| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017366264.1, is a part of gene, LOC108198511. |
| The genetic_marker, MK003628 K1072, is located in gene, LOC108198511. |
| 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. |
| Transcript Name | Identifier | Type | Location |
|---|---|---|---|
| XM_017366264.1 | XM_017366264.1 | mRNA | DCARv2_Chr8:28056711..28062648 |
TATGTGTGGTGTAAGTTCATGGATTTTACAATGTTGTGAAACCAGTTATA
ATAATTTTAAGTACAACCATATCTCAAAATGGGTGGTAACTGAGTTTAGT
GTAACTAAAATAAGCCAAACACTCTTGATTTGTACTTGAACAAATCTTAT
ATACCATCATTTAGGTGAAAATATGTCATATTAATGTTACTTAAAATGTT
AACTGAATAAAACAAAATCAGACATAAAAAACATGCTCAATGTAGTTCAA
AATTGAGATGAAGAACACAAAAGGAGAAAAGCTATCGGCTGGCTCTGAGC
AAGGGCACTTTGTTTAATGAGTGAAGACAATATTCTTACATAAACGGCTA
TAAAGTGCGTTCACAAGTTGAACATGCTAAGAAACTCATAAGTCTCAGCC
TCTCAGGTATGCTACTCATAACTATTCTTCTATGTTTGCATCTTAGCGGT
TTTTGTTTTTGATATATAACTCTAAATGTTAAACAATAGATGTCTTTGTC
GACGCATGCTTTAACAGATTAGCTTGAGCCTTGCTGATTCATTCAGTTAT
GTCTTGTTTGAATCCAATTTATGATCCGATTAAGGCCATGAATCTATGTT
TTTCCCATTGTGTGATTTTCTATAGTTCAGTTACTGTCATTTAATACACA
TATGATCTTTGCTACTTTATAACTTATAAGCAACTTTAATTTGATTGTGT
ACAGCAGATAAGAAAAGGGCATGGAGTGGAACTGGAATCATGTTATTTGG
CTGGCGTTGATAAGTTTGGTTTCACTTGTTTGGCACTTGAAGAATAGACG
CGGACGTTCTAAACTCCCCCCTGGTCCTAAGGGCTGGCCACTTATCGGCA
ATCTTCTTGAACTTGGAAGCTTGCCACATAGGAGACTGGAAGCTCTTAAA
AAGGACTATGGTCCTGTTGTGTGGTTGAATATAGGTCCTATCAAGACCAT
GGTGATTCTCTCTGCTGGTGCAGCCGAAGAGTTGTTCAAGAATCACGACA
TCAACTTTGCTGACCGGTTTGGAAACGACTCAATGAGATCACATGATTAC
TACATGAGCTCTATGGCTGTAGGTGCATATACCAGCTACTGGCGCACTTT
GAGGAAAATATGTACTGTCGAGCTCTTCACTAATAAGAGAATCAATGAAA
CGGTTTTAGTTAGGAGAAGATCCGTGGATGAGCTGCTGGTGTGGATAGAA
AAGGAAGCAGACAAAGGTGCAAGTGATGGAATTGAAGTTATCAGCTTTGT
GTTTGCAGCATTGTTTAATATGGTGGGGAATCTCACGCTGTCTCGGGATT
TGGTGGATCCATATTCGACGATATCCTCTGAATTTTGCGACACTTTGTCA
GGATTCCATCAGTGTCTGCTCCATCCTAATATTTCTGATTTGTTTCCCTG
GCTAAGTAGGTTTGACCTGCAAGGAATAAGGAGGAGAATGGACGGATATT
TAGGCAAAGCCATAGAAATAATCTCCGGATTTGTGAAGGAGCGTGTGAAA
GAGAGACAAAAAACGCAGAAATTATCATCAGAGCAAAAGAAGGACTTCTT
GGATGTGCTGTTAGATTATAGGGGAACCGGAAGGGATGAACTAGATTCAC
TATCAGAGCACCAAGTCACAATTTTCCTAATGGTAAGTACTTCTAATTGT
ATATTTTGCGGATTAGTATTTGGTGAAAACACTAATTTTACAAGTGCATA
ACATGCAGGAAATGTTCATTGCTGGAACACACACGTCAAGCACCACGACT
GAGTGGGCGCTGAGTGAGCTCTTGCAGAATCCTGATCAAATGAAGAAGGT
TAAAGCCGAGCTTGCTAGAGTCGTTGGAGCCAAGACTAGACTACAAGAGA
GTGACATTGATAATCTCCCTTACTTGCAAGCAATTATGGAGGAAACGCTA
CGCCTCCATCCTCCAGCTCCAATTTTACTTCCAAGAAAGGCGGCTCAAGA
TACCACTTTCATGGGCTATAACATCCCGAAAAATACACAAGTTCTAGTCA
ATAGCTGGGCAATTGGAAGAGATGAGGAGAATTGGAAGGATGCTTTGTCA
TTTAGGCCTGAAAGGTTTCTCAACTCGAATATTAATTCCAAGGGTCAGAA
CTACGAGCTTTTACCATTTGGCGCTGGGAGGAGGATTTGTCCGGGCATTC
CATTAGCTCATCGCATGGTGCCCTTAGTCCTCGGCTCCCTGCTTCACCAT
TTTGAGTGGGAGCTTTGTGATGGTCTGAAGAAGATAGACATGACGGAGAC
GTTGGGGGCAACTGCAACTAAACGAGAACTCTTGCGTGCAATCCCAAAGC
TCAAGACAATATAAATACAGAGTTTGTGTGATCGAAATAATGTCAAGTGT
GTTTACTTTTATTATGTTTAACCATTTCAACGCGTTAAAAGATTGTTGCC
AATAATCATTTGTCACACGGTGAATATGTCAGGTTTTGAGGGCCTCAAGT
CTGCAAATTCTGTCCTTTAAAATTTTTCTGAACTGTCAGTACTTCTTACG
AGTTCAGATTATGTATCATTAGATACCGTTATGGCTTTATTATCACCTTG
ATACTCTTGCTGATCATTTTGATATGTGACTCATTGGGCGATCAATCGGA
AAATTATCAGATATCTGTAAATGTATGTAAAGAAGGAAAAACATGCATTT
TTCAAGCAGTGTTGTAAAAAATGAAAATCATCATTCATCGTAATACCAGA
GTTTTAGAACACTAGTTGTTAAACAACCTTGTAAAGTTTGAAAATCTATG
CATTCGACTTAACTGAACACTGCCAATTTCAAATATACAACTAGTCGAGC
CGCGCAACACACATTAACTCCACATTGTCCGCCTGGGCCGTGACCAAACT
CGCATGGATTTATTTTTGGACTCCTCCCGAAAGACCTCATACTAATGGGG
TTGTTTTGGCTGCTTATATTCAAAACAAATCTTTTCCTTCTTTATGATGT
CGGACTACGGTTGACACCCACTCAACATGTACAACTACTTTTGGGTGTGA
TCAATCGAGTGAAAATCGGATACAAACACTTTCTGCAGAGAACTTGTACT
AATAGTTTGCCATGCATATTAGTTCTTCTGGCTAAATGAGCAGTTCTGGA
ACCATTCTGCTGTGTGTGTAATGATGCAACTGAAACTTTATTTTGTTTAA
GCAAGTAGTGGCCCTTTATCGTGGTGTCACAAGCCCCTTTCGCTGAGGCC
TTGGCATGCAGAGAGGTTTTAAGTTGGTCGAAGAGGATTGCCAGATGCTC
TGCAGAATGTTAGTTCCAAGGCACATGTTTAGTGTTTTATTTCTCTTTTT
TGAACTTTATTAAATAACAAAAGATTCGATTGTGTTATCAGTTTCCTGAA
AATTGAACTTGGGAACAGACGTAATTAGTATAGTAATGAGTAGCACGTTA
TAGAGGCCGAGACGTGGCAGTTGGATTCCTTCTTGGTGGATTGTACTGTC
TTTTAGGTCCGTGAACTTGGCGTGCTCAATAATTGAAGGAGCGTGCTGCT
TCGCTAAAATGTGCCCAAACATGGCACAGAACATGAAACACAACTTTGGA
AATCAGCGGAGTGTCACTTATAGTATAAAGTAAGAAATCAGTTAGAACGC
GAATGGAGAAAAAAATATCACCCTGTCAGTTGTCACTAGCTGATAATATA
GAATATGATGGGGCTGACAATTTGGAAAATGAAGGGCGTTAATGATTTAC
GTCGACTCATGGCTGGCTCTGGCTATAAACTGTGCTCATAACTTCAACAT
GCTAGCCGACGTAGTGTGTTCACAGGTTCAGTTGCTAAGAAGTTCACAAG
TCTCAGCTTCTCAGGTATGCAGAATTTTTGCAGAATCTCAAAAATAATTT
CACAGAATTTTTGGGGAATTTTTCACTTTGAGGAATTGATTCATGCATGT
AGACATTACAGGTATAACTGTTCAATTTATAAGAAATTTTATTTTGACTC
TGAACAGCAGATCTGAAATTGTGTCATGGAGTGGAACTGGAACTATGTCA
TATGGTCCGCATTGATATGTTTGATTTCACTTGTTTGGAGCTTGAGGAAG
AATAGTTACAGACGTTCAAAGCTCCCTCCTGGCCCTAAGGGCTGGCCATT
GTTCGGAAATCTTTTTGATCTTGGAAGCTTGCCTCACAGGAGTTTGGAAG
CACTAAAACAGGACTATGGTCCTGTTGTGTGGTTAGATCTTGGCAGCGTC
AAGACCATGGTGCTTCTTTCTGCTGCCCCTGTCGAAGAGTTATTCAAGAG
TCATGATCTCTCCTTCATCAACCGGATCACTAATGATGCAATGAGGTCAC
ATGATTACTACCAGAGCTCTATAGCATTTGGTCCATATAGTGTCTACTGG
CGCACCTTGAGGCGGATATGTACCTCTGAGCTCTTTGCAAATAAGAGGCT
CAATGAAACGATGATGAATAGGCAAAAAAGCGTGGATGAAATGTTGCTAT
GGATCCAGAAGGAAGCAGAAAGAGGTACTAGTGGAATCATAGTTCGACAT
TATGTGTTTCCAGCATTGTTCAACATGATTGGGAATGTCACGCTGTCTCA
GGACCTAGTGGATCCACAGTCGAAGACCTCCTCTGATTTTGGCATCGCGT
TGGATGGTTTCCATCAATGTCTAGGCCGTCCCAATATATCTGATCTGTTA
CCCTGGCTAAGAAGGTTCGACCTCCAAGGAATAAGGAGGAAAATGGATCA
AGATTTAGGAAAATGCCTAGAAATTATTTCAGTATTCGTCAAGGAGCGTG
TGAAGCAGAGGCAACTACAAGAATCATCACAACAGAGGCAACTACAAGAA
TCATCACAACAGGACTTTTTGGATGTGTTGTTAGATTACAGGGGCAGTGG
AAATGACGAACCAGCTAAACTATCAGAATTCCAAGTCACAATTTTTCTAA
TGGTAAGTCCAAGAACAGAATTTGATAACAGTCTCTCTACTTTAAGGATA
GGGGCAAGACTGCGTACATTTTACCCTCCTCAGACCCTGCTCTAAGCGGG
ATATACTGAGTATGTATGGTATGGTATCTATACTTTTGTTGTTTGTGAAC
TACAATAGTAGAGTTATCTGACTGCTTATATTCTAGCTATATGCTCCTTC
CACAACCGATGTGAGACAGCTCCTAACACTAAGCGGGTAAGATTTGTGCA
GGAAATGTTTATTGCTGGAACGGATACAACAAGCAGCACGACTGAGTGGG
CGCTGAGTGAGCTCTTACAAAATCCTGAGCAAATGAAGAGAGTTAAAGCT
GAGATTTCCAGTGTCGTTGGAGCAAACAAACAACTGAAAGAGAGCGACAC
TGATAAGCTACATTATCTGCAGGCCATTGTGGACGAGACACTACGCCTGC
ACCCTCCTGCTCCAATTTTACTTCCCAGAAAGGCGGTCCGAGAGACCAAC
TTCATGGGCTATACTATTCCCAAGGACACACAAGTCTTAATCAATAACTG
GGCAATAGGGAGAGACAAAGATTTATGGGAGGATCCTTTGTCATTTAAGC
CTGAGAGGTTCTTGGACTCGAAGATCAACTACAAGGGTCAGAATTACGAG
TTTTTACCATTCGGAGCAGGGAGAAGAATTTGCCCGGGCCTTCCATTGGC
TCATCGCATGGTACCCTTAGTTCTAGGCTCCCTACTTCACCACTTTGAGT
GGGAGCTTTGTGATGGTGTGAAGACTATTGACATGAGGGAGACTCTGGGG
TCAGCATCGAAAAAACTAGAACTCTTACGAGCAGTTCCAAAACGAAAGAT
GACTTAATAGTAGTTACTAAAGCTTATAAGCTGGTTTTTTGGAACAGGCC
AGATGAAATAAAGTCAGGTAAGGTAGTTTGGAAACAAGCAAAAATAAAGA
CAGTTGAGGTACTGGATTTGTGATTGTTGTACTATCTTGTTTGATGATTG
AGTATTATGTTCGTGTCGGACACTCGACACTTCCACC