| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017393196.1, is a part of gene, LOC108219695. |
| The genetic_marker, MK003968 K1412, is located in gene, LOC108219695. |
| The mRNA, XM_017393195.1, is a part of gene, LOC108219695. |
| 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_017393195.1 | XM_017393195.1 | mRNA | DCARv2_Chr5:34663423..34668669 |
| XM_017393196.1 | XM_017393196.1 | mRNA | DCARv2_Chr5:34663423..34667842 |
AAAATAAAGGAAAAAGGAGTGCAAATTCTAGAGTTGCAGGTCTTTCTTTT
ACTCTGAGAAGATGCTTCCTTGCCTCTGCCTAAACAATGACAGTACGCCG
CCACACAGATCTGTGTAAGTTTTACATACATGCATTCTTTCATATTTGAT
AGATTTCGTTATATTAATATATTAAGTGACTACTCGAACATGACTATGGA
TCATAGAAGAATAGGAGAGATTGACACTTAACTGTCAAAGGCCAACAAAT
TCACAATCATTTTCATATAAGTGTGCAGCATGCATGCATCTGCATGTGTA
TTCATATGCGTATTAGAGCAAGACAGCAAGTTCAAGAGTGTTTTAGTGAT
TGTTTTATAAATATTATAAAATATAGTTTCCTACTAGTTTAGAACATCAT
TTTTGTACGTTCCAAGTACGAAAAAAGAGGGAATATCAATATCTTATTAT
TAATAAAACGAGATTGCGCAGTCTTAAAAATATCCGTCTTAAAAATAGAG
ACACTTATTTTTGTCAATTGCCCTAAATTTTGATTTAGAAGACCAAATAA
GGCATATATCTGTTGGACTTGTATTGATCTACGACACTTTTCTATAACTT
TGCCAAATTTATAATGATCAAAATATGTAAAAAAAATTATGTTATGCAAA
TCAGGTGCTTCAACTGTTAAACACATGGATACTCTGAACTTTAGACCATG
ACTGCAGACAGAAATTCTCTCCATTATAATAAGGGACAGCTGAATCTTAA
TACAGTAATAACTATTAAAAATAATGTCTCAGCCATGTATCTTTATATAT
ATATATATAAGAACTAATAAGCACGGCTATAAAATACTTGGACATAGCAT
GTTATGTACATCAACTCATAAAACAGTAAAGCACAGAAGCGTCACTTCCT
GTATATGCTGTAAGACTAGCAATGTGAGGTCGCTGATCTGCACTACACAG
CTTTATTTCTAGTTGTTTCTGCACAATTCACACACACACACTCGCATAGA
AGCTGATTCTTGGAATTGTACACTATGATGCCAAATATACTACTCTCTTC
CTACCAACAGGATCGTTTCGGGTAACTTCTTCTTATTTACCTAACTTCTC
AACTTCTTTGTTATTCCTTTTATGATCTGAATTTTAGCATTCTTCATCAA
ATAAGTATAATAATATATATAGTTCCTTGAGTAAAACAGCCAGAATTCTG
GCTTTAATCTTATGATGAATCCTTGCTTGTTTATGTCCGGGAAGCAATAA
GATCCAGGTTGTGTATGTAAATATGCCGGATAGATTTCTTATTTTAATGT
ATGTACACAGGTTTAATAGTTATTAATTTGTTATGGGTTTTGTATATGTG
TAATCATCATATATACATGATCAGAACAACAAAGAAGAAGACAAATGGAG
TACTGAAGATGGATGAGTCGACACACAAGCATCACCACCGTGGTTACTAC
AGAGACCCCGTCGTAAAACAATCCCAAGTAGCAAGGTTTTCTTTCCTTAC
CCTTCCCGCCTCTCTACCATGTTTGAGTATTATGTTACTGTGTGAGTCAA
TGAGTGATGTGCTGTGTGCACAACTTGTATAAACACCTCAACTGCTCTAC
AAAATTTTGTTGTATTTAAATAAGACAGTGTCACTAAATAAATTTACAAT
TATCATGCATAGCACGTATTTTGATCACTTAAACAAATTATTATATTTGA
GTTAGAAAACACTAAAATATATTTTTTTGGAGGAATTTCGATAAGTAAAT
TAATTATATGCGCTAATCTTTATAATCTCATGTAGTTTGTTATGGATATT
TTGAAATATAACTGATATTAATACCAAACTATATACTATATTTTATAATA
ATTATATTGTATATTCATTATTCAATATTTTATAATTTTTATATCTACGT
TTATCTAGAATATATTTTTAAATAAAATTGTCCTTCAATGATGAGAGTAA
AATTTTTTAGATCCGTCAAATTGTTTTAAATATCTTCATGTGGATACTGT
TTTAAAACTTTAAAATAGTCTACATATTTTATTCATATGATAAATTAAAA
AATTATTTGCCATCTAAATTTAAAATTGACGAAAGCATTGCTCTCTATCT
TATCTTAAAGTGCTTGATAATACTCAAAAGTAATTAAAAATAATTTGAAT
AATTATATGATTAATAAAATGATTGGTTATATAAATATAGTATATATATA
TTAACTATAAAAATAGTACTTAATTAAGTTATGTGGAAATTAAGTTACAC
GTTTTTTAAATTTGACTTAAATCTGTTCTTTACAATAGTAAATTTATTTT
TAACATTTATGTTGGTTATATCTTGGCGAAGTGTTTAAAAGTAAAAAAAA
AAAAACCAACTTAAAATAAGATTCATTACTTCCAGCTTAACATGATTTTC
AAATCAATTAAGATTACTTTTATTTAATTGAAAAAAAACACTGTAACAGC
TTGATTAAGACAAAAGGAAAACATTATAAAATTATAAAAGGTTATTCATT
CCAAATTCCAGACACAAGAAACACAAGTAGAGATCCTAAATTACTGTTGG
GTAGATTCACTTCACTTAATTTAACAGTGACTTGAGTAGTTCACTAGTTC
ACTTCACTTGTGTTTGGTCTTCACTAAACACACTGTGTGTATGTGTGTGT
TTTTATGTGTCCACATCTGAAGAAAGAGCAGCAGCACTGGAATCAAGAAA
ATGGCCATTAACAAAGTCTCCAACTTCTCCGATCTCATCCACCGTGTCAC
CGCCTCTTGTTTCCTCCACCCTCTCGCCGCCGACCGCCACCACTCCTCCC
AAATCTCCCCCTCCGACGACTCCGACGACTCTGATGACTACCCACCCAAC
CCCAGAATCTCCGAGTACTTAGCCCAGCAAGAAGAAGATATCGAAAACAC
CGAAAACGGCAGCATTGCCAGGGCACGGAGAAGTGATGGGGAATTTGGGG
ATGTGGAGGTGTTGATTGGTGAGGTTTTTGAGGCGTTTTCGGCTGTGAAG
AAGGCTTATGTGAGTTTACAGGAGGCGCATTGTCCTTGGGATCCTGATAG
AATGCGGGTTTGCGATGCGGCGGTGGTGGCTGAGCTGCGGAGAATTGGGG
TTTTGAGGGAGAGGTTTAGGAGGAAGAATGTGGGTGGGGAGAGGGGGAGG
AGGGTTGTGGGAGCTACTTTGAGGGAGGTTGTCGCGCCTTATGAGGCCGC
GGTGGAGGAGTTGAAGAGGGAGCTTAAGGTGAAGGAAGTTGAAGTGGAGA
ATTTGAAGGACAAGTTGAAGAATGCGGTGGTGGTGACTGGTGGGAGTGGA
GGGAAGAAAAATGGGAGGGGCCATCATCAGTCCAAGCGGAGAGTTGGGTG
CAGTACTCAGACTCCTGGTAATTTCTACATACATTTTGCATATAAATTTC
TATCGAATAAGTCATTTGGAATTGCATTTGAGTTAATTAATTCATGTGGT
GCTATGTTTAGATTTTGTGGATCAAGCTGGGTTCTTGGTCATGGGTTGTG
TTTTTGTGTGAGAAATTGTCGCCTAATTTTGTAGAAAACAGTTGGAGTTG
GGGTTGAGAGTGAAAAAGATAACCCAAAATTAAATTTTGAATATATTTTT
GTTAAGTTAATCAGAGTGCTATAATTATGTTAAGATCTAGTCCAAGCATC
ATCCTGTTAGGGGTTATCATTTTATACAATGTATGCATTTCTTTTGTGCT
TGTACTTTTTTGTATTTATTGACTCAGTCCAGGGATGATTACTTTGTAAA
AATGTTATAAGCATTGCTTCACATACTTTTCTTAGATTATGATGTTATAT
GATTTGAACTAGGAATTAAGATTCTGACTTCGAGACAGTTATAAAGCATT
GCTTCACATACTTTTCTTAGATTATGATGTTACTTGAACTAGGAATTAAG
ATTCTGACTTCGAGACAGTTATAAGTTACAAGTTAAAAGCAATAATCTTC
GGACACAATGTGAAGATGTGTGAGTAGAAAGTGTTCTCTACTTATTACAA
CTTGAGCATATATACAGTTGTATTAAAGATGTGTAAATGAGGCCCGAGTA
GAAAGTGTCCTTTAGTGATTAGAACTTAAACAATTTTGTAATAGCATTGA
AACAGGTTCAAGACATCCTCTATTAAACTCTAATTTCTAACTTCACACTT
GATTATCTTTTGCTAACAAGGTGTCATCTTCAAGGTTAATCAAGTTCCTA
GCTATTCTTATTTTATTGTGGCAAGACAATTGTCATTCGGTATCTTTATC
TTATGTTAGAGAAAGTATTTTTTTAACACCAAAAGCTTGTCTTGCATGAA
ATTTTGGTATGTTGCAATCTATCTAAACTATATATACCAATGTCCAGTAT
CACTGTCGCCGGCACCAGAGGTATTTGAAGCAACAATGAGCATGGTAAGA
GAAGCATCAAAGTCATTTACAGCTCTCCTTCTCTCACTCATGAAATCAGC
CCACTGGGACATTACAGCTGCTGTAAGATCAATTGAAGCTGCTGCAGGGG
CAACTACCAATGCTACTATGGACTCCATTGTGGGACCAAATCATGCAAAG
TACGCAATGGAATCGTATGTCAACCGGAAATTCTTCCAAGGTTTTGACCA
TGAGACATTCTACATGGATGGCAGCCTCTCATCTCTACTGCACCCTGATC
AGTTCCGCCGAGATTGCTTCACTCAGTACCGAGACATGAAAGCAATGGAC
CCCATTGAACTCCTTGGCATTCTTCCCACTTGTGACTTTGGCAAATTCTG
CTGTAAAAAATATCTCTCCATTATCCATCCCAAAATGGAGGAGTCTTTGT
TTGGTGATTTGGAACAGCGCTGTCAAGTTTTGGCTGGAAATCACCCTAGG
AGTCGATTCTATGGGGATTTTCTGGGGCTTGCAAAAGCAATTTGGCTGCT
GCATTTGCTTGCATTCTCGTTGGAGCCACCACCTAGTTATTTTGAAGGTA
GCAAGGGTGCAGATTTCCATTCTCAGTACATGGAGAGTGTGGTGAGGTTT
CCGGGTGGAAGAGTTGTAGGTGGTCAGGTAGTGGGGTTTCCAGTTAGCCC
TGGGTTTAAGCTGGCCAGTGGTTCTGTTATAAAGGCTAGGGTTTACCTTG
TGCCCAAAAATGATTTTTAGGCAAGAGACTTCCTAATAAATGTCTATTAC
GAGCTAATGTAGAGTGTTTTTAAAATTGTATTGTTTGTGTAATGGGTTGG
TGGTAGCTTGCTATGGCTAGTGCTATAAACTTGCAGATTTTAATCA