| 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. |
ATTGTTATCAAACCAAACACAGCCCTCTCTTAAAATTACAATCATCATCA
CCCGGGTCGATCATTCTCCAAGTTACCCACAGATTCACGAAGTATTAGAT
ATCAGTGAAACCCATCTAATACATAACTGTTTCCAGTATTATTAACTTGT
ATATATGTATATACATATATGTTTGTAGTTGCAGCCTTGCAGGTGTTATT
GTAAATCAATTATGGAGTTGGATTATGCTATTGAGCTTCAAGACGAAGAT
AGTTTCGGATTTGGTGACAGTAATGTTGATAATTCAGCCCTTGAAGGTGA
AAAATGTGGAATATGCATGGATATTGTCATTGATAGGGGAGTTCTGGATT
GCTGTCAACACTGGTACTGTTTTTCATGCATTGATAACTGGGCTACCATT
ACAAATTTATGTCCACTGTGCCAGAATGAGTTTCAACTGATTACTTGTGT
GCCTGTATATGATACCATTGGAAATAACAGCACTGATGAGGACTTGCAAT
CCAGAGATGATGACTGGTGCATTGAAGGAAAAAATAACACTTTATCTTTT
CCATCATACTATATTGATGAAAATGCAGTTGTCTGTTTGGATGGAGATGG
CTGCAAAGTCAGAAGTATGTCAGCATCAGTTGAAGAAGGCTTGGATTTCG
ATACATCAATTGCTTGTGATTCATGTGATTTATGGTATCATGCTTTCTGT
GTTGGATTTGATACTGAAGGCACATGTGAGAACTCATGGTTATGCCCAAG
GTGTACGGTGCAACATAGGTCAGATGAACTTTTATTGGGTCGGCCAAGCA
ACCAATGTGCTTCAGAAAATTCTAGCGATCAATGTCCTGTTGACCCTGGT
TTGTCAGGAAAATTAGTAGTATCTGTTGCTGATGCTGGAGAAACAGCTTT
GGTTGTGTCGATGCTTGAAGGGAAGCAAGAAACTAAGAGAAAGTTTCAAA
CCATGTCCAGTGTAGAAATGTGCGAGATGAAAGAACCATGGCAACTGTCA
GATTCTGTGGCTGAGGCTGGAAGGAAGTCTGGTACAGTAGCAGTTGAAAA
AACTGAAGAACAAGAAATGACAAAAGTCTTCCCAAGTTCTAATATACCCG
AGGATGTGAAAATGCATGCATCTCTTCCTAGTTCTTTCTTTAACAAGCAG
TTGTCGGAAACAACCATGTCTTTGAAAATGTGCGAGATAAAAGCACCAAC
TCAAGTGTCAGATTCTGTTGCTGATGCTGGAAGGAAATCTGCTACAGTAG
CAGTTGAAGAAACTGAAGAACAAGAAAGGACTAAGGTCTTTGCAAGTTCA
AATATACCGGAGGATGTGAAAATGCATTCATCTCTTTCTAGTTCTTTGGT
TAACGAGCAGAAGTTGGAAACACCATTAGAGAACAGGCATAGTGTTGGAC
CAAATTCAGTGGCGGAGGTACATAAATTGGCTGTATTACAAGAGTCATCA
GGCATGTTACCTTCAATTTCTGGATCTGCTTTTGGTGATGAAGGAATGAG
TGCACTACCTAATGGATCTGTAACTTCTATAAGCAAGTTACTAGATCAAC
ATTGCAGTAAAGCAACTCCTAGATCTGCTGACAACCAAGTGGGTATAGGT
GACACTGTTAAAGAATGCCCACTTCAAGCGGATGAGACCATGAAGAAGGA
TGCTAATGGAAGTCTTGGTACAAAGAGAAAGAATAGAGATTGGAGAGGTA
CCGAAGAAGTTAAAGCTAAAACGGCAAAAAAGAAAGTCAATGCTGAGGGG
AGCATGCAACAGATTCATGCAAACGATCATGCTGATGAGTGTGTTAAAAA
AAACACTCCAAAGGCATCTGGTGTTACTGTTTCGCAAAATAAAAAAATAA
TAGCAAATTCTACCATGCAGACAGCAACTACTAGCATAATGGACATAGTT
CGCGAGACGGATCGACTTGCAGAGACTTCCTCTAGGAGCCGAGAAAATGC
AGCTGGCTTGAGGGTAAAAAAAATATTGAGGCGACCTACTGAGGACAAGG
AGTCTTCTATCTTAGTTCAAAAGCTAAGAAAAGAAATCAGAGATGCTGTC
CGAAACAAAACATCCAAAGAGCTTGGAGACAACCATTTTGATCCAAAACT
TTTAACGGCTTTTCGGGCTGCTGTGGTTGGACAGGTGCCTGAATCAAAAA
ATTCTTTGCCTGTGGATATGAAGGCCAAAAAGTCACTACTTCAAAAGGGA
AAAATACGTGAAAATTTAACCAAAAAAATATATGGTATGGGGGGGAGGAG
GCGTAGGGCTTGGACCCGAGATTGTGACATTGAATTTTGGAAGTATCGGT
GCTCAAAAATTTCGAAGCCTGAAAAAATTGAGACGTTGAAATCTGTCCTC
AACCTGTTAAGGAAGAGTCCAGAGAGAACAGAAATCAAACATAAAAATGA
AAGTGCTGGTTCAAGTTCTATCCTATCACGATTATATTTAGCTGATTCAT
CTCTATTTCCTCGGAAGGAGGACATCAAACCTGTGTCAACACTGAAAGCT
GCTGCTATTGCTGCACAGAATAAAAATGTTAGATCTACAGAAAATCCTCT
GACTTCGGGTTACGGAAACAACTGTTTGGAAACTCTGGTTACAGAAGTTA
GTGCCTCACAGATGAAAGTTCCTCCGCCTAATATTGCAGCTACTACATCT
ATTGTTCCAACTTTGAAAGGTGAAGTTCCTTCCCATAAATCAAAGTCAAA
TAGATGTACAGTTGGGTCATCGATTCCTACAATAGCTGCTTCCCAATCCC
AGAAGGATCCAAATGGAAAACATGATATGCATACTGACAAAAGAAAATGG
GCCCAGCAGTTTCTTGCACGGAAAGCTGCAGTAGCAGGAAATAATGCATT
ACAAGAACAAGATGACACTGCTGTGCTCAAAGGACAGCACCCTTTATTAG
CTCAGTTACCAAGAGATATGCGGCCAGTATTGGCAGTCAGTCGTCATAAT
AAAATTCCCCTATCAATTAGGCAGGCTCAACTTTACCGCCTAACCGAACA
CTTTCTAAGAAAAACAAATATGCCAGTCAATCGCAGAACTGCCCAAATCG
AGTTGGCTGTGGCAGATGCAGTTAATATCGAAAAAGAGGTTGCTAACAGG
TCAAACAGCAAGCTAGTATATGTAAATCTATGTTCCCAGGAGTTGTTACA
TAGATCTGAGAGTACTTTGTCTAGTAAAGCAATGGAGTCTATCTCTAATC
CAGTTCCAGAAATTTCTGCTGATAGATTGGTGAAATCTACCATTGATTGT
TCAACCAGCTTGGCTGTTGACGAGGCATTAAGAAATGCAGGGCTTCTATC
CGATTCCCCACCAAGTAGTCCACATCGTCAATTAGAGGAAATAGAGAAAG
CTGATGATTCAAAAAGGTTTGTACACGAGGGACCTGATAGTGTATTTGAA
ATTGATTCTGAACCTGAACTGGATATATATGGTGATTTTGAGTATGATTT
GCAAGATGAAGACTTCATTGGTGCTAGTACATTAAAAGGATCTGAGTCGC
AAGCAGAAGAACCGAAATTGAAAGTGGTTTTCTCCACTATTGACTCTGAC
CGACCAAATGATACTGTGAAATTGGATAATATAGAAAAGCCAGTAATTGC
TGGGGAACCTGATAATTCTTCCAATTGTATTGACAGCCGAGCTGATACAA
CAAGCACTGGGAGTTTAATTATTAGTGGTAAGGCGGACAGGTCTGATCCT
CAGAGTTCTTTACTTGATGAAGGTGAAGAGCTTTCTCTTGCAGAATGTGA
AGAGTTATATGGCCCGGACAGAGAACCTTTAATCACAAAGTTTCCTGAAA
GTGTCTGTATGAAGCCTTATGATTTAACAGCCACAAACTTGGTCCCTGAT
AATAATAAAGACAATCTATCGAGTCAAACTCTTGAAGCATCTGACGAGAA
AAAGGCTTTGGCGAGAAACCAGGCACTGACCGCTGTTGTTGGCGATGTAG
AATATGAGTCCAAGCAATCCCGAGAATGCGTAATTATAAAGGAGAAAACA
GATAGCAGAAAGCAGCAAGATGGCTGCAATTCTGTTCATAAGAAGGTAGA
AGCTTATATAAAAGAGCACATCAGACCTCTCTGCAAAAGTGGTGTAATCA
ATGTTGAACAGTACCGATGGGCTGTCGGGAAGACAACTGAAAAAATTATG
AAGTATCACCACAAAGACAAAAATGCAAATTTTCTTATCAAGGAAGGTGA
GAAAGTGAAGAAACTTGCAGAGCAGTACGTCGAAGCTGCCCAAACCCAGA
GAGGATAATGAAATAATCAAGCAGTCACGGTTTGGAAATAGTCTGGCTTT
CAATTTCTATTCTTCAAGTTGATGACTTCAACAAACTTCGAAGGTGTATA
ATTTAAGTCCTATGTATTCTGTAATTATATTTACAGCAGAAAAATATATA
CCTGGCCTTGTAAATTTAGGACGGAAGTTATAACTCTTGAAATTAAGTTT
GAAAGTAACCGGAGTAACACTTTAAGAAATCACTGGTTTTGATTA
MELDYAIELQDEDSFGFGDSNVDNSALEGEKCGICMDIVIDRGVLDCCQH
WYCFSCIDNWATITNLCPLCQNEFQLITCVPVYDTIGNNSTDEDLQSRDD
DWCIEGKNNTLSFPSYYIDENAVVCLDGDGCKVRSMSASVEEGLDFDTSI
ACDSCDLWYHAFCVGFDTEGTCENSWLCPRCTVQHRSDELLLGRPSNQCA
SENSSDQCPVDPGLSGKLVVSVADAGETALVVSMLEGKQETKRKFQTMSS
VEMCEMKEPWQLSDSVAEAGRKSGTVAVEKTEEQEMTKVFPSSNIPEDVK
MHASLPSSFFNKQLSETTMSLKMCEIKAPTQVSDSVADAGRKSATVAVEE
TEEQERTKVFASSNIPEDVKMHSSLSSSLVNEQKLETPLENRHSVGPNSV
AEVHKLAVLQESSGMLPSISGSAFGDEGMSALPNGSVTSISKLLDQHCSK
ATPRSADNQVGIGDTVKECPLQADETMKKDANGSLGTKRKNRDWRGTEEV
KAKTAKKKVNAEGSMQQIHANDHADECVKKNTPKASGVTVSQNKKIIANS
TMQTATTSIMDIVRETDRLAETSSRSRENAAGLRVKKILRRPTEDKESSI
LVQKLRKEIRDAVRNKTSKELGDNHFDPKLLTAFRAAVVGQVPESKNSLP
VDMKAKKSLLQKGKIRENLTKKIYGMGGRRRRAWTRDCDIEFWKYRCSKI
SKPEKIETLKSVLNLLRKSPERTEIKHKNESAGSSSILSRLYLADSSLFP
RKEDIKPVSTLKAAAIAAQNKNVRSTENPLTSGYGNNCLETLVTEVSASQ
MKVPPPNIAATTSIVPTLKGEVPSHKSKSNRCTVGSSIPTIAASQSQKDP
NGKHDMHTDKRKWAQQFLARKAAVAGNNALQEQDDTAVLKGQHPLLAQLP
RDMRPVLAVSRHNKIPLSIRQAQLYRLTEHFLRKTNMPVNRRTAQIELAV
ADAVNIEKEVANRSNSKLVYVNLCSQELLHRSESTLSSKAMESISNPVPE
ISADRLVKSTIDCSTSLAVDEALRNAGLLSDSPPSSPHRQLEEIEKADDS
KRFVHEGPDSVFEIDSEPELDIYGDFEYDLQDEDFIGASTLKGSESQAEE
PKLKVVFSTIDSDRPNDTVKLDNIEKPVIAGEPDNSSNCIDSRADTTSTG
SLIISGKADRSDPQSSLLDEGEELSLAECEELYGPDREPLITKFPESVCM
KPYDLTATNLVPDNNKDNLSSQTLEASDEKKALARNQALTAVVGDVEYES
KQSRECVIIKEKTDSRKQQDGCNSVHKKVEAYIKEHIRPLCKSGVINVEQ
YRWAVGKTTEKIMKYHHKDKNANFLIKEGEKVKKLAEQYVEAAQTQRG
| Relationships |
|---|
| The mRNA, XM_017371094.1, is a part of gene, LOC108202616. |
| The polypeptide, XM_017371094.1, derives from mRNA, XM_017371094.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |