCCAGAGCTCTTGCTCTTGCCTCC
TTATGTTGATGTCAATGTCAACAGGCCTTTACTAAATGTCAGATTCCATC
AGGCACAAGTAAATGTTATTGGTTCAGTCATGTGCCTGGAAAATTGTGGC
TCTTCTGTTTATGTTACCCTTGTAAGATTGGGTGGGAGCAGTAAAAAAGA
GAGAAAGACAGTTAGTTTGACTGATCAGAGTAGTGAATTTCTGTTTCCTA
ACATCCTACCAGGGAAATACAGACTTGAGGTCAAGCGCCAGTTTCCAGGA
TTGTCAGAAGATAACTGGTGCTGGGATCAAAATTTTTTTGATGTGGATGT
TGGGACAGAGGATGTTAATGGGATTTCATTTGTTCAAAAGGGTTACTGGG
TCAATGTTGTCTCCACTCATGCGGTAGATGCGTACTTCACTCAGCCAGAT
GGCTCTCACGTGAACTTGAAAATTGAGAAGGGTTCACAAAAAATTTGTGT
AGGAACTCCTGGAGTACATGAACTTCACTTTGTAAACTCGTGTATTTTCT
TTGGTAGCTCACCCGTGAAAATTGATACATCTAATCCTTCGCCTGTGAGT
CTAAAAGGAGAAAAATATCTTCTGAAAGGTCAAATATCTATTGAATCAAG
CTCCCTCGATGGTTTAGACACGAGCGCTGACACAATTTTAGTAGACATTC
TAAACAGTGAGGGTTTATTTGTTGAGGGTACTAGTGCCAGATTTGTAGGT
GCTAGGAATGGTCAATCCGACGCGTCTATCTTCGAATATTCATTATGGGC
TAATCCTGGCGAGAAGCTTACATTTGTTCCTCGGGATGCAAGAGATAATG
GTGAAAGGAAAATCTTATTTTATCCTAGACAACATAAAGTCGCAGTATCA
CAAGATGGTTGCCAAGCTGCCATTCCCTTATTTTTGGGTCGTCTGGGGTT
GTACATTGAAGGATCAGTCTCTCCTCCCCTTTCTGATGTATACATCAGAA
TTATTGCTGGAGCAAATAAAGAAAATGCTCCAATGAAGCCAGCTGAAGTA
GTACTTGAAACCACCACAGGAGGAGATGGTGTTTTTGTTGGTGGACCCCT
ATATGATGACATTACTTACAATGTTGAAGCTTCGAAGCCTGGCTATCATG
TAAAGGCAGTCGGACCTTATTCATTTTCCTGTCAGAAGCTCAGTCAGATT
TCGGTACATATATATTCAGAAGAAAATCCCAATGAACTTTTTCCTTCCGT
TCTATTATCATTAAGTGGTGAAGATGGTTATAGAAACAATTCAGTGGCTG
GTGCTGGTGGTACTTTCCTCTTTGATAACTTATTTCCCGGGAGCTTTTAT
CTCAGACCTTTGCTTAAGGAGTATGCTTTCTCGCCTGCAGCACAGGCAAT
TGAACTTGGTTCTGGGGAGTCTCAGAAAGTAGTTTTCCAGGCTACTCGTG
TTGCTTACAGTGTGATGGGTTCTGTTACTCTGTTATCTGGGCAGCCCAAA
GAAGGTGTTTTAGTTGAAGCCCGGTCAGAATCAAAAGGCTATTATGAGGA
GACCCTGACAGATTCATCAGGAAGTTATCGCCTTAGAGGTCTCCTACCCA
ATACAGTCTATGTAATTAAAGTTGGGAAAAAGGGTGACCTTGATAATCAA
ATTGAACGCGCATCTCCTGATTCTGTTGTTGCGGAGATTGGAGTAGGGGA
TATCAAGGATTTGAATTTTTTGGTGTTCGAACAACCACACATGACAATCA
TCAGTGGTCACATAGAAGGAAATAGAATTAAAGAGTTACGGGAGCATCTC
AGGGTGGAAATCAGATCAGCAAATGACCCATCCAAGGTTGAATCCACCTT
ACCATTACCTTTATCCAACTTCTTCCAGGTAAAAGATTTGCCAAAAGGCA
AGTATCTTTTACAGCTTCGATCTGTACTCCCTCCAAACATCCACAGATTT
AAAACAGAAGTTATTGAGGTCGACTTAGAGAAACATACCCAGATTCATGT
GGGCCCCCTGAATTATACTCTGGTAGAGGAGCACCACAAACAGGAATTGA
CTCCAGCTCCTGTATATCCACTAATTGTAGGAGTCTCGTTGATTGGTCTT
CTTCTCGGCATGCCAAGATTAAAGGATCTATATCAAGGCACAATAGGAGC
ATCATTATCAGGATCCATGGCAAGTGCCAAGAAAGAAATGAGAAGGCCAA
CTATTAGGAAGAAGACATATTGAGGGACCCGTTTAGATCCAGATTTTGGC
ATAGAGATAGATCAAGGGTTAACACTAGTAAGACATTCTTCAGTTTCAAG
TTATGCTATGAAGAACAATAGCTGCTTTTAGGTGAGGCCCTCTCAAGTTT
TGTACCAAGTGAATATATGAATCTTTATCATGTTGTATCATTCCAAATTA
TAGTCTAACATTGAGGGCTTCTATATTAATAGTCCGAGATGAAAGTTGAC
AAAAAGCATCAATGCAATTTCATATCTAATTAAGCTAATAAAAGCTGAAC
TTAAATACA
MTILHHLLLIACIFISLNPIIPAIADSILGCGGFVEASSALIKSRKATDA
KLDYSHITVELRTVDGLMKDRTQCAPNGYYFIPVYDKGSFVIKIKGPQGW
SWDPIQVPVVVDHNGCNANEDINFQFTGFTVSGRVVGAVGGESCSHKTGG
PSSVTVELLHHPSGAVASSVLTSTDGSYSFSNIIPGNYNVRAAHNDLPIE
VKGSTEVELGFGNAVIDDIFYVPGYDIHGLVVAQGNPLLGVHIYLYSDDV
LEVNCPQGFGDPPGESKALCHAISDADGVFKFKSIPCGLYKLIPYYKGEN
TVFDVSPPFLFVSVQHEHATVPQKFQVTGFSVGGRVVDGNNKGVDGVKII
VDGQEKSITDKEGFYKLDQVTSKRYTIEAKKEHYKFDKLHDFMVLPNMAL
VDDIKAISYDVCGLVETVSPGYKAKVALTHGPENVKPQVKQTDNNGNFCF
EVLPGEYRLSSFAAKPESSPELLLLPPYVDVNVNRPLLNVRFHQAQVNVI
GSVMCLENCGSSVYVTLVRLGGSSKKERKTVSLTDQSSEFLFPNILPGKY
RLEVKRQFPGLSEDNWCWDQNFFDVDVGTEDVNGISFVQKGYWVNVVSTH
AVDAYFTQPDGSHVNLKIEKGSQKICVGTPGVHELHFVNSCIFFGSSPVK
IDTSNPSPVSLKGEKYLLKGQISIESSSLDGLDTSADTILVDILNSEGLF
VEGTSARFVGARNGQSDASIFEYSLWANPGEKLTFVPRDARDNGERKILF
YPRQHKVAVSQDGCQAAIPLFLGRLGLYIEGSVSPPLSDVYIRIIAGANK
ENAPMKPAEVVLETTTGGDGVFVGGPLYDDITYNVEASKPGYHVKAVGPY
SFSCQKLSQISVHIYSEENPNELFPSVLLSLSGEDGYRNNSVAGAGGTFL
FDNLFPGSFYLRPLLKEYAFSPAAQAIELGSGESQKVVFQATRVAYSVMG
SVTLLSGQPKEGVLVEARSESKGYYEETLTDSSGSYRLRGLLPNTVYVIK
VGKKGDLDNQIERASPDSVVAEIGVGDIKDLNFLVFEQPHMTIISGHIEG
NRIKELREHLRVEIRSANDPSKVESTLPLPLSNFFQVKDLPKGKYLLQLR
SVLPPNIHRFKTEVIEVDLEKHTQIHVGPLNYTLVEEHHKQELTPAPVYP
LIVGVSLIGLLLGMPRLKDLYQGTIGASLSGSMASAKKEMRRPTIRKKTY
| Relationships |
|---|
| The mRNA, XM_017396954.1, is a part of gene, LOC108222957. |
| The polypeptide, XM_017396954.1, derives from mRNA, XM_017396954.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |