| 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. |
TATACTGTATGTTGTTAAAACTCTTCTTGTTCTTAAGGTTGTCTAGCTGA
AGGGTTTTGTATGTCTGTCTGTATGTATATGTCACACAAAACAAAGTACT
AAGATATCCGTGTGTGTGCCTTGATTTTAATTCAAAAACACAAGTACAAC
AGAGAGTACTAGAGCTATTGTGTGCTTGAATGAGAAACTTGGATGATGCT
TATCTCAGTTCCAAAACAATGATCAAAGCTCTTGTTTTTGTGATACTATT
ATCCCTTTCATTTAGGTCAATCTCTGCCGTTGATTTTGAAGATGAAGATG
GACTAGTACAATGGCAGATCCTCACTAAATTCAATTTCTCTTCTCAGATC
CGGACCCATCCTCACATCCTGCTCCTGATCACTGTTCCATGGTTCGGCGA
ATCTCGATCTCTTATGAGGGATTTGGCTCAAGTGGTTAATAGTAAGCAAA
AGAAATTTGGTACTCTGAAGCTCATGTTTGTACATAGAAATAGTGATAAG
GTGCTTGCTGAAGCTCTTGGCGCTAAAGACGGAATAAAATTTTTGTATTT
TCGCCAATCTTTGTCTTACAAATACCAAGGCCCGCTTCGGGTACAGAACA
TATTGTCTTCTGTTTATCATCTTATGTCACTTCCGCCGAAAGATATTCCC
CTCAAATTTTTAACCACGGCCGAGGACTTGAAATCATTTACCGAATCAAC
TGACAAGGTATTACTAGTCATGGAATTCTGCGGATGGACCTCCAGATTAC
TGACCAAGGCCAAGAACAGTGTGACTGATAATGGATTTGAGAGTATCTTT
AACATTGCTAATGGAACATTTTCTCCAGGAGGGAAGAATATGCAGAAGAT
CGAAAGCGAACAGAACTGTGGTGCTTACAGTGGAAATCTTTGGACTGGAG
AGTTTTCCGCAAATAATATGAGTCAATTCCCGGGATCTGGGCTGCCTACT
GACGGGGATTTCTGTAGCTCTGAAGAGTTCCATAAGTATGAAACTTTTTT
GGTAGAGTTGTCGGTAATTGCAAAAGAATTTTTCCTGCCACCTGAAAGGA
TAAGATTTGGTTTGGTCCAGGAGAGAGCTCTGCTTTCATTCCTTGGTATC
AAATATTCTGGTCCATGGTTGGCGATGCTTCACTTTGCAGGATGCCCTAG
TTGTTCAAAGGTTCTGGGAGAAGGTGATGATATCAGACATGCTATAAAGA
TGCAAGCTTCACCTGTTTTAGAGCTTGAGGGTGATGCGAATGGTCTTGAT
CCTCCTATTCCTGCAAACAAGCCATCAATAGTTCTTTTTATTGATAGATC
ATCTGAGTCATTGGATGTTAGGAAAAAGAGCAGTGAAGCCCTTGGTGTAT
TCAGAGAATTGGCTCTGCACCATCAAATGAATGAGGAAACAACTGCAAAG
TCTCAAAGAACTTCCATGGGAAATTACCAATCGTCACTTAGTACTCTTGG
ACATCCTAAATTTGATATGTCTCCTTCATCTCAAAAGATAACGGAACTGA
AAGATAAGATGTCTGTCATGTTATTGGACAAGGGAAAACACATTACCATC
AATAAAGCTGTTACAGATTTACAAGGTGGCTCTTTGCAGGAGATACTGAC
GTATCTTATTCAGCATAAGAAAGAAATCAAAATAAGCTCACTTGCCAAAA
ATGCAGGATTTCAACTTTTATCGGATGATTTTACTGTAAAAGTTGCAGAA
GAGTCACCGGCAGACTTAAATGTGCAGTCTAATCAGGTTTCGACAGAAGT
ACAGGAAGAACATCCTGAAGGCAGTGACAGTGGTCATCTTCGCCAGAATC
AGACACCACATATGGCTGGTGGCAGAGTTGAAAAACCTGAAAATTCTGCA
GATGGTAAACAGAAAGAAGTCAAGGAAACTATTGTTGATTCAACCAAAGT
ATTATCTGCAGGTATCGATTCTCGTTATAATGTTGACCACATTGCTAATA
CTGCACACAGTGAGAAAATTCCTCCAAATGTTGATCACAATTTCCCAGGT
TCTGTGGGGTCCTTTTTCTTTTCTGATGGTGGATTTCGGCTACTTAAGGC
TCTGGCTCCATCGTCATCGATTCCAATAGTTGTAATAATCGACCCCCTTT
CCCACAAGCATTACTTGTTTCCTGAAGAGGAAGTTTTCGGATATTCTTCA
CTTAGTAATTTTCTGGAGAGGTTTAATAATGGTAGTCTTGTTCCATATAA
ACACTCCGAGACTTTTACGCGGGCCTCTAGGGAGTCTCCGAGGCCACCTT
TTGTAAATTCAAATTTTCATGCAGTGAACTCTGTCCCTCGACTTACCACC
AATACATTTTTGGAGTTAGTTGTTGGCAATCAATCAGATATGGCAAATTC
CAGTAATGCTTGGAAGAAGGATGTTTTAGTTCTTTTTAGCAATACTTGGT
GTGGTTTTTGCCAAAGAATGGAACTTGTTGTTCGTGAAGTATACTCGGCT
TTTAAGGGGTACTCGAGGATGCTGAAGGATAAACCTTCATTGATATCTGA
TAATGTGGAAAACACTAATCTGAAGCTCCCGTTGATTTACCTAATGGATT
GTACACTGAATGATTGCAGTTTGATCCTGAATTCATCTCTGCAGAGGGAT
CTCTATCCTTCTCTGCTGTTATTCCCAGCAGAAAGGAAAGAAGCTGTTCC
TTATGGAGGTGATATCACAGTAACTCAAATTATTAATTTTATTGCTGAAT
ATGGAAGTAACTCGGAGAGGCTTTTCGGAGAAAATGGTTTTTTATGGAAT
AAAGCCTCACAAAGAGTCAAGTATGGAAATTTGCATAAAGATGTGACACA
GACTTCAAATATTAAGGATCCTTCTTCATTGACAAATATATACCATGAGG
TTCTACTGAAAGACAGAGCACAGAAAATAGAAGTTAAAGATTATGAAATG
AGTCCGCAAAGGTACAATCGCCCACATGAAATAGGCACTGACCTGGTTGC
TGGTTCAATACTTGTTGCAAGTGAGAAGCTTGTCAATGTACATCCTTTTG
ACGGATCTAAAATTCTCATTGTTAAAGTAAATCAAAGTACGGGATTCCAA
GGTGTAATTATCAACAAGCATATCAGTTGGGACACACTAGGAAAATTAGA
TGAAGGTTTGGAACTACTAAAACGGGCACCTTTATCTCTTGGGGGTCCTG
TGATAATACGAGGAATGCCTCTTGTTTCTCTATCTCGAAAGCTTATGAAA
TATCGTGATCAGACTGCAGAACCTGAGATCCACTTTCTTGATCAGTGGGA
GACGCTTGATGTCATAAAAGCATTACAGGCGGGAGACCGTTCTATTTCAG
ACTACTGGTTTTTTATGGGGTACTCAAGTTGGGAATGGAAGCAGCTTTTC
GATGAGATTGCAGAAGGATCCTGGAAAATAAGCAATGGTATGGAACATTT
AGAATGGCCTGAGAGTGATTAGGCTCGCATGTTAAATTATTCAAAGTTTT
GGAGCTTTTTAATCAAGATTTTTAAGACCAGGAAAAGAAGGTAGACTGAG
TATCAAAGTTTTGAGGTTAGCAAATAGCAGCACATGAATCTGATGGGTAA
TCCCAAAAAAAGATCCTACTCCACACATTTTACTTTTGACAGATCAGTGT
AACAAAACATGTACATTAGTGATTTTGTATTCTATCTTACCATTTTTATT
TTTGACAGCCAA
MRNLDDAYLSSKTMIKALVFVILLSLSFRSISAVDFEDEDGLVQWQILTK
FNFSSQIRTHPHILLLITVPWFGESRSLMRDLAQVVNSKQKKFGTLKLMF
VHRNSDKVLAEALGAKDGIKFLYFRQSLSYKYQGPLRVQNILSSVYHLMS
LPPKDIPLKFLTTAEDLKSFTESTDKVLLVMEFCGWTSRLLTKAKNSVTD
NGFESIFNIANGTFSPGGKNMQKIESEQNCGAYSGNLWTGEFSANNMSQF
PGSGLPTDGDFCSSEEFHKYETFLVELSVIAKEFFLPPERIRFGLVQERA
LLSFLGIKYSGPWLAMLHFAGCPSCSKVLGEGDDIRHAIKMQASPVLELE
GDANGLDPPIPANKPSIVLFIDRSSESLDVRKKSSEALGVFRELALHHQM
NEETTAKSQRTSMGNYQSSLSTLGHPKFDMSPSSQKITELKDKMSVMLLD
KGKHITINKAVTDLQGGSLQEILTYLIQHKKEIKISSLAKNAGFQLLSDD
FTVKVAEESPADLNVQSNQVSTEVQEEHPEGSDSGHLRQNQTPHMAGGRV
EKPENSADGKQKEVKETIVDSTKVLSAGIDSRYNVDHIANTAHSEKIPPN
VDHNFPGSVGSFFFSDGGFRLLKALAPSSSIPIVVIIDPLSHKHYLFPEE
EVFGYSSLSNFLERFNNGSLVPYKHSETFTRASRESPRPPFVNSNFHAVN
SVPRLTTNTFLELVVGNQSDMANSSNAWKKDVLVLFSNTWCGFCQRMELV
VREVYSAFKGYSRMLKDKPSLISDNVENTNLKLPLIYLMDCTLNDCSLIL
NSSLQRDLYPSLLLFPAERKEAVPYGGDITVTQIINFIAEYGSNSERLFG
ENGFLWNKASQRVKYGNLHKDVTQTSNIKDPSSLTNIYHEVLLKDRAQKI
EVKDYEMSPQRYNRPHEIGTDLVAGSILVASEKLVNVHPFDGSKILIVKV
NQSTGFQGVIINKHISWDTLGKLDEGLELLKRAPLSLGGPVIIRGMPLVS
LSRKLMKYRDQTAEPEIHFLDQWETLDVIKALQAGDRSISDYWFFMGYSS
WEWKQLFDEIAEGSWKISNGMEHLEWPESD
| Relationships |
|---|
| The mRNA, XM_017374249.1, is a part of gene, LOC108204684. |
| The polypeptide, XM_017374249.1, derives from mRNA, XM_017374249.1. |
| NCBI Gene | |
|---|---|
| NCBI Nuccore | |