| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017368380.1, is a part of gene, LOC108200280. |
| The genetic_marker, MK004059 K1503, is located in gene, LOC108200280. |
| The mRNA, XM_017368379.1, is a part of gene, LOC108200280. |
| The mRNA, XM_017368381.1, is a part of gene, LOC108200280. |
| 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_017368380.1 | XM_017368380.1 | mRNA | DCARv2_Chr9:659454..664358 |
| XM_017368379.1 | XM_017368379.1 | mRNA | DCARv2_Chr9:659455..663663 |
| XM_017368381.1 | XM_017368381.1 | mRNA | DCARv2_Chr9:659455..663663 |
ATCAAAATCTAGTACGCGTTTTGACGTTGAAGAATTAGTCATTGCCCCCC
TCACCAAAGTCTTTTCAAGTCTTCTCTTCAAGTCTCACGTTCTTTTACTT
TCATGGTATCTTTAATCATAACAAGAGTGATCACTCTTATTCTTTCATTT
GTTTTTTATGTGCAATTTTGATCTAATTGTTGTACATGCATGAAAGTAAT
CTTGGGTTTCAATTGGTAAGTGATCAAGTACTAGATGATTCTTTTTTTCC
TTGTATATATAATTGAATACACTCTCGCTTGTCTTATACTCCGTTTGTCC
CATTTATTTATATACGTTTCTTTTCAACTGCTCGACACGCATTTTAATGC
TCTTATAAAATATAGTTCTGTAACTTATTTTTGAGTTCTCGATGTTTGGT
TAAAGCTGTTGATATTAGATTTTTTTGTTTACCGGAGATAGAATAGACAG
GAAGGTGGTTTTTGTTGATTCAGTATGAAGGCTGTTTTCTGATGGGGTTT
AGGATTATATTTTTGAAATCGAAAATTTGGATTGAAGTTCTGTAATGGCT
AGTGTTTTTAAAAGATTTGTCCCGGAGAAACGGTTAGGTTCTGATGTTGA
TGATGAGTACAATTCGGAGTACTCTTTTGCGACAGAGTACACTGGCCCTC
TTGTTAGTTATGATGTTCCTTGTGTAGCCCCGGTGCACGTTGATCGAATT
CCGATAGCAGCTAGTATAGCCACACCTGATAGGACTAAGAATATGGCACT
TCCAGTTGTTCAACCTGTTGCAAGGGTTGATTCTGGGAAGTTGTCAAAGA
AGTCGAAAAAGGGGTTATTAGGAGATGCTTCTTCGATGTCAGTTACCCAT
TCGAATGAACTTGATGTTGCTCGTGTACTCGATGTTTCTAAGAGGCATAG
GACAGATTTTAGAGTGGTTAATGTGCTTGATACATCGGGTGAGTTAGAGT
TTTTGGAGACTGAGGAATGCATCCACCGCAATTTGAATAGATGTGCTAGT
TCTGGTACTTTGGGGTTTTCTGGGAGTCATGAGACTTCCTGTGAGCTGTC
AGAAAGCTCGGGTATGGAGTCCTTACATGAGGATAAATATAACGGTGCTT
CCTTTAAGGGCCATGAACAGGAAGCGGTGAAATGTACAGTGAGGAAAGGG
TCATGTCATCGATGCCTTGTTAAAATTAGGTTCAGGGAGAAGGAAGTTTG
CATAGTCTGCAGCGCAAAGTATTGCTCTAGTTGTGTACTAAGAGCAATGG
GGTCAATGCCAGAAGGAAGAAAATGCATTACTTGCATTGGTTGTAGAATA
GACGAGTCCAAGCGATCTACCCTTGGAAAAAGTTCTAGGATGCTTAGGCG
TCTGCTCACTGATTCGAGAGCTAAAGAGATCATGAGCCATGAGATATCAT
GTGCAGTGAATCAAATACCACCTGAACTTGTCATTGTGAACGGGAAGCCT
CTCTGTCACGAAGAGCTAGTTCAATTGCTTGGCTGTCCAAATCCCCCCAG
AAAGCTAAAGCCCAGAAAGTATTGGTATGACAAGCAATCTGGACTTTGGG
GCATGGTAAGAAGTTGGTCCTTAAGTTACTTTTCTATAAATCATAGTTGC
TATCAGTTGTTATCTTACATTTAAGCTTAATCAAACAGGAAGGAGAGAAA
CCTTGCCAGATTATTACTCCACAACTGGCTGTTGGCGATCCCATCATGAA
AAATGCGAGCAATGGGAACACAAATATCTTGGTTAATAATCGGGAAATTA
CCAAACCTGAGCTCTGGATAATGCAGGTTTGTTTTCTCAAGTGAATAAAC
ACATCAGTCTTTTCTCCCTTTCCTCTCTTTGTTTTCTTTCTTTCACAAAG
GCAGGTTTCTATGTTGTCTATGATAATATGCTTGACCATTACGTTAAAAT
TTGTAGTTTGCAGGAATCCGTTGTGAAGGGCAGCCACACTTTTGGTGTAG
CGCTGACGGTTCCTTCCAGGAAGAGGGACATGGGAATGTAAAGGAGCGAA
TATGGTTCAAGGTACATATTCTTGCAACGATCGTCATGCTAGTTCATCCT
TAATCAACAATATTATGTTATCTATTCATTTATTGTAACCTTTAAAATTC
TGTTTTTAGCCAAAAATCAAACTACTGTGTTCAGTCCTGTCATTGCCCAT
CCCGCCAGAATCTGCAAACTCTGATCAAGGGAAAGTTGACGATAAAGTTG
TGTTTAGCACTCAAAAGAGAAACGAACCATATAAATTACTCATGGTTGGT
TATGAAAAATCTGGCACGAGTACCATATTCAAACAGGTATGATTTCCTTC
CGACAATATTGTGAACTTTGATGTTAAATTTAGTTTCAAAAGTTCCATTT
AAGGTATCTATATCTCCATTTCTGTGAAAGTAGAAGCTCGTCTTTAGGAA
CTGTATCCTGTTTACGTCTCCATGTTTAAACTTTTATGGGAAAATAATTT
CATGTTTTAAGCTTGTGATCTTATATTCATATTTCAGGCAAAACTTCTAT
ACAAAATTCCTTTCACTGAAGATGAGCGGCAGAATATGAAAAACATCATT
CAGAGCAACTTATACCGTTACATAGGTATTCTGCTCGAAGCACGTGAACA
ATTTGAAGAAGAAACTCTAAATGAAATGAGGATGAAATTCATTAATCAAC
CTGGTCTTTCAGGTACAAAAAGTATCAAATTCACTTATTTTCTTTGTTAA
CAGCATACTCGTGCACATAATTTCTCTCCTGCAAGTGGCTTGTAGTCAAT
TCTAGTCCATTATGATTAACCAAATTCCAGCTTAATATGTTTTCTTTTGT
TGTTGATATAAGTGACTTGATTATAATTGTACAGATACAGCAGATATTAA
TCAGATTGACAAGGCAAACATTTACTCCATTGGTCCCAGGCTTAGAGGAT
TCTCTGATTGGTTACTCCAAATTATAATGTCTGGAAATTTGACAGCGGTT
TTCCCTGCTTCCACTCGCGAGTATGCACCCTATGTGGAGGAACTCTGGAA
GGATAAAGCCTTTCAAGCCACATTGGATCGAAGGAATGAGATACAAACGC
TTCCTAGAGTTGCTAACTATTTCTTGAATCGGGTAAGCTCGTGATTTCTG
TTCCTCAGTTATGCTTCGAGTTCTGTATGCTCAAGGTAACATAATATTAA
TAGACACATTGATGGTAACACTCAAATTTGACTTTTTTGTTTTCCAATCA
AGGCTGTTGAGATCTCGTCAATGTACTACGAGCCTTCTGACATGGACATA
TTATATGCCGAGGGGATTGCTGCTTCAAACGGTATAGCTAGCATGGATTT
TTCCTTCTCAAAGTCGAAAAAGGATAGCATCTTGGACTCTAATGATGAAG
ATGATCCCTTGATAAGGTTTAGTACTTTTTTATGCTTTACTCATTAAACC
GATATCTTGCCTAAGCCGTTTAACCATTGAATTGTTAGTATACATCCTTG
TTCCTTATCACAGCTTAATATGGTAAACTGCAGTTACCAACTTATGAGAG
TTCATTCAAGCAACCTCGGCAAAAACTGCAAGTGGATGGAAATGTTTGAG
GATATGGATCTAATTATATACTGTGTTTCCTTAACGGATTATGATGAGTA
CTGCTCTGATATCAACGGAGTTTCTACCAACAGAATGATGGAAAGTAAGA
AGCTATTCGAGACCATAGTGACACATCCAATCTGTTCTCACAAAAACTTC
CTTCTGGTGCTCAACAAATATGACCTCTTGGAAGAGAAAATTGAACAGGT
TCCTCTTACTCGTTGTGAGTGGTTCCGCGACTTTAATCCTCTGATCAGCG
GTCAACAGAGCAGCAGGAGCAGCAGCAGCAAGAATCCAGTTGCAACACTG
GCTCAAAGTGCATTCCATTATATTGCGGGGAAATTTAAACGGCAGTTTCA
GTCCTTGACCGGAAATAAATTGTATGTTTTTCGGGTTACAGGGCTCGAAT
CAGACAGTGTTGATGAAGCAATTAAATATGCAACAGAGATTTTGAAGTGG
GAGAATGAAAAGCCAAACTTCAGTATGAATGACTGGTCATCTGGCAGCAT
TGAGGCTACCACTACTACATGATTGTAGGTACATTCCTTTTTCTAGTGTA
CTTGCCACAAAACTTGTAGAATCACAGATCAGAAATAACTTCTTACATAT
ATATGTACAAAGAAGCTTATCATCAAGCTTACATATAAAATTTTGAAAAT
TTTACATAATTTTGGTCTGATACACATGTTCAAGTGTCGAGCGTCTGATA
ATTATAATGAGAGTCAAGGCAAAATAAAGAGTCGGGGCAACGGATGTTTA
CATATATTTTCTTTTTCATTACAAGCAAAGAAAACAACTGCATCACAAAG
CTCACTCCTATACTTGCTACATACTCCACAAAACACACACATATCTACAA
ACATCTCGAAACCTCAGTAAATTCTGATCTGCAGCCAAGTATAGCTGGAG
TTAGCACATACCACCAACCCTAGTTCTTGGTTTCAAGATGGTGCAAACCT
GTCCATGATCATGAAAATGGTAGCTTCCGAAAAACCACCATCTTCTCCCT
TAGCCTCCACCGACGACTTCACATCGCGTAAAGAAGCAGTTTTGCCTTCT
TTTCCTTGTTCTCCAGGAGAAACTTCTGTTGCACATCTGTTTCTGAACAA
GAAAGACTTGTTCACCTGCATTTTGTCCTTGAGTTTTGCTACCTCTCTCA
TGCATGCACTTACCATCTGTGACATTTTCTACAAAACCTAGAATTCTTTG
TCTATTTAAGTTGTGTTTAGCTCACTGATATGATTGTGTAGACATGTTGT
TGATATTTATATGGTCATGGATTAAACAGAAGATAAGTGAAGGGTGAGGA
ATCAGTGTGCTGTGCAACCAGGCAACTTGAGAAAACAGGGATTTTGTAGT
GCAT