| 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. |
ATTTTTGCCCCTCTATTTTTTTTCCCTTCACAATTATACTCCCCTGTTTT
AACTCCCCCCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
TCTCTCTCACACACACACACACAGACACACCACCTGCACAAACAGTTGTC
CTCGGGGCTCGCGCAATGTTTCACCAATTCGGCGCAACAGCAGACTCCCT
GAGCAAAGCATCAACCCTGGTCTTTCGTATCGGCACCGACGCTCATCTCT
ACGACGATCCCGATGACGTCAGCATCGCACCTCTCCTCGACAGCAAATTT
GACTCAGAGAAATGCGAAGCTCTCAAACGACTTCTCGCTCTTATCGCACA
AGGGTTCGATGTCTCCAATTACTTCCCTCAGGTTGTTAAAAATGTGGCAT
CTCAATCGTTGGAGGTGAAGAAGCTGGTTTACTTGTATCTGCTGCATTAT
GCTGAAAAGCGTCCGAATGAAGCTTTACTCTCAATCAATTATTTCCAGAA
AGACTTGGGGGATCCAAATCCATTAGTGCGAGCATGGGCACTCCGTACTA
TGGCAGGAATACGTCTACATGTAGTTGCACCTATTGTTGTCGTTGCAGTG
GCGAAATGTGCAAGAGACCCATCAGTATATGTTAGAAAATGTGCTGCCAA
TGCTCTTCCCAAGCTGCATGATTTGCGCTTGGAGGAGAACACTGGGGGAA
TTGAGGAGATAGTTGGAATCTTGCTGAATGACAACTCTCCTTCTGTAGTT
GGAGCTGCTGCAGCAGCATTTGCTTCTGTATGTCCGAACAATCTGAATTT
AATTGGTAGACACTATAAAAAGTTATGCGAGACACTTCCTGATGTCGAGG
AGTGGGGCCAGATTGTCTTAATTGAGATTCTTTTACGCTATGTGATTGCT
AGGCAAGGGCTTGTAAGAGAATCCATTATGGCATCTCCTTATTCCGAATA
CCTTGATTCTGAAATTGATGGTCCAGATAGAGACTTTGCGGTTAAGGAAG
AGACTAATGTTGTTAGCATTGGGGCATATCAGTCTCAATTATTACAGATG
GCTTCTAAGAGCTACCTTGAAGGACCAGAAAAATATCTTTCACAAATGAA
TTTTGAAGACAAGGGCGCATTCCAATCGGGATTACCAAAGTTTACATCTG
CCAAAAATGATGATGTAAAGATCCTGCTTCAGTGTACTTCACCTTTGTTA
TGGAGTCATAATAGTGCAGTGATACTTGCTGCTGCTGGGCTACACTGGAT
TATGGCACCCAAAGAGGATCTCAGAAGAATTGTCAAACCACTCTTGTTTA
TCTTGAGATCGTCTAGTGCCTCGGCATATGTGGCGCTCTGCAATATTCAA
GTGTTTGCTAAAGCGATGCCTTCTCTCTTTGCTTCTTACAGTGAAGACTT
CTTTATATGTTCCTCTGATACATATCAAATAAAGGCCCTCAAACTTGAGA
TATTATCTAACATTGCCACAGAGTCATCTATCCCGGTTATATTCCAAGAG
TTTCAGGATTATGTTAGAGATTCCGATAGGAGATTTGCAGCAGATACTGT
AGCTGCAATAGGTTTGTGTGCACAAAGGCTTCCAAATGTAGCTAATACCT
GTTTGGAAGGATTATTAGCTCTGACTATACCCCAATCTTTGAATAATGAT
ACCGAGTCTTCAGGTGGAGATTCAATTGTTCTAATTCAAGCAATCATATC
AATCAGATCAATCATAAAACTAGATCCACCACGTCATGAGAAGGTAATTG
TTCATCTGGTGCGAACTTTGGATTCAATTAAAGTACCCACAGCCAGGGCA
ATGGTTATTCGTATGATGGGAGAGTACAACTCCTCTGGTCACATTCTTCC
AAAGATGTTGACCTCAGTACTTACGTATCTTGCTTGCTGCTTTACTAAAG
AAGCACTTGAAACTAAGCTCCAGATTCTATATGCTGCTGTCAAGGTCGTA
TTATGTGCAAGAGGGGATGATCTATGTGCTTCCAAAAAACTCTTAAGCTA
TGTGCTTGAACTTGCCAAATGTGATATAAATTATGACATCCGTGACCGAG
CTCGTGTTATAAGAAAACTTCTTACGCAGTACTTATTTTCCTTTGAACTG
GTGGAAGAAGCACGATATATATCAGAATCAAAGAACATGTCATGTCTACT
AGCAGAACGATTATTTTTGGAAAAACCTAAATCAATGTCAACTGAACCCA
ATAACTATCGATTTTATCTTCCTGGATCGCTTTCTCAGATAGTTCTTCAT
GCAGCTCCAGGGTATAATCCTTTACCGGAGCCATGTAGTTTGACCATTGG
TGATAGTAGTTTCGGTTCAAATATCGTTAAGGGTGGCACTCACAGTGATT
TATACGGAGTAGATGATTCTGAAAGAGCATCGGGTTCTTCAGATGATGAT
AGTAACTCAAGTGACGGTTCTGAAATTTCTGAAGCTGGCTCAAGTGGCAA
TGATGTTGGTGATGAGAGTGGGTCTGCAAGCGAGGGTGACGAGAACACTG
GGTTATTAATTAATTTTTCAGATGTTGGTAATGCTGCATATGCAAACCTT
AATGGAAACTCAGAGGTGAATGATCCTCAATCCAGACCTAATGATTTTGG
CGAGCTCATGTCTAACCGAGCTCTTGAATCTTGGTTGGATGAAAGCCCTG
ATTCAAGCCGAAATGCTCCTGAATCAAGTAGTTTCCAGAATTCATCAGCT
AGAATATCTGTCGGGTCCCTCTCTGAGAGGGTAAAACCAAAATCTTATAC
ACTCTTAGACACTGTAAATGGAAATGGCTTGAGGGTGGATTATGTATTCT
CATCTGAAATGTCAAGCAAATCCAAATTTGTTTGTTTAGAAGTATCTTTC
AAAAATTGTTCCAATGAACCTAAAGAGAAAATTTTGCTGTTTGATGAGGA
CATTGAAGGGGGCCAAGATAACTCAGAGCAAGCATTGAGAACAAACGAGA
GTTCCTCAGCACCACATAACAATGATGTTAAAGTTATAGTTCCTGTGGAA
GAAATTCCTTGTCTAGAACCTGGTCAGAGTTCAAAGAAAATCATGGAAGT
TCATTTCCATCATCATCTCTTGCCTATAAAGCTAGTTCTACGATGCAGTG
GATTAAAGCTTCCTGTTAAGTTGTGGCCTGACATTGGATACTTTGTAAAA
CCCCTGCCAATGGATGATGAAGAATTCTTCAGGAAGGAATCTCAACTCCG
TGGGATGTTTGAATACAATAGAAGGTGTACCTTCATTGATCATGTGAGGG
AGCTGAAAGATGAAAAGGGTGAAATCTCTCTGGTAAAAGACAAGTTTCTT
GTCGTATGTGAAACTCTAGGATTAAAGATGCTCAGTAATGCAAATCTTTC
TCTCATTTCGGTGGACATGCCTGTTACTACAAACCATGATGATGTGTCAG
GTTTGTGCTTGCGGTTCGCTTGTGAGATTCTGAGTAACTCGATGCCTTGT
TTGATCACTGTTACCCTCAGAGGTAATTGCTCTGAACCGCTTAATACAAC
TGTGAAAGTCAACTGTGAAGAAACTGTATTTGGATTGAATCTGTTAAACA
AAATAGTCAGTTTCTTAGCTGAGCCCCCTCTTTAAGGTGCTAAATCTGTC
AAGTGATCAAATGTTTTGGCATCTGTAGTTTTGCGGAACTTTAAGTTGTG
TGCTTTCATATCCCATTGAGCTTGGGGATGCAATTGCATTTGTTGTCCCA
TTAGAAATACAAAATATATTTCATGACCATTATAAAAAATCCCTTCTCTT
TTTGGCTACTGTACTGCTGCTTAACTTGATATACATTTCAATGTTTGCGG
CTTTTAAGTGTCTTCTCTAGTTTAAAAAGCATATTTAATAGCCACAATAT
ATCAGGGGATGTTTGCTGTCTA
MFHQFGATADSLSKASTLVFRIGTDAHLYDDPDDVSIAPLLDSKFDSEKC
EALKRLLALIAQGFDVSNYFPQVVKNVASQSLEVKKLVYLYLLHYAEKRP
NEALLSINYFQKDLGDPNPLVRAWALRTMAGIRLHVVAPIVVVAVAKCAR
DPSVYVRKCAANALPKLHDLRLEENTGGIEEIVGILLNDNSPSVVGAAAA
AFASVCPNNLNLIGRHYKKLCETLPDVEEWGQIVLIEILLRYVIARQGLV
RESIMASPYSEYLDSEIDGPDRDFAVKEETNVVSIGAYQSQLLQMASKSY
LEGPEKYLSQMNFEDKGAFQSGLPKFTSAKNDDVKILLQCTSPLLWSHNS
AVILAAAGLHWIMAPKEDLRRIVKPLLFILRSSSASAYVALCNIQVFAKA
MPSLFASYSEDFFICSSDTYQIKALKLEILSNIATESSIPVIFQEFQDYV
RDSDRRFAADTVAAIGLCAQRLPNVANTCLEGLLALTIPQSLNNDTESSG
GDSIVLIQAIISIRSIIKLDPPRHEKVIVHLVRTLDSIKVPTARAMVIRM
MGEYNSSGHILPKMLTSVLTYLACCFTKEALETKLQILYAAVKVVLCARG
DDLCASKKLLSYVLELAKCDINYDIRDRARVIRKLLTQYLFSFELVEEAR
YISESKNMSCLLAERLFLEKPKSMSTEPNNYRFYLPGSLSQIVLHAAPGY
NPLPEPCSLTIGDSSFGSNIVKGGTHSDLYGVDDSERASGSSDDDSNSSD
GSEISEAGSSGNDVGDESGSASEGDENTGLLINFSDVGNAAYANLNGNSE
VNDPQSRPNDFGELMSNRALESWLDESPDSSRNAPESSSFQNSSARISVG
SLSERVKPKSYTLLDTVNGNGLRVDYVFSSEMSSKSKFVCLEVSFKNCSN
EPKEKILLFDEDIEGGQDNSEQALRTNESSSAPHNNDVKVIVPVEEIPCL
EPGQSSKKIMEVHFHHHLLPIKLVLRCSGLKLPVKLWPDIGYFVKPLPMD
DEEFFRKESQLRGMFEYNRRCTFIDHVRELKDEKGEISLVKDKFLVVCET
LGLKMLSNANLSLISVDMPVTTNHDDVSGLCLRFACEILSNSMPCLITVT
LRGNCSEPLNTTVKVNCEETVFGLNLLNKIVSFLAEPPL
| Relationships |
|---|
| The mRNA, XM_017367587.1, is a part of gene, LOC108199664. |
| The polypeptide, XM_017367587.1, derives from mRNA, XM_017367587.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |