| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017398068.1, is a part of gene, LOC108223691. |
| The genetic_marker, MK006287 K3731, is located in gene, LOC108223691. |
| The genetic_marker, MK006443 K3887, is located in gene, LOC108223691. |
| The mRNA, XM_017398069.1, is a part of gene, LOC108223691. |
| 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_017398069.1 | XM_017398069.1 | mRNA | DCARv2_Chr5:39681118..39685959 |
| XM_017398068.1 | XM_017398068.1 | mRNA | DCARv2_Chr5:39681118..39685959 |
GTTGGCCTCTGTGAATCCAAATTTGAGTCAAACTGTACTCTTCTCACTCC
CTAGTCCCTCTCTCTACAAATATTTACACTTTGTATTTCTATTTTCTAGG
GTTTGCTCTGACTCTTTGAGCTCTGCCCCCAAAATCCAAATCCACCTAAT
CAAGAGCCTCCCTTTTAATTCGCCTATATTTTCATTGCCCCATATCCAAT
TCTTGCTCATATACAAAACCCAGCAATTGGATTCTAGGGTTTGATCAGTT
CAAGAACAGAGACCAAGATTCACTTCACGAATAAGGTGAGATTTTTAAGT
GGCCCTTTTGTTTATAGAATCTGGGTGATCTCTTTTCTTGTAGATTATTG
TTAATATCAATGTTGTTATCGATCTTTTTTGTGATTATAAATAGTTTTAA
GCTCATGGTTTTGTAAGTAGTTGTATGGATTGAAAGAGATTAGCATATGG
GTGATTGGATGTGCCAAAAGATTAGTGGTGATGTTAGTTAAAAAAATCTT
GTTTTTTTTAATCCTAATGTGTAGCGTTGCTCTTTTTATTATTGTGTTGG
TTGGATAGATAAGTACTAATTTTCAAGTGTTATATCCTTGGAAAATAGAA
TGTATTGATTTTGCAAATTGGTGGAAGGTTGTAAATTAATGTTTGATTGA
GATTTGATGATGCAGATATACTTTAGAAAGCTTTATGTGACATTATCGCT
ACAACTACAAGCTAAGAAATACGTAGACGACACAGAAGTAGCAATAAATA
AACGCGGAATATATCTGTTATATGGCCCAAAAGTGAAGCTCCTTACTGAT
AAACCAACTATTCAGTAACTAAAAGATAATAAGTAAAATAGGAAATTGAA
CTGTCCTAAACGGCAATGTTTTTATATGTTCGACCAATTACTAAATTAAC
CCTATTTAAGAGGACACTGTTTCAGCAACAATATAAAACGTAAGAGTAGC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCACACACC
CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGAAACGGGTAC
GCTACCACGTACCGCGATCCAAATCGTTCGTACCCGAAACGCAAACGGAA
ACGTTCGGGGTCGCGACCTAGATCGCCGGAAGTGACGACCCGCAAGAACA
CACTTCATTCTTGTTCTGAACAATAGATCCATGTTTATGTCATATGATAA
GTAGTTTATTTTATCAATAAATGTGTACTTTTATTTGTTATTCAACATCT
TTTTCTCTAAAAAAATTTATAAATGTATAAATTATCAACTAAAATTGTAT
ATTATAATGGAATTTATATATATGATTATAGAATTCTTTTTAAAAGGACC
AGGTGTACCCATACGTTCCATCGTACTCATACGTTTCATCGTACCGGATT
CACTAAAACTAATGTTCCGCGTACCCGATTTCGTTCCCCGTTTCGAATCG
AACCAAGTCTTATGTAACTATGGAATGTGTTTTAGCTTCTTAATTACGAT
TTACTTATTTACAAATATTGCATGTAATGGTTTGAAGATATGTCACTTTT
TGAAATACCCGATAACTTTGGGGGAACTTGAATCTGTGCATTTTTCTAGC
TAGTTTACTAGTTATAGTAGAAGTGAGAACCTAAGAAACCCTAGGTCCAA
TGCATTAAAGGAACCATATAGAACAAATGTTTTGTTTACAGTTTTATGGT
CTATATTTTTGCTAATAGTTTTTGGTAATAAAGTTGTTTTTTGTTTTATA
TCCTGCTTTACCTTTATGTGTTTACGGTTCAGGTCTTTAACTTCCTTTGT
GAAGGCAAGTGGAGGTTCTTGCTTTCTGATTTATTCGTGGATGTGCTCTA
AGTTATGATATTATTCATAGGAAATAAAGCAGTGCAAGTAACAATAAATC
GTGTGAGGGGCTAAGATGCCATCTACTCATCTTTCTACACTGAGGAGTGC
CATCAGGCAGGGAATAAAAAGTTCATCTACCGGAGCAAAAGTTAGCATCC
AGGATTCTGTGGAAGTTGGTGTTAGCCTAGGCAAAATAATTGGCAACTCC
AGGCTGTTGCATTCTCTATCAGACTCATGTTTTTCTAAACTGAATGTGCT
TTTAGAACCTGGTACTACTGTTAATGCTCAATCAAATTTACATATAGTGA
ACCGAAGAAAAAATATTTCAGTTGTTGGAGCTGTCCCTCGTACATTTTCT
ACTCCATCAGTTTCTGGGCCATCCTTTGAAGTCTGTGGGTATCACTTAGA
TCACCTATTTATTGAGTCCGGTCATTCATCGTCCAACATTCACACTCAGA
AAACACCTATGGCCATCAGTATTTCCAGAGCTTTGGTCGGTGACTGTTCA
GTACCTAATGTAACATCTAAGCATGGGCATTCACTACGGCAAACAAGTAA
AGGCAGTTCTGCTTACAGGAATCTAAGTTTTGACAATTGCAGAAAAGCCT
GCATGAAATTGAGCAATAATGAGCAACCTAATAATAATAGTTCTCTATAC
GGATTCTTCTCATATCATGTGGTGAAGAGCAGTGGAAATTCCTATCCAGC
ATTGGGGTTTGGCCTGAGAAGTTTCCACATCTCGGCACCTGCTTCGTTCT
CTGCAGGGACTGCTCCAGATGTGTCCTTTGAGAACCCTGTTAGAGAGGAA
CAGGTTGCTAATGCTGCTGATTCTTCAGAACAGTATGTTTTCTTTCCTTG
TCCAATTATTTCATCATTTTTTTTTTAATAATCCTTGATATTAAGAGCTT
TTTGGATTGTGAATTGTAATTATAAGTGAATGATTTGGACTCCAGTGACC
CTATTGGTGTACTGTATTATAGCCTTATAGGGAATTAGGGCTGATTATGC
GATTAATATGTACAGCAGTTAATAATAAATAATAACAGAAGTAAGTTTAT
CTTGTTATCTGTGTTTGACTGCAGGAAAATCATAGCAGACAGATCTTTGA
AACTAAATTCAGGATCATGTTATCTCCCCCATCCCGATAAAGAAGAAACT
GGTGGGGAGGATGCTCACTTTATCTGCTCAGATGAACAAGCCATTGGCGT
GGCGGATGGCGTTGGTGGCTGGGCTGATCTTGGTGTTAATGCAGGGCTTT
ATGCACGAGAACTTATGTCAAATTCGGTAGCTGCAATTCAGGATGAACCT
AAGGGTTCTATTGACCCATCTCGGGTGCTGGAGAAAGCATACTCAAGCAC
CAAAGCCAGAGGGTCTTCAACTGCTTGCATCATTGCTCTCACAGAACAGG
TACTCGGATCCTGTCATCTTTAAGTTTTGGACTTTTGCCTAAGTTAAGAT
TTCGACCAATTGCAAATAATAGATTTGAATTCTACCGGTAAATTTGGATT
CACTTTGCTCTATGTGCAGGGTATCCATGCTATTAACTTAGGTGATAGTG
GGTTTATGGTGGTAAGAGATGGATGCACCATTTTTCGGTCCACTGCGCAA
CAGCATGATTTTAATTTCACATATCAGCTGGAGAATGGTAGTGATGGTGA
TTTGCCTAGCTCTGGTGAGGTTAGTTGTTGCGAGCTCATGGTTGTCATGT
CGATAAGTCGAGTCGAGTCGATAGAGGTCTAGCTTGTGGACTAGTAGACT
AGTCAACTAGTCGCTAATTAGTCGAAAAAGTTAATTAATAATTAATTAAA
TAATATATGTTAATAACTATTATATATGTGGTTTCCTATAACTAATCATA
TGTATATCAATCACAAAACAGATGTGTCAATTACAAAATATATCTTTTTT
CCTCTTTCATGTACACACATCAACACACTGATTGTATCAATATATAAACA
GATTATATTACATGTATATTCAGTTTTCATCAACTTGTGCATACATACAC
ACACACACACACAAAGATCTATAAACTTAGATTAACATGTTGATTATTGC
TGTTTTTGAGCAAGTTCATAGAATTTATTTATTTTTCATTATAAGTTTTG
ATTGAATTTTGCACTTGTCGACCGACTAGTCGACCGACTAGTTGAGCAAG
TCGACCGACTAGTGGAGCAAGTCGATCCATTAGTCGACCGACTAGTCGAC
AATTCGCAAGTCGACCTCTCCAGTCAATTTTCTCAACCCGACTAGTCGAT
TAGTCGTGACTAGTCGAGCGCTGTGACAACAATGCTAGAACTTGTATATG
ACGGAAGAATGTCTCATAATTTTGCAGTACTGCACATACCACACTCTTAC
TGATTTTATATCCTTCATGTATAACTCAACCTAACAGGAGTTACATTTGG
TGCAGGTGATTACAGTCCCTGTAGCTGCCGGGGATGTAATAATTGCTGGG
ACAGATGGGCTATTTGATAACTTGTACAACAATGATATTACTGCTGTGGT
AGTTCATGCTGTCAGAGCTGGTTTTGGCCCTCAAGTAACAGCTCAGAAGA
TAGCTGCCTTGGCACGCCAAAGGGCACAGGATAAAAATCGACAGACACCA
TTTTCCTCTGCAGCCCAAGAAGCCGGATTTCGCTACTATGGCGGAAAGCT
TGATGACATTACTGTCGTTGTTTCATACATAACCAATGCTGATGCCAAGT
AACGCGTGTCTGCTCATTCTTTCCTGTGCTCACACATTCACATACATGCC
TATCCGAAAATGAGATTTGTACGATTAGCTTGAATAAACTTGTCAGCTAT
CTGATTTGCCGAAAACGTTTTGCGAACAATGTCATCGGCTACACATCCTC
CTACAATGGAGATTAGCTCATAAAAAAGAGTTTGTTAGCTTTCTGTACAG
TTTCATGGTAATATAGGTTGGACTCAATTATTTGATGGATTATTCTTTAG
TGTTCATGGTAACGAAGGTTGTGGATTATTCTTCGCAGCAA