| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017398200.1, is a part of gene, LOC108223781. |
| The genetic_marker, MK004504 K1948, is located in gene, LOC108223781. |
| 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_017398200.1 | XM_017398200.1 | mRNA | DCARv2_Chr5:40134058..40136723 |
TCCCCCAAAATCCAAATCTCAAAATTTATCGAGCACACATATGTACACGC
ACTATAAATATAGTGGATTACTCTGTTGGCTCTTGTAGAAGTTTGGATTG
TATTTGGTGAGCAACCTTTCTCTCCCCTCTCCCTCTCTCTCTGTCTCTCT
CTGCAGGTGAATTAGGTTAAAGAAATAGAAGATCAAATGGGTCGAACTGC
TTCTTCAAAACACAAATCTTCAAACAAGAAAAAATCCAAACTTTCCTCTC
AGGTACTCTTAATTACTCTCTCTATTTCATCAATTTAGTTCAATTTGATT
GTTTCATCATTCTTGCTGCTTTATTTTATTGTTTTAATGATTGAATCTCT
TTAATGTAAGGTTCATATTGAAATTATACTAATTGGGGCAAATATTAGGA
TCAAGATTCAATTTTTATACCAGTACTCAACAAGTTTCAATGTTCTTGAT
TATAGTGTATGATAGATTGATGAAGTACTAATGGGTTTTGTGTCAAACTA
ATTTTTAATGTATGGGTTTTGTGGTTAGACCCGAAGGAAGAAGACGAGTA
AAAGAAATAAATCGAAGAGGGTTTATAGCGATGATTCTGTTTCTTCGGAT
TCTGATGAGTCGTTGAGGTCTGTGTCTGTATCGTTGTCTGATAGTGAGGA
TGGTGATATTGGCAGAAAGGGACGGTCTCGCGCGAGAGGTAAGGTGAAGG
GTAGTAAGAAGAGGGTTCGAAGAAGCTCTTCTAGTGATGATAGCAGTGTA
GATGTTAAGGTGAGGAAACATTCAAAAAGAATTGGGGATTCTAAGGTTAG
GAAGAGAACACATAAGAAGAAGAAGAAGAAGATTAGGAGAAAAGTCAGTG
TTAGTTCTTCGAGCAGTGATTCGGGAATTGTGAGGACTCGTCGTCATGAC
AGTTCTAGTGGTACGGAGGAGAGTGAACATGAGAGGAAGAGGGGAAGGTC
TAGGAAGAGGAAAAGCGACAGAACAAGTTCAGGTAAACTTGGATCTAAAA
AGAGTAGATTGAGGTCTAGGAGTTATTCTTCAGGCAGCCGTTATAGTAAT
AACAGTGATGATGTGATTAAGGATAATGTGGCAAGTGAGATTGATCAGAA
CAGGGAAATAGTTGCGAGTGAGATTTTGCCAAGGCGTTTAAAATCAATTA
TTACTGTTGTACGACCACAATATGAAGAAGAAGCAAGTGGACAGGATAAG
GATGAAAACAAAGAAGAGATTTTTTACGATCAGGATGATTACCCTTCCTG
CAGAAGCAATGACAGTAACGATGGGGGTAAGAGGGACTTGGCACACAAAT
CTTACGATGGATCTGAGAAGGAAAGAGCTGAAGATATGGTGGGACAAGAA
GATTTTTCTTATGAACTTGTAGCAAATGAGTCTAAATTAAGTAGCATAGA
TAGGATTGATCAATCTTATAGAGCGTCAATAGAACATCCCGGTAATAAAA
ATGAGATTGATACATCTACTCCCATTGGAGGATTTGGCAGTGAGGATCTA
GAGACAATCTTGAGGCAAAAGGCTCTAGAGAATCTTATGAGGTTTCGAGG
TCCTCAGAAAAATGCAAAACCGACATCTTATCACGAATATGAGACCGAGA
GAAATGTTAAATCATTCGCTGCAAAGGCTGATGATGTTCAAAACAAGTCA
TCTAAGCAGGATCCCACGATTGGAGTTGGTGAAACTGGAGGAAAGAATCA
GCAGAATAGGCAGACACTGAGGACAAATTCGTCTCGTTTTGTGCAGACTG
AGGATATGAAGGTGGATGGAAGAGAAATTGAAATTGAAATTAGCACAGCC
AAACCGATGGAACAACCGCCAGAAAGTAGCCTGGAGAAACTGCCACAATC
ACCTGTGTCTGCAAATGTACGGGGAACGTCTGTTATACACAAGAGTGCCG
CTGAAAAGGCTGAAACTGTAGCCGGGAGTATTGTTAATAATGAGAATGTA
GGAGCTAATGATGCCTCTCATGTGGTTCCAGAATCTTCTTGTAGTAAACC
AATATCTGATGAACATAACTCTAAACAATGCCAAGAAGAATCCAAAGGCA
ACTCATTTGAACAGAAAACTATGTCTGTGATGAGAGGTGGTGAAATGGTG
CAGGTGACGGCTATTTAATATACATTGTGGAGGATATAAAATTTTACAGT
TGTGAATACTAAGCTAAAACTGGTTTTAATCTGCAATTGTTTAATAAATT
GACTTTATCTGCTTCTTTTGATCAGGTGAGCTACAAGGTCTACATTCCAA
ATAAAGCCCCTGCTCTAGCTAGAAGGAAACTCCAGCGATGACTAATATGC
TTCTGGTGGTAACGGGCACCATTTTTGTATACATGTGATTCTATCCCAGT
ATAGACAGGACAGAAGCTGTCATTGGCCTTTTGCTGTCCCCATGAAGATA
GATAAATCTATCTGTACAAACTGAAAGCTGCTCGTAGGGAAGTTCTGAAG
TAGGGTATGTCAAAAACATGGAGAAAATGGAAAAATACGCGGCTCTTGCT
TTGCAAATAATAAAATGTATTAAGATTATTCGGGAAATACAATATACAAT
TTTGCTTACCCATTCCCCAAGCAGTTGTTTTGCTCCATTTCAATGTTGTT
AACTTGAGCCGCAGTTGGATATTATGCTATACGAAGTAACCCTCTAGTAT
AGAATTCTTTGTTAA