| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017376047.1, is a part of gene, LOC108205921. |
| The genetic_marker, MK009464 2_26496567, is located in gene, LOC108205921. |
| 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_017376047.1 | XM_017376047.1 | mRNA | DCARv2_Chr2:26493020..26498599 |
TCGAATAAGTTAAAGCAAAGCAAGCTACAACAGCCAAATGGCTCGAGCCT
TAGCCGCGCACTCCACCTCCCTCTTCACCTCCGCGGCGGCTCCGACTAAC
CATTTCCGGCGCCGATCTCTCCGACTTTATCGGGTCCACGTCATCAAGCC
ACCGAAAATGTCGTACCACCACCCATCAGTGGAAGTTATCGGAGACTTGC
TGGTCCCACAACTCCACACTCTAAAACGGCCTTATAATCCCTATCCTCTG
ATTGGTTGGAACTGCCACGTGGAAACTATATTTGCTGCGTGGTTTCGCAC
GCTTCCCGAGGTGAGGTTTAAGAGACAGTGTCTGAGGAGCCAGGATGGTG
GGTCCCTTGCTCTTGATTGGGTCGCTGGTGACGTGTCCAAGTTGCCTGCT
GATTCTCCCATTCTCATTCTGCTCGTAAGTCGATCAACGAATAATTACGA
ATAATTATAAAATTTTATGTACAGACATTGCTTTAGTATGTGGCGTTTGC
AAGTTATTGGTCGTTTAATTTTGCTGTGAATGTAGGTGTAGGGGGTGTTT
ATCGGATTTCATTCGATGAAGTTGTTAACTTGATATTGAATTTGAGGATA
TTCGATAATTATTTGAAGTAGATGATCTTGAAATGATACTAATACTTAAG
GCCAAGGCCGGGAGTTTGCACTTTGCTTTGAAAAAACCTTAAGCTATGCG
CTTTCTATCTTGCTCTGTGATCAAGTAGGTTGATTAAGGTGGATGTACTT
TTGAAATCGTGGCTCACAATTTTCTTCATATAAAACCGGAAATTTTTGAC
TGCGGGCAACTTAAAGAATGAACACAATCTTCATACGCCAGAGCTACTCG
AGCTTGGCTCATGAAAATATTCTAATTCGGCTTTGACTAAATTGTGCATG
AAATTATTAAGTTCGTGGCTCGCGAGCTAATCGAGCTTTTATTATTATTT
ATATATTATTGTATTACCATTTACTATATATTACTTATATTATATATTTA
ATTGAGCTGAATTGCATTCGAGCTTTTTTGAATATGTAGTTAAGTTGATT
TGAGCTTTTGTTTCGAGTCGAGCCAGAACATATCAAACTTTTGTCCAGCG
CCAGCCGAGTTTTAAACTTGAAATTTATGGCTCGTTGAACTCAGATTCGA
GCTCGAACCCGAAATTTTTAAGTCGAACTTGAATTTGAGGCTGACAGTGA
TTGACTCGGCTCGGCTCATTTACAGCCCTATGTGAACAATTTGCACTTAG
GTGTCGTAATTACATACTCCCTTCCACTATACCTCCACAAGGCTTACTGT
ATAAGCAAGAGAAGAGGGGTATCCTCGGGCCAAGTCTTGCAGAAGTTGTG
TATTGTAGATTATATAGTATATATGACTAAAAGTTTTTGCTTAACATTTA
TTATTTGGTTAATATATATTTGATTTTATTAATGTGAAGAATTTTTTTTA
GTAAAGCTTATATCGGATGCATACCATAACAATGAATTAGCATGATGATG
CAGCCAGGTCTTACAGGGGGAAGTGAGGACTCCTATGTAAGGCATATGCT
GTTAAGAGCAAGAAGTATGGGATGGAGAGTAGTCGTGTTTAATAGCCGTG
GTTGTGGAGATAGTCCTGTCACTACATCCCAGGTATACTGTACTCTCTTC
TTTTTTGTTACATACAGAGACAATTTTATCTTGAAAACTCGTTAGTGGCA
CTACTGAAGTCATAATATCAAGTTGCGTGCTGATTTTGATTGCTCGCTCT
AGTATGTTACCATCAGTGACTTAAAGCAAGAAAAAAATAGTCATATGTTG
TTCATGTTTGCCCCCATATTGCAGTTCTATTCAGCTTCCTACACAGAAGA
TATCCGTCAAGTAGTCAGACATGTGGGCTGCCGGTATCCTGAAGCCAAAT
TATATGCTGCCGGTTGGTCTATTGGGGCAAATATCCTTGTTCACTACTTG
GGTCAGGTTGGATCATTGGATCATTATATGCTTTTGTTATTTCTGAATGT
TATATTTCCGAAAACTACCTGCCTCATAAGTGTCTAGTTCTACCTTATTC
GATTATTCTGCCCAGAAGAAGAAAGAATGATCAGATTGAAAGAAGACTAT
TTTAGAAGTCAACAAAGAACATAAGTACTCCCATTTCTATTGAGCGTAGT
ACATTATGTTCTTGTTTAGTGTCTGGAACAAGTATTAGCCTTATTATTAT
TACTCGTCTGATATACTGAAACATTTTATTGGGCTAATCTCAATAGGAAT
ATTATCATTAGATATTTTAGAACATTTAATTAATCAATGCTCTATGTTCA
TAAAGGAAATCATTTGTTTATCTTCTCTAAAGTCTTCAGTGGCATACCTG
TAGTTGTTGCCTGCTATCGAATGTAAAAGCTATATACTTTCTATTGGATC
AATATTGGCTCCTTGTGGTCCTATTGGCCTTCCATGGTAGAAATCTACTA
TATTCATAATTTCTTTATTATCTTTTACTCTAATATTTATTAAAAACATA
TTCACATCTTTAAACATAGGCCCTGTTTGAGCAAAGTTGGAAAGTAGAAA
CTGGTGATTTTCATGGTTATGAAGTGGCAACCATTACTTATATCTTTGAC
CATAGTAACTCTTTCTTGAAAAATGCACCAGAACTGAATTTTATTTTATT
TATTTTATTTTATTTTAATTGTTGCCCTGATACAGCAGCTGGATACTGCA
TGCTTCTTTATTATTTCAATTATGTCCCATCACACTGTTCCCTAGCAACT
CTTATGAATTATGAATCTATGATGTATGGACAGAACTGAAAGTTGTGTCA
TTGGTGCCCTGAGGCTCAGCTAAATGCTTCATGCTTCTTTATCATTTCAT
GTATGTCCAATCTCACCTCGGACCTAATTAAAAATAAAAATAAAAACATG
AACATTTTCGACCTTTCAACTTTGGATTCTCGACATGTGATATTATTTAA
GGAGTAACAAGAGATAACCAACATCCTGAAGCTAGCATCAAATTGCTTGT
AATTTGATCATGATCGATTTTTTAAATAACATATTTTAGATTTGAAGTTC
TACCTAATACTGGAAGAAAGAAGGGGTAACTTAGTAGTTTTAATAGCCAC
ATTCTCAAAATGGCAAACATTTTTCTGCTGTAATTATCGAACATCAAAAT
GCGTGAATGTTATCACTCGTCACTGCTTTGTAATATGGAGTGTGATTGCA
GGAATCTGACACTTGCCTTCTTTCTGGTGCTGTGTCCTTGTGTAATCCTT
TCGATTTGGTCATCGCAGATGAAGATTTCCATAAGGGCTTTAACAATGTC
TATGACAAAGCTCTTGCAAGTTCTCTCCGCAAGATTTTTAAGAAGTAATA
CTTTGTGACGATTTTTGGTCCTCATGTCTGAATATTTGTTTAGATCTTCG
TATGTAATCTACATTGCAAGTATCTTTGATTTTTCCAGACATGCTCCTCT
GTTTGAAGACATGGGAGGTGAATATAATATCCCTCTAGCTGCCAGTGCGA
AGACTGTCAGAGAATTTGATGATGGAATCACTCGAGGTAAAGTCATATAG
ATATCAACATGGCTGCACTATATTCCATAATTTCCATTGTTCACCTTGTT
AACGGATTTTTTGTGACACCTGGCAGTTTCATTCGGTTTCAAGTCAGTGG
ATGACTACTATTCATACTCGAGCAGTTCTAAAGTTATAAAAAATGTTCGC
ATACCATTACTTTGCATACAGGTACATCCTAGATAATGCATTTATGCCAT
GAAGTCAAATTCCTTGAAACTCATCAAAATCAACTAAATCGATTTAATTT
TTTAGGGGAGATGTATTCTTCTGTAGGAGAAATGTACACCAAATTCTGAT
ATCAGCTCCATCTGGATCTCTTTCTCTCTCTCTCATGATCTAGTCTATGC
AATCACCCCACCTTTTTTTTAGCTTCTTATGGTGTACCTTTGAGTTCAGA
ATTCAACTCTAACAGTGTTATTACAAAGCACATAGGATATTTACGTATCA
ATTTGACACCCTTCAAATTACCGATTGAATTTATAATGACTATTAATAAT
TCTTGATGACATTTACAAGGCTAAGTCTTGCCATTTGTATATTCTTCTTC
TTCAAATGGAAATAGCATTGTGTTTATTGTGGCTTCAGCTCTGCTCTCAT
ATTTGGGTGCTAGTAGTGGATTATTCTTCTGGAGGAGACCTTTGTCATAG
TATGTCTAAATTTTCTAGTGACTTTACAGGCTGAAAATGATCCAATTGCT
CCATCTAGAGGAATTCCTTACGAAGACATTAAGGTATGAGTCCCTGTCTT
GTAAAAATGGTTCATCACTTCATCTTCAACAACTTTGTCAGAGCAGCAAG
TTTATTATTTACCAATACTACTCTTTTCATCTCTAGCTATCACCTACAGC
CTATTTGGTCTTATTGTTAGGTTTCAGACAGTTTGTGAATTAGAACTGAA
ATTTTTATGATATATTGTTGTTAAAATGGTATTATGTTCATATAGCTTTC
CTTGTTTCATTTAAGTGTCAGCACTGCGAAGATTTACTTGCCTTTTGTAC
TACTGCAGCCTGTCACCTAAAGAAATGAGAAAAAGAAGTTTAATCTTTCC
ATCTATAAAATCTGTGAAGTTGATCATGCCTTCTGTAAACTTCGTGCTAA
AAATTGCTTTTCTCCACCTTACAATTTTCTTTCGTCTCACTGATCTTTGC
TTTGCAAGTTTATGTTTCATATAATCTCAGCTCGTTTGTTGAATAATTTG
ACAACATTTGTGCAGCCTGTGCCAGCTATTGAGTTCAAATATCTAATAAA
TATCACTTAATGTATATATTGCATATATTATTCTGCTAGAACTTGGATAA
TTGTTTACATTGAATACGTTACAACATTGCCATGTCATTCCCCTAGTGCC
TGCCTTGATGAATAATTGAATGTTGCTTCAGGGAAACCCAAACTGTTTAT
TGATAGTTACACCAAAAGGTGGACATTTAGGGTGGGTTGCAGGCGATGAA
GCTCCTCGTGGAGCTCCATGGACTGATCCTCTGGTGATGGATTTCTTGCA
AAATTTAGAAACTAATGCAGGATCACATACCTCTTCATCTAATTCTAGCA
GGCCAAATGAAAACGTCCACCAATCGACGGATCAAATGGACCCCCTTAAG
GTATAGCAGAAGCAAAGCACAGTCATATTCTTGTGCATCAAATAAAGATG
CATATGTCTAGTTGTACTGGGTATGATTCAACAACCAAAATTATTGTTAT
ATAAGCTGGTGGGCACCAATATGAATCATCTGATTATATCCATTCATTCC
TTGGAGGGTGTCTTCTACATGTGACAAACAAGAATCTTTGGCACCTTTGC
AGATACCATAGAAGTAATATACTTGTGTAATTATGAAAACTGGTAGACAA
CATTATTGCTGTGGAGTCATTGAATCTTTTGCAAAGTGAGGCCGTATGGG
GGTCATGACTCATGTGTGATGCATGTCAGTGTGCTCTCCTGCCCTACCCG
AGTCCCTTTTCAGCCCTGTATCATCATTGCACCAAGTAATGGAATGTGTA
AAAATCTCATGCATACAGATTTAACTACA