| 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. |
CAAATCTATAACGATCAAGTAAGTCTCTTCGGTGACTAACCTATACATAC
AACCTATACACACAGAAAAGTCTTGCTGAATTCAACTCCACCGTCTTCTC
CAAGGTACTCTCTTGTAAAATGGGGAAAGGAAGACCTAGGTCAGTAGAGA
AAGGTGGATTAGGGCAAAATTCAAGTCTAGGGTTAGTTAATTCGATATGT
ATACCATCTGCGCCTGTGTATTATCCAACTGAAGATGAATTTAAGGATCC
TCTAGAGTTTATTTACAAGATTAGGCCTGAGGCCGAGAGGTTTGGGATTT
GTAAAATCGTTCCGCCCGAGAGCTGGAAGCCTCCGTTTGCTCTTGATTTG
GAAAAGTTTATGTTTCCGACTAAGACGCAGGCCATTCATAGGTTGCAAGT
TAGGGCTGCGTCCTGTGACTCGAAGACGTTTGAGTTGGAGTATAGTAGGT
TTTTGGAGGGGAGTGGGGGGAAGAAGGCGAAGAAGAGGGTTGTGTTTGAG
GGGGAGGATTTGGATTTGTGTAAGTTGTTTAATGCGGTGAAGAGGTTTGG
GGGGTATGATAGGGTTGTCAAGGAGAAGAAGTGGGGGGAGGTTTCAAAGT
TTGTGAGGTCGGTGAGGAAGGTTTCGGAGTGTGCTAAGCATGTGTTGTGT
CAGTTGTATAGGGAGCATTTGTATGATTATGAGGTTTATTATAGTGAGTT
GAATCGTGTGGCGGAGAAGAGTGGTGTGCGTGATGAGAGGAAATGTGAGC
CAGAGGTGGATATGTTGAGTTCGAAAAGGAAAGGGAAGAATCAAGGGGAC
GGGGGAGTTGAGTTGGTTAAAGTGGAGGAGGGAGAGCTTGATCAAATATG
TGAGCAATGTAGAAGCGGGCTGCATGGTGAAGTAATGCTGTTGTGCGACA
GGTGTAATAAGGGTTGGCATATATATTGTTTGTCACCTCCTTTGAAACAG
ATTCCAGCTGGGAATTGGTACTGTTTAGATTGCTTAAATTCTGAGAAAGA
ATGTTTTGGATTTGTACCTGGTAGGCATATTTCACTAGAAGCTTTTAGGC
GTGTAGCTGACAGAGCGAAGAAAAGATGGTTTGGTTCGGGACCTACCTCA
AGAGTCCAACTGGAGAAGAAGTTTTGGGAAATTGTAGAGGGTTCAGCTGG
TCCGGTTGAAGTTAAGTACGGTAGTGACTTGGATACGTCCGTGTATGGGA
GTGGGTTTCCTCGGGTTAGCGACCAAAAACCAGAAGCTCTAGGAGAAGAC
GTTTGGGATGAATATCGTGCAAGTCCATGGAATCTCAATAACTTGCCCAA
GCTACAAGGATCAATGCTTCGAACGGTTCATCATAGTATTGCTGGTGTTA
TGGTACCTTGGCTTTATATTGGAATGCTGTTTTCATCTTTCTGTTGGCAT
TTTGAAGATCATTGTTTTTACTCGATGAATTATCATCACTGGGGAGAACC
AAAATGTTGGTACAGTGTCCCTGGCAGTGAAGCAAGTGCTTTCGAGAAGG
TGATGAGAAATTCCCTTCCCGATCTATTCGATGCTCAACCAGATTTGCTT
TTTCAGCTTGTCACCATGTTAAATCCATCTGTCCTGCAAAACAGTAATGT
TCCGGTTTACAGTGTACTGCAGGAGCCAGGAAACTTTGTCATCACCTTCC
CCAGATCATATCATGGAGGTTTCAACTGTGGCTTAAATTGTGCAGAAGCA
GTCAACTTTGCTCCTGCTGATTGGCTACCTCATGGAGGTTCCGGTGCGGA
TCTTTATAAACTTTATCGTAAATCTCCTGTTTTATCTCACGAGGAGCTTA
TCTGTGTTGTGGCCAAGACTGAATTTGATAGCAAAGTAACACCTTACCTA
ATGAAGGAATTGCTCCGTATTTACAACAAAGAGAAAAGCTGGAGAGCTAG
ACTTTGGAGAAATGGCATTGTGCGGTCTTCCTTAATGTCGCCTCGGGAGC
AGCCTCAGTATGTGGGTGTCGAAGAGGATCCTACGTGCATCATATGCCAA
CAATATTTGTATCTATCTGCTGTTGCTTGCCGTTGTAGGCCGTCTACTTT
TGTGTGTCTTGAGCACTGGAAGCACCTTTGTGAATGCAAAGCAAATAAAC
ATCGCCTCCTTTACCGTCATTCACTAGCAGAGTTAAATAATCTAATTCTG
AATGTTGCTGGGAGGGGTGACTACACAGAGGCTACCCAAGATAAAAATTT
ACAAAAGCAGCAACTCTATTCGCTTGATATTGGTACATTGTCAAAAAAGG
TAGGAAGTGTCCACGTCAACCTTGTGCAACTTGCTGAAGAGTGGCTTTCA
AGATCTTGTAAGCTTCTTCAGATGCCATACTCCATTGTTGCTTTTGCAAA
TGCACTAAAGGAAGCTGAACAGTTTCTTTGGGGTGGTTCTGAAATGGACT
CGGTGCGGGAAGCAACAAAGAACTTGATTGAAGCTCAGAATTGGGTAGAA
GGTGTAAAAGATTGTGTAGACAAAGTGGAATTGCGGTTATGCCATGGCAA
CAATGACATGGACAGAGTACATATGAAACATGTTCGTGGGTTGCTGAATA
TCGATTCTGTGCCTTGCAATGAGCCTGAATTTCTCAAACTGAAGGAATAT
GCAGAAGAAGCTGAAGTATTAATTCAGGACATTGAGTCTGCTCTTTCTAT
GTGCCCCCAAGTCTCCATTGTTGATTGGGAGATTTTGCATAGCAGAGCGT
TTGCCTTGGGGATCTTTGTCGAAGAAAGTGAAAAATTATCTAATAAGCTT
TCTTTTGTGAAGATCTGGGTCGAAGGTGTAAGAAAATGCATTATGGAAAA
ATCTCCAGCAGCGATTGAGGTAGACAGCTTGGACAAGTTGAAGTCTGAGG
TCTCAGAACTCCAAATTCAACTCCCTGAAATCGAAATGCTTGGGGATTTA
ATGAGGCGAGTGGAATCATGTCAATCTCGGTGTAACAAGATATTGGATGG
TTCTGTGAACCTAAAGCAACTTGAATTGTTTCTCCAGGAAATGGATGGTT
TCACTGTCAATGTGCCCGAGTTGAAACTTTTGAGGCAATATCAGAAGGAT
GCTGTCTTATGGATCTCCCGCTTTCAAATTGCTGTGCAAAATTCTGAACA
ATGTAATGATCTGGAGAATGTTGTTACTGAGTTGACACGCATCATAAAAG
ATGGGACTCTTCTGAAAATTCAAGTTGATGAGCTGTCACATGCTGAGATT
GAGCTAAAAAAGGCGGAGTGCAGGCTGAATGGACTTGAGGCTCTTCGACG
TAAAGTGCCTTTAGAAACTTTCAAAGAAGTACTGGGTGAGGCAAGCAGAC
TGCAGATTGGTGATGAGAAACTGTTTATCAATATTTTTGAAGTACTTACT
GCTGCTTTGTCTTGGGAGGAGAGAGCAAATCATATACTTTCAAGTGACGC
TCAAATATCTGATTTTGAGGATCTTATAAGGACATCTGAGGGCATTTCAG
TGTTTTTACCTTCTCTGGAAAATGTCAAGGAAGCAGTATCAACAGCTAGG
TCATGGCTGAATGAATCCAAACCTTTTTTGTATCCGTGTATCCCTGTTAC
ACCAGACTCAGATGGTTTGCTGAAATCGGAGGCCCTGAAGGAGTTGGTTG
CACAGTCAGAGAAACTGAAAATACGTTTGATAGAAATATCTATGCTTCAG
AAAATATTAGATAATTGCATTCAGTGGGAGGTACAGGCATACTCTGTACT
TGATTATACAGAGAGCCTACTAAAAATCAATTTAGAGGATGGTAGTGCCA
TTGGCTTAACAGCAAAAATTGAACTTCAAATTCATTCATTGGAATCCGTT
CTCAAAATGGGTTCTTGTCTTCCTATTGACTTTGCTGTGACTCAGAGACT
TGATGATGCTTCTGCTGTTCTTCGTTGTTGCTTAAAGTCTCTCTCCTTTC
GTGATACAACTCCAGTAATTGAGGAAGTTATGATGTTACTGGAGGTTGCC
AGCCACCTCCCCACTACTTATGCATCCTGTGAATTATGGAGTTCCCTGGT
TGGTGGGATGAGCTGGCTTAAGAATGCATTGGAAATATTCTTGCCTTGTA
ATCGTAGGAAATTCAAGTTGAGTTATGTTGAAGAAGTTTTTCGGCAATCA
CAGATTTTAAATGTATCTTTCCCAGCGATAGTAGATCAACTTAAAAACGC
TATCAAGAAGCACAATTTGTGGCTTGAGCAAGTCCAACAATATGCCAGTG
TGAAGTCTGGTGACCGGTCATCGTTTTTGCTGTTCCAGATTAAGGAACTT
GGCAGCACTGATGCCTTTAATTGTTTGGAACTGGAAATGGTCTTTTCTGA
TGTGGAACGGGTTGAGCAATGGAGGCACAACTGTGAAAATATTGCTGGGT
TGGTTGGAAATGTTAAGTCACTACCAGATGCTTTGGCTGAGATAAGCGGT
ACCCTTGATAGGTCCCTGCATATATATAATTGTAAGGGACGCAAACTAGA
ACAATTATGCATACACTGCTTCTGTGGGTCAAAGGATCAGAAGCTCTTGA
CTTGTTCTATCTGCAATGACTGCTACCATTTCAGGTGCATTGAGCCGATA
GGACACGGTGATCCAAATAATTGTTTAAAATGTATATGCCCGTATTGTAA
CTTTATAAGAAGTGGGAACATAGCTAGAAGTGGAGGGGGCTATTTGACAA
AGAGAAAGCAGTTACCTAGCCTGACTAAGCTCACTCGAATTTTATCTGAA
GCGAAGCTTCTGTGTGTGTGGATCAAGGAGAGGGATATACTTCTCCAAAT
TGTTGAAAAAGCTGAATTGTGCAGAACACGCTTAACAGAAGTAGCTGATA
GAGTCTTGGCGCATGTTGACAAGGATCTCGATATAGTGGCTGAAAAGCTT
TCCACAGCATTAAAGGCAGTTGAAGCTGCAGGAGTGTATGACCATGATAG
CAACTGCAAATTTGAGATGGCATTAGCAAGGAATTCATGGAGGGTTAGAG
CCCAGAAACTGTTAGAATCTTCGCTCAAGCCTACAGTTCAACAGATTCAA
CGTCATTTAAAAGAGGGTTCTGCCATCAGCATACCGGTGGGAGATTACTT
CAGGGAGAAACTTATTGAAGTGAAGCATCGCTGCGTGCAATGGGTCGATA
CGGCGAAGAAGGTTTCGGTGGATTCTGGGGAACTTGAGTTGGATAAAGTT
TATGACCTAATAATAGAGGGGAATGATTTGCTTGTTGACGTTGAAAAAGA
ACTCAAGCTTTTGCAAGATAGAAGTATGCTCTACTGCATATGTCGAAAGC
CCTATGATCAGAGAGCAATGATTGCTTGTGATAAATGTGATGAATGGTAT
CATTTTGATTGCATCAAGTTAACTTCACCACCAAAGGTTTACACTTGCCC
TGCATGTAAGCTGGACAATGAATATTTGTCTTCGTCACTATCATCATCAC
AGGAGAGGTCTACCAACAAATGTGAAGAGCCCCAGACACCTTCTCCAGGA
AGACCAGGTTCAAGGAGGAGAACAAAACAGACGGATTCTCTCTGTAGAAA
GAGAGACAAACCAGACAGCACTGAAAATAATATTATCTCAAGGCTTCCAA
CTGGTTTTGGAAATTTGTTGTGGAGAAATAGGAAGCCTTTTAGAAGAGTA
GCCAGAAAACGTGAAGAGTTTAACATTCTGTCCCTTTATCATTTACAACA
ATGACTTTTATTTACTCTTAACATTTAATTTATTCAATTAATTCATATAT
C
MGKGRPRSVEKGGLGQNSSLGLVNSICIPSAPVYYPTEDEFKDPLEFIYK
IRPEAERFGICKIVPPESWKPPFALDLEKFMFPTKTQAIHRLQVRAASCD
SKTFELEYSRFLEGSGGKKAKKRVVFEGEDLDLCKLFNAVKRFGGYDRVV
KEKKWGEVSKFVRSVRKVSECAKHVLCQLYREHLYDYEVYYSELNRVAEK
SGVRDERKCEPEVDMLSSKRKGKNQGDGGVELVKVEEGELDQICEQCRSG
LHGEVMLLCDRCNKGWHIYCLSPPLKQIPAGNWYCLDCLNSEKECFGFVP
GRHISLEAFRRVADRAKKRWFGSGPTSRVQLEKKFWEIVEGSAGPVEVKY
GSDLDTSVYGSGFPRVSDQKPEALGEDVWDEYRASPWNLNNLPKLQGSML
RTVHHSIAGVMVPWLYIGMLFSSFCWHFEDHCFYSMNYHHWGEPKCWYSV
PGSEASAFEKVMRNSLPDLFDAQPDLLFQLVTMLNPSVLQNSNVPVYSVL
QEPGNFVITFPRSYHGGFNCGLNCAEAVNFAPADWLPHGGSGADLYKLYR
KSPVLSHEELICVVAKTEFDSKVTPYLMKELLRIYNKEKSWRARLWRNGI
VRSSLMSPREQPQYVGVEEDPTCIICQQYLYLSAVACRCRPSTFVCLEHW
KHLCECKANKHRLLYRHSLAELNNLILNVAGRGDYTEATQDKNLQKQQLY
SLDIGTLSKKVGSVHVNLVQLAEEWLSRSCKLLQMPYSIVAFANALKEAE
QFLWGGSEMDSVREATKNLIEAQNWVEGVKDCVDKVELRLCHGNNDMDRV
HMKHVRGLLNIDSVPCNEPEFLKLKEYAEEAEVLIQDIESALSMCPQVSI
VDWEILHSRAFALGIFVEESEKLSNKLSFVKIWVEGVRKCIMEKSPAAIE
VDSLDKLKSEVSELQIQLPEIEMLGDLMRRVESCQSRCNKILDGSVNLKQ
LELFLQEMDGFTVNVPELKLLRQYQKDAVLWISRFQIAVQNSEQCNDLEN
VVTELTRIIKDGTLLKIQVDELSHAEIELKKAECRLNGLEALRRKVPLET
FKEVLGEASRLQIGDEKLFINIFEVLTAALSWEERANHILSSDAQISDFE
DLIRTSEGISVFLPSLENVKEAVSTARSWLNESKPFLYPCIPVTPDSDGL
LKSEALKELVAQSEKLKIRLIEISMLQKILDNCIQWEVQAYSVLDYTESL
LKINLEDGSAIGLTAKIELQIHSLESVLKMGSCLPIDFAVTQRLDDASAV
LRCCLKSLSFRDTTPVIEEVMMLLEVASHLPTTYASCELWSSLVGGMSWL
KNALEIFLPCNRRKFKLSYVEEVFRQSQILNVSFPAIVDQLKNAIKKHNL
WLEQVQQYASVKSGDRSSFLLFQIKELGSTDAFNCLELEMVFSDVERVEQ
WRHNCENIAGLVGNVKSLPDALAEISGTLDRSLHIYNCKGRKLEQLCIHC
FCGSKDQKLLTCSICNDCYHFRCIEPIGHGDPNNCLKCICPYCNFIRSGN
IARSGGGYLTKRKQLPSLTKLTRILSEAKLLCVWIKERDILLQIVEKAEL
CRTRLTEVADRVLAHVDKDLDIVAEKLSTALKAVEAAGVYDHDSNCKFEM
ALARNSWRVRAQKLLESSLKPTVQQIQRHLKEGSAISIPVGDYFREKLIE
VKHRCVQWVDTAKKVSVDSGELELDKVYDLIIEGNDLLVDVEKELKLLQD
RSMLYCICRKPYDQRAMIACDKCDEWYHFDCIKLTSPPKVYTCPACKLDN
EYLSSSLSSSQERSTNKCEEPQTPSPGRPGSRRRTKQTDSLCRKRDKPDS
TENNIISRLPTGFGNLLWRNRKPFRRVARKREEFNILSLYHLQQ
| Relationships |
|---|
| The mRNA, XM_017379505.1, is a part of gene, LOC108208906. |
| The polypeptide, XM_017379505.1, derives from mRNA, XM_017379505.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |