| 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. |
GTTGTATCTCGTAATTACTGAATTTGCTTCTTCGGTAGCTCGTTCGTCTT
GGTTGATTGCAAACACAGACAAGGAAGACAGCCCAGCGACATCGTGATAT
ACACACACATATACATACAACATATAGCTCAGCATACACTCTTCTTCTCC
GTAAGACTTCTCCGATCTGTACTTTCCCTTTGATTTTCAACACTCTCTTC
GCCATTACATACACATATAGATACACAATTCTGCAGATTCATTTCCACAG
CTTTGTCAACTTCTAGGGTTTGTGATTGTTCGATTTCTAGGGTCTGATTG
CTGTTATGAACTTGCTTTGAAGTGTCTAGGGTTTGAATTGAAGTTTCAAT
TTCTGAGAATTTTAGGTTAGGTTTTGTGATGATTTGATCTGGAATGGCGA
GGCTATTGGGATTGACTCGCGGCGAATACGAGTCGCCGCGAGAGGTTACG
AGAACAATCCCAACTAGTGATACTAGTACTGAGAATGGCTGGTTGATTAG
GTTTTTTGATTCTGCGTTTTTTTGTGAGTGGATTGCGGTTAGTTATTTGT
ATAAACATGATCATCCCGGTGTGCGGGATTATTTGTGCAATAGGATGTAT
ACGTTGCCGTTGTCTGGTATTGAGAGTTACTTGTTTCAAGTGTGTTATAT
GTTAGTTCATAAACCGAGTCCGTCGTTGGATAAGTTTGTTATTGATATTT
GTTCAAAGTCGCTGCAAATTGCGTTGAAAGTGCACTGGTTTTTGATGGCG
GAGTTGGAGGATTCGGATGATAATGAAGGGATTAGTAGGATTCAGGAGAA
GTGTCAGATTGCGGCTACTTTGATGGGGGAGTGGCCTACTTTGATTAGGC
CGCAGAATGTGTCTTCGAATCCACTAGGTAAGAATCAAGTTCTTAATAGG
CTGTTATCATCGAAGCAGAAGCTTTTGTCACTGACTTCGTCACCCCCTAC
TCAGCGTTCAGCATCGTTAACAGTCCCGTCAGGCAACTCTTTGCAGGAGG
ATGGTAGTAAAATATCATCTGACGAGAGTAAGATTTTTAAGAAATTTATG
CCGGGTCAAAAAGTAAGAGATGCATTACTTTTTAGAAAATCAGTGGAGAA
AGATGACGGGGAGACGGACAAGGATGGGTTTTTCAAGAGGCTCTTAAGAG
ACAGCAAAGACGAGGATGTTAGGAAGTCGACTGATAAAGATGAGGAGGAG
ACCGAGAAGGATGGTTTTTTCAGAAGGTTTTTAAGAGACAGTAAGGACGA
AGACGAGGAGCTCACATCGAGCTCAGAGGGTTTCTTTAAAAGGTTGTTTC
GTGACAAAGCTGATTTAGAGGTGGTTACCAAATCTGTAGAAGATGATGAC
AAGGAAGGTTTTTTTAGGAAGTTTTTCAAGGATAAATTTGAGGACAAGAA
GGATGGCATTGACCAAAAGGACATTGATTTGATAAAATCTGTTGAAGATG
ATGAAAAAGAAGGGTTCTTCCGGAAACTTTTTAAAGATAAATTTGATGAC
AAAAAAGATAATTTAGACAGAACTGATGAGGAGACCAAGGGGCCAACCAA
TGAAGACGAAGAAGAACATTCTGAAGTTCCATTATTCCGTAGATTTTTCA
GCCTGAACCATGGAGATAAGAAGACTCCTGGAACTGATGAACACAGTAAT
GGTTTGCATGAAGGCGGTGCAGGTAGTCCGGGGACGGAGAAATTTTTCCG
CAAGTTGTTTAGGGATCGTGATCGTTCTGTGGAGGACTCTGAAATTTTTG
GTTTAAAGAAGCAAAAGGAGAAACATCCTGGTTCGCCTAAGCAGCACAAT
GATAAATCAAATGTCAAGCCCCCTCTTCCATATAATGCTTCACAGTTTAG
GAAAGGGACGTATCATGAGTCACTGGACTTTGTGCAATCGCTCTGTGATA
CATCGTATGGTTTAGTAGATGTATTTCCTGTTGAAGATCGCAAAAGTGCT
CTTTCTGAGTCACTTACTGAGATCAATGCGCATATAACTGCTGCTCAAAG
TAGTGGAGGTGTGTGCTTCCCTATGGGAAAGGGTATGTACCGTGTTGTTC
ATATACCTGAAGATGAAGCTGTTCTTTTAAATTCCAGAGAGAAGGCACCA
TACCTGATTTGCGTAGAAGTTCTGAAAAGTGAGACAGTGAGCAACACAAA
GGATGTAAATAATAGTCAAAAACTTTTTAAAGGAGGAATCCCTGTAGCAA
ACGGAGATGCATTTTTGCCGAAGCCTCCTCCATGGGCTTATCCATTGGCA
GGACAGGACCGTTATGGTGGTTATGATAGGATGTCAAGATCTGCTTCAGA
TGCTATTGATCAGGCTATGGCTCAATTATGGGATGCAAAAGCTAAAGTTG
TTCATCTTGCTCTTTCAGTGGAGAAGCAACAGCTCAGCCAGTCGACAGAA
ACCGCAGATCATGATTCTAATTGTGTCATTCATCCTTGTGATCAATTTGA
TTCAGACAAAGAAGGTACAAACTGTGCAGCCAGAGGTGGTAGTCGTGACT
TGGAAAGAGTAAGGGTAGTTCTGACAGCAGATCCTGGGGTTAGCATGGAT
GACACGGAGGATCAAGAGCCACCACATCGGAAGGAACACCGACGTGTTCC
AAGTACAATAGCTTTTGAGGAAGTTAAGGCTGCTGCTTTGAAAGGAGAAG
CTCCTCTTGGACTTCCTATAAAAGGCGCTGGTCAAGATTCATCTGACTCC
CGATCACATGTTAGTAATGGTGATACGCCAAAAGCAAGCGATGCTTTATC
TGGTGAGCTATGGGAAGTAAAGAAACTGAGAATTCGTAATGCATCAGTAC
ATGGAAAATTACCTGGCTGGGACTTGCGCTCTTTAATTGTCAAGAGTGGT
GATGATTGTAGACAAGAGCATCTTGCAGTGCAACTAATCTCTCACTTTTA
TGATATATTTCAAGAAGCTGGTCTGCCACTTTGGTTGCGCCCGTATGAAG
TGCTAGTTACTTCTTCGTACACTGCACTCATTGAAACAATTCCAGACACG
GCATCACTTCATTCTCTCAAAAGTAGATACCCCAACATTTCCAGTTTAAG
ACAGTTCTTTGTCGATAAGTATCAGGAGAATTCTCCGAACTTTAAGCTTG
CCCAGAGAAATTTTGTGGAAAGCATGGCTGGTTATTCTCTTGTTTGCTAC
CTGTTGCAGGTCAAGGACAGGCATAATGGAAACCTTTTGTTGGATGAAGA
AGGCCATATTATACACATCGACTTCGGGTTTATGTTGTCCAATTCTCCTG
GAGGTGTTAATTTTGAGAGTGCACCATTTAAGTTAACCCGTGAACTTCTT
GAGGTCATGGATTCTGATGCCGAGGGAGTTCCAAGTGAATTTTTTGATTA
TTTCAAGGTTTTATGTATTCAAGGCTTTTTAACTTGTCGGAAGCATGCTG
AACGCGTAATTCTTCTTGTTGAGATGTTGCAGGATTCTGGTTTCCCGTGT
TTTAAAGGTGGACCTCGGGCAATACAGAATTTAAGGAAAAGATTTCATCT
AAGTTTAACCGAAGAGCAATGTGTGTCGTTGGTGCTTTCTCTCATCAGCA
GCAGCTTAGATGCTTGGCGGACACGTCAATATGATTACTATCAGAGGGTG
TTGAATGGAATTTTATGATGTAGATCTCACTGCTATGTTCTCAATTCTCA
TGATGAGCAGTCAGTAAGATGAAGCACTGTGAAGAACCAACTACGTCTGT
GAATCGTATTGTGATGGGGAGCAGTTGATTCATTTAGTGATGGGCTATAG
AGGTTTTGTTTGGACATCTGATAGCAGTTTGTGCCCTGCAATGGATCAAT
GTCAGAGCTCTATTATGGCTATATCCATCAGCATGAGTAATTTTCTTTTG
CACCAATTTTTGAATTATCATTTTGTTTCAAGGAATATGGACTGCGCTGT
CTAGAAGAAAATATATCAATTATGAAGCTGCAACGATATTATTCTTCGTA
TTCATGTTGGCCAGCCGGGACATAGTGTACAGGATTATGGAAATCAGCAA
ATTCTCTAGAAATGAGATTGTTATCAGGACCATACTCTCAAAGTTTTTAC
GCATTTGCGCAAAGAATCGGATTCCGCGCAATAGTCAGCTTGTACAATCC
ACTTCGTTCTATTTTCTGTGTCGAGGTCATTAACATATTAGTAGCCATTG
GAAAAGGCAAGCAGATTCTTGTTGATAACACCACCGAAGATATGCCATTT
AAGCTTTCTTCCAGATTCTGCAGTCGTCGGCAGAGACGCAAATTTGCAAC
ATAGGACGATTTCTGTGTAATATCTTGTTCATTAAGTTGGTTTTAAGGGT
CTTTCTTTTTTCTTCCCCATTTGATGAGTGCATACTTGTTTCATATTACA
ATCTTTTGCAACTTGATATGGAAAGTTAAGTGAGTTTGGTGTCCTACAGT
GTAGAGCCTTTTTAGCATTGTCCACAGATTTCAGGCGCAGAATGTACATT
ACTGTAATCTTTTACTTGAAACCAATTTTGATACAGGGTTTAAACTATTG
CACGTTTCTCGCA
MARLLGLTRGEYESPREVTRTIPTSDTSTENGWLIRFFDSAFFCEWIAVS
YLYKHDHPGVRDYLCNRMYTLPLSGIESYLFQVCYMLVHKPSPSLDKFVI
DICSKSLQIALKVHWFLMAELEDSDDNEGISRIQEKCQIAATLMGEWPTL
IRPQNVSSNPLGKNQVLNRLLSSKQKLLSLTSSPPTQRSASLTVPSGNSL
QEDGSKISSDESKIFKKFMPGQKVRDALLFRKSVEKDDGETDKDGFFKRL
LRDSKDEDVRKSTDKDEEETEKDGFFRRFLRDSKDEDEELTSSSEGFFKR
LFRDKADLEVVTKSVEDDDKEGFFRKFFKDKFEDKKDGIDQKDIDLIKSV
EDDEKEGFFRKLFKDKFDDKKDNLDRTDEETKGPTNEDEEEHSEVPLFRR
FFSLNHGDKKTPGTDEHSNGLHEGGAGSPGTEKFFRKLFRDRDRSVEDSE
IFGLKKQKEKHPGSPKQHNDKSNVKPPLPYNASQFRKGTYHESLDFVQSL
CDTSYGLVDVFPVEDRKSALSESLTEINAHITAAQSSGGVCFPMGKGMYR
VVHIPEDEAVLLNSREKAPYLICVEVLKSETVSNTKDVNNSQKLFKGGIP
VANGDAFLPKPPPWAYPLAGQDRYGGYDRMSRSASDAIDQAMAQLWDAKA
KVVHLALSVEKQQLSQSTETADHDSNCVIHPCDQFDSDKEGTNCAARGGS
RDLERVRVVLTADPGVSMDDTEDQEPPHRKEHRRVPSTIAFEEVKAAALK
GEAPLGLPIKGAGQDSSDSRSHVSNGDTPKASDALSGELWEVKKLRIRNA
SVHGKLPGWDLRSLIVKSGDDCRQEHLAVQLISHFYDIFQEAGLPLWLRP
YEVLVTSSYTALIETIPDTASLHSLKSRYPNISSLRQFFVDKYQENSPNF
KLAQRNFVESMAGYSLVCYLLQVKDRHNGNLLLDEEGHIIHIDFGFMLSN
SPGGVNFESAPFKLTRELLEVMDSDAEGVPSEFFDYFKVLCIQGFLTCRK
HAERVILLVEMLQDSGFPCFKGGPRAIQNLRKRFHLSLTEEQCVSLVLSL
ISSSLDAWRTRQYDYYQRVLNGIL
| Relationships |
|---|
| The mRNA, XM_017391591.1, is a part of gene, LOC108218589. |
| The polypeptide, XM_017391591.1, derives from mRNA, XM_017391591.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |