| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017402687.1, is a part of gene, LOC108227507. |
| The genetic_marker, MK006307 K3751, is located in gene, LOC108227507. |
| The genetic_marker, MK010273 6_27301983, is located in gene, LOC108227507. |
| The genetic_marker, MK010275 6_27301992, is located in gene, LOC108227507. |
| 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_017402687.1 | XM_017402687.1 | mRNA | DCARv2_Chr6:27297147..27302326 |
TGATATATAACACAAACACTGTAACCTTCACCCGGTGCGGTGCAGTCTTT
GTCTGCCCTCCCAAATCAAAAAAATAATCTCTCTCTCTCTCTCTCCCCCC
CTCTCTCTCATCATCGTCAATTTTTCATCTCTCGACGATTTATCCCAAAA
AATCTCAAAAAATATAAACACAAATTATATCTATTTCTATATAATCACTA
GTATTCTACCCTAGGGTTTTAAAAAAAAATCTAAAAAAGGAGAATCGAAT
CAAATCAATGGCTCAGATTCAAGTTCAACCTCAGCAGCAGCAACAGCAGA
TTCCTGTTTCTGGATCTAACGGAGTTTCGGCCGGAGCGGCGGCAAACGCC
GGCGGCAGCAATCAGTTCACGACGACGTCGTTGTATGTTGGAGATTTGGA
TCAAAGCGTGACTGATTCGCAGCTGTATGACTTGTTTAACCAAGTCGGTC
AGGTTGTGTCGGTTAGGGTTTGTAGAGATTTGAGTACTGGCCGCTCTCTG
GGTTACGGTTATGTTAACTATAGCAATCAGCAAGATGGTAACCAATCCTC
TCTCTCTGTGTGTATTGTTTGATTTGATTTGTGGTTGATGATTTTTATGT
ATGCATGTTGGTTAATTATTATAATTGTTGCTTTATGAATTAGGGTTTAG
TGGTTTTTGATTCGTAATTGAGCTGTGAATTGCGATTGTTAGTTTGTGAT
TGAAATGTTATCGAGATTATGTTGGTTTTGAATTGGGATCGCTTGGAGTG
ATATGTACTGTTGGGGATATATGCATGTTGATTAATTATTAGAGCTGTCC
CTAATATGAATTTAGGGATAGCCAGTTCTGTAGGTTTTGAAATGTAATTG
ATGGCAACGTAATTGAAACATTACTCAACTGAAATGTCCGTTCTGTTTAT
TGAGCTTGCCATTGAGTATTGTTGGAGTATTACAGCAAAATTAATGGCTG
TGCTAAAGTAGATGGAGCTATTGTTTTGGTGTCAAATTATGGCTATGACA
CCATCGACACACTATTGGATAAGAGTCACCATAATTTAGACGGGACGGGT
TTTACATTTTTGTCAATTCCTCGCATATTTTCTGTCTGTATTTTATATAT
CAGTTGGTATTTATATCCTGTCTGTATTTTTATATCTCAGTTGGTATTTA
TAGCCTTAAGTGACCAGACCGTTGTCAGTGCTTTTGATGTTTGCGGCGGT
TCTCTTATCATTCTCATTTATATGGGTGTGGTTGTGAAAATATTGCGTTG
TCCTTTAATTAGTTTGATTAATTATTTGCTCTGTTTTGAGTCTTGTTGTG
GATATATCAGTTGCTATTTTTTCTTCACTCAGAGAAAGCGATGAGTTAAT
TAATGTGTACAGTCATTATACACTGCTTCATCAGTAATAATTTAACTTTT
CCATTATGTATTTGTTTTAGCGACGAGGGCTATTGATGTCTTGAATTTCA
CTCCGCTGAATAACAAGACAATTCGAGTGAGTGTTTCTCGTCGGGATCCT
ACTGATCGGAAGAGTGGAGCTGGTAATATTTTTATCAAGGTACTAAAAAA
CTTTAGAGTGCTTTAAACGTTTTCTTCATAACATGAGTATATGTATTAAT
TTCTTAGATGTTAAGTCATGCATTTTGAATGGGTAAGTAAGTTTGGCATC
ATTTGGTAAACCTTTGCCCATTATTTAATAACGTTACCTGATGATTGCCA
TTCTGAAATGAATTTTAATTTTTCTGTAATTATATTATTTGTTGAAAGAA
GGCTATTACTTGAGTTTTTTTCTGAAAACGTTTTTGCGGTGTTAAATATA
ACTTTTTTGTTTTATCAGAAGAAAATATACATACATGTATTATGTATATG
AGATTACAATTTTTTGTCTGCTTTGGCGGGCACCAACCCATATTTTTTGA
TATCATTCTGTGGCTAACTCTAGGGGTCTCTCTGTGTGTTATATTAGGGT
TTTGTTGTTTCTGGTTTCTCGTTGGCCTGGTAAAGATATACTTAAAAAGT
CATTTATATTTTTTTTCCATTTTTGTGTTGTGCAGAACTTGGACAAGTCA
ATAGATATCAAAGCCTTGCATGAAACATTTTCAAGCTTCGGAACTATCAT
TTCCTGCAAGATAGCAACTGATGCCTCTGGCCAGTCTAAAGGCTATGGGT
TTGTTCAGTATGATAGTGAAGAAGCTGCTCAGACTGCTATTGACAAGCTA
AATGGCATGTTGATGAATGACAAGCAAGTTTATGTTGGTGTATTTTTGCG
CAAGCAAGATAGAGATAGTGAGATGAGCAAAACTAAATTTAACAACATAT
ATGTGAAAAATCTTTCTGATTCTACATCTGAAGATGATCTCAGGAAAACC
TTTGGTGAGTATGGAACAATTACCAGTGTAGTAGTAATGAGAGATGCAGA
TGGAAAATCAAAGTGTTTTGGCTTTGTCAACTTTGAGAATCCCGAAGATG
CTGCTAAAGCTGTTGATGCACTGAACGGGAAGAAGTTCGACGATAAAGAA
TGGTATGTTGGTAAAGCTCAGAAAAAATCAGAAAGAGAAGTCGAGCTCAA
AAGTAGGTTTGAGCAAACTGTGAAGGAGCAGGTCGACAAATACCAAGGGG
TTAATTTGTATGTCAAAAACTTAGATGACACCATTGATGATGAAAAACTG
AAGGAGTTGTTCTCTGAATATGGAACTATCACTTCATGCAAGGTTTGTTT
TTTCTCATTTCATTATATGTTGTTTAAGGAAGTTTATCTTGGAGATTACT
CAATTTGTTGTTGATGGCCTTACAGGTCATGCGTGATCCTAGCGGTATCA
GCCGGGGATCTGGATTTGTTGCATTTTCAACTCCTGAAGAAGCTTCTAGA
GCTGTAAGTGCTCTGTCTATACTTTGTTCAGCCTCACCCAAATTCTTATT
GTAGTAAGCTGATCAGTTTTTTGACCAAACTACAGCTTGGTGAGATGAAT
GGAAAAATGATTGTCAGCAAACCACTCTATGTTGCACTTGCTCAGAGGAA
AGAAGAAAGAAGAGCTAGGTTACAGGTACAAAATGTTTATTTTAGTCATC
TCTGGCCTGCTGGAATGTTCATGGAATCATAGATAAATGTTGTCTGGTGA
ACTTTGCACAAACATGTGTACTCATTTTAATGAAATGATATGCCTTTGTG
TTAACTAAACATATTACATTTATTTCTCTCTTTGCATTGATAGTACAAAG
TTATAAGAAATAGTTCACTGTTTTTCAACTTTTAATAGACATGCAAATCT
GGGGAAGTCAGGAATATATGGTTTGATAAGTGCCAAGCGGTCAAGCTTCA
GTAGTTTTCAGCATCTGATGTGATAAAGTTCTTTTTTGTGAGGCTACGGA
ACTAATTTCAAACCTTCCAAGTGAAGTTCTGTTGCATATTATTCTACCTC
TAAAGTGGTTGTTTCTTAAATGAATTTATACTGCAATGGGGACTTGAAGT
CCTAATCATTTGGTGCGAATATAACTATTGATTTATTGCTTATAAACTAA
TTTGTTTTTGTAATATCTGGGATATCTTTTGCTTGTTTTACAAGACAGTG
TTATATTATATTGTATAACAAATAGTGAATGATTACAGGCCCAGTTTTCA
CAGATGAGGCCTGTTGCAATGCCTCCATCCATGGGCCCTCGTATGCCGAT
GTATTCACCTGGTGCTCCTGGTATGGGACAGCAACTCTTTTATGGACAAG
CACCTCCTGCAATGATTGCACCCCAGGTATTTTTTCTTTTACAAGTTGGA
CTCCTTATGGAGTGTTATAAATGTATTACTGATATGAAAGCTAAAAGAGT
TTGATGTACTGGCTCCAAAAGCATTTTGTTATTCTTTTGTTAGTAGAAAA
ATAAGGCTGAAAAGTGAACGGCCTGTTACAGTTGGTTATACAAGCCATCT
TAGCTTCCTCTAGTTTCTGGGTTTAGTGGTAGACTGGTATTAGTTTTTTA
ATGCGAGATAAATTCGAACTCCAATAAATGAGAGGGGAATAACATTGTTT
TTACTTCAGCATATACATCTGTATCTATATCTACATCTATCTATATATAA
TATGAGGCTGAAATAATCCTTCTTGTAGGCTGGTTTTGGCTACCAGCAAC
AGCTGGTTCCAGGGATGAGGCCTGGTGGAGGGCCAATGCCAAATTTCTTC
ATGCCAATGGTACAGCAAGGTCAGCAGGGACAGAGACCTGGTGGAAGGCG
TGGTGCAGGTCCAGCACAACAGACTCAGCAACCTGTTCCTATGATGCCCC
AACAGGTATGTTGAAATTGTATACTGCATCTTTTACGCTGTTTCTCAGTT
GTACTCTTTTAAGGTATATATCTGGTTTAATTAAATGGGCATTTCTTTTT
CAGCTCATGCCCAGGGGCCGCATGTATCGTTTCCCACCTGGTCGCAATGT
TGGTGATGTTACCATGCCAGGTGTTGGAGGGGGAATGCTTCCAGTTCCCT
ACAACATGGGTGGCATGCTTCCTAGAGAGGCTGCTATGGGTCAGCCTATG
CCAATTACAGCATTGGCTTCTGCACTTGCTAATGCTCCAGCAGACCAGCA
AAGGACTGTAAGTTTTTGTGCAGATTTTAGGATTTTATCTTTAGTTTCAT
ACAAAGGTATGTAATTTTAACCCTTTTGATTTATGGCAGATGCTTGGGGA
AAATCTATACCCGCTTGTCGACCAGTTAGAGCATGATCATGCAGCCAAAG
TCACAGGCATGCTTTTAGAGATGGACCAAACTGAAGTTCTGCATTTGTTA
GAGTCACCTGATGCTCTGAAGGCAAAAGTGGCCGAGGCCATGGATGTTTT
GAGGAATGTATCTCAGCCTAATGTAGCTGATCAACTAGGTGGACTCTCTT
TAAACGAGAACCTCGTTTCTTAAGATCTGTCCAGGCTGGCGATTCTCGTT
TGACCTTGGGATCCTTTTCTGTGAAGGCTGGAGGTTCTAGTCTTTGTTTC
TTTATCATCTAGTGTCTCGGACCACGAACCGAACTGTGTTAAGTTTAATA
CTGAACGTAAGTGCATCTTGTTTCCTTGACAGTTTCTCTTTGACTATTGA
ATTTGGTTTGGAGCTACGGCTTTGGTTTGATATTTACCTTTTACTATGTC
ATTAGTCAAATCCGTTAGAAATCGTTGTTATTGTGTTGATTTCTAATGAT
AGTAATAATAATATTATTGGGTACTATAA