| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017362348.1, is a part of gene, LOC108195385. |
| The genetic_marker, MK010754 1_39625408, is located in gene, LOC108195385. |
| The genetic_marker, MK010749 1_39625487, is located in gene, LOC108195385. |
| The genetic_marker, MK009405 1_39625492, is located in gene, LOC108195385. |
| The genetic_marker, MK009408 1_39625516, is located in gene, LOC108195385. |
| 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_017362348.1 | XM_017362348.1 | mRNA | DCARv2_Chr1:39619989..39626634 |
TTCCAAACAGTCTTTCTTATATCCTGGGAAACCCAGAATCGCTCGTTAGG
TACTCACCTCCCCAGGTTTCCTGCTTATTCATCATCCATCTGCATGCCTT
TGGTTATGAATATATGATTCTATAATTTTAATTATTGTTTTGATCAATCA
TTTATTGTTTAAGTTGATGCATTATCTTTTTTTTCCCTCAATTTTGTCAT
TTGAATATTATTTGTTGTTGTGTATTATCAAAATTCATTTTTGTTGACAT
GTTTGTGTATTGAACATGAAGAAGATATTGGATATTTTCCATGTCGGATT
TGAAAATTTTGAAAATTTTCTGGGCTTAGAAATGCAAAGTGTGAAATTTG
ATGTAAATTTAATTGTTTTGGCTTTGAATTAGCAGAGAGCGAAGATTCTG
GGTTTTGTTGCCGCTAGAAGCACTGCCAAATGGATTCTCATTTGGCTGAT
GCTCTTTGACGTTTTTCTTCTTTGACTATTATCATGAGAAGTGCTCTGTT
AGTTGTAATTCAAGATATTGGAAAACTGAGGTATTCGAAAAACTGCAGAA
TCTTGGTTTTGAAAGCTTAATATAAGGAGGTTGTTTAGTGTAAAATGGGC
TGCCTTTGCTCCAAGGCAACCTGGTCTAATGATTTTGTTGTTGATTATGA
GAGAGAGAAAGAGAAGGAGAGTAGAAAGTCTTCGGTGCAGTTAGTTCCTC
CAAAAGAGGAATTTGTGGCCGAGTCAAGAAGAGGCTCTGTGCATCGGATA
TCTAATGAAAATGTGGGTTCAGTTCGCGGGACCAAGGATGGTGAGGACAG
AATTGTGGAAAGGCCTAAGAGTGGGCATCATAAACGGACAGGATCAGAGT
CGATACATGGTCGGATAAGTAGCAATCCAGGTGCTGCTGAAGGGGAAGCA
ACAGAATGGCCCTCTTGGCTAATTTCAGTTGCTAAAGACGCTGTACATGG
ATGGACTCCTAGAAGTGCAGACTCGTATGAGAAGTTAAAGAAAGTCAGTT
TTTTGACCCTCTATCATACTATATATATTACAAGTACTTGCAGTACCAAT
TTTTTGCTGTTTTTGAGATTTCCACTTCCAGCTGCACTTCATGTTATTAG
TTTGAGATTCTTGCATTTCATACGAGCAAATTTTATATTAAGTGATTTGC
AAAACAAGTTGGCAAGTGGTTCGAGATTGAGGCTCTAAGATGGATCATGG
TGTATCTTTTGGCTGTAAACTTTTGCTGAACCAATCCTTCCTTGTTCTTT
TTCTGAAAATAAAGAAAGGCCCTTATATCACTTCATGTCTTGTAGTTCAG
AAAATTAAAATAAGCAAAAGGAAATGGGAAAGGGAAAGGGTCATAGTGAT
GTGAGGATGGTTGTGGTAGCTAATTTTCAGCTTATTAGTGAAAATAAGTA
ACTGATTATTTAATTGAGTTAAATTAGTGATTTCAGACACTTATCTGGTA
TGTAATGCTTTAAGCACTTTCACATGTAGACGTGCTGTAGGCGCATGTAT
GAGTTTATAATAATTTAATAGTGGATCATTAAATCAGTCAAGTTAATCTC
CTAGCATAGGAGTTAAATTTGATTTTCTTCTATTACTCCGGGGCCTAATC
ATAGTTAAGGTGCTTATATATTGGTGTAAGCCTCACAATTAGCTTACATG
ATAGTGGTGACTAGAATTTAGACTTCTCAAATTTCTGATAGCCTACTGAT
GTTGTTTTGCCATGCAGATTGGCCAAGGAACCTACAGCAGTGTTTACAAA
GCACGTGACCTGAAGACCAACAAAATAGTTGCAATGAAGAAAGTGAGGTT
TGTTAACATGGATCCAGAAAGTGTACGTTTTATGGCTAGGGAAATTTGTA
TTTTGCGTAGACTAGATCACCCAAATGTTATGAGACTTGAGGCTATCGTC
ACATCCAGAATGTCAGATAACTTGTATCTTGTGTTTGAGTACATGGAGCA
TGATCTCACTGGGCTTTTAGCATCGCCTGATGTCAAATTCACTGTACCAC
AGGTATGTTTTCACTTTCTTATGCGGGTTCAACTTCTAATATACGACATG
AAACTGAACTTGCATTTTCAACTATACAGAGCTTTCTATGAATGAAATGA
GATTTTCACTAAGTGTATTAGGAGACATTTAAAATTTATTTTTTTCACTA
TAGCTTGCCTCTAGGACAGTCAGATCAACACCACCAACATATTACTTTCT
GTGTTTTTCCTAAATAGGAATTTCTTGCTTTGATACCAGCACCTAATAAA
GGATACTTTTTATTCAGTTTTAAGTTTGTGAAATTGAGTTCCTTATGTAA
GTAGTTGGTGACAGTACCAACTACTTAGCGATAAATGGCATTCACATTAG
CAGCTTATCTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNTCTTAATACAGGATCATTCAAATCTGGT
TTTTTTTTTTTATTAGAGCTTTTTTTTTTTTTTTTTTTTTTTTTTGCCTA
CACCTTCAGATTAAATGTTATATGCAACAACTGCTTTCTGGACTCGAACA
CTGCCATCGTCGCGGTGTCCTGCATCGAGACATCAAGGGTTCAAATCTTC
TAATTGACAACAAAGGAGTTCTAAAGATCGGAGACTTTGGTCTAGCTACC
TTTTTTAACCCTGACAAAAAACAACTATTAACTAGTCGAGTTGTAACTCT
ATGGTATAGGGCTCCAGAGCTTTTGCTTGGTGCTACATCTTATGGAGCTG
CCATTGATATGTGGAGTGTAGGATGCATTCTTGCGGAACTATTTGTTGGG
AAGCCTATCATGCCAGGAAGAACAGAGGTAGAGTAATCTAAACAATAACT
ATCTGCACTTTATATAGCTTAAACAAGTAGTAGCACAAGCAAGGACATAC
ACTTGCATTTTTATGCCTGCCTTATTATAGAGTTCATCATTTTGCCCAAA
TAACGTCATCTAACATAATATTCTTTTGAGTTTTAAAAAATCTGATTTAA
AAACACCTGTCCAATCTTAAATTTGACTTGAATGATTGTGTTATATTGAT
AAAGAAGTTTCTAGTGAAACCTCAATTCATCACAGAAAAATTGATAATTT
TTTTGTGCTTTAAGAGGGCTGCGCATGTTGATGCTATCTGGGAACATATG
AAGATTAATGATTTTGGTATGGGAATTCTACCTCAAAATTTCAAGAAAGT
GATAGGTTATTGATCCACGTGGTTAAAATGGTTACACGCGTGCATCCAGC
TCACTTCATATTGCATGTTGTACACACTTCTTTTTTCTTTTCATGCATCT
GTAGCCACTTGTTCGAGGCCCACTCTTAGGTTCTGAATTTTTTCCAACTT
TCTGTATGTCAGAGTTTACTACTCTTCCTTAATTAAGAAAATTGCTAATA
ATCTTGAGCCATTCAGGTTGAGCAAATGCATAAAATTTTCAAGCTTTGTG
GATCTCCTTCTGAGCAGTACTGGAAAAAAACCAAATTACCACATGCTACT
AGTTTTAAACCTCAACAACCTTACAAGCGTCAGGTTGCAGAGACTTTTAA
GGATTTGCCCTCATCAGCTTTGGAACTTGTCGATGTTCTTCTTTCAGTGG
AACCGGAAGCACGGAGTACTGCTTCTTCTGCTCTTAAAAGCGAGGTAGTG
CTTATGACTCTTAACCTCAGTTATTTGTTAAAATTATACGGTAAATTTCA
ATGATTCTGCATCGTAAAGTAGCCGTTGCATGCTGCTAAGTGCAGAAATT
AGAAATTTAGACATCTTGGCAATAAGATACTTCCCCTTCTTTTAATGATT
TTCTTTCTTTGCATTAAATTCTCCGTGCTATACTATTAACTAGTACACGT
CCCTCCACTATCTTCCCTGGTTCCAGATGGATGGTGTGAGACTTCTGATT
TTCCAAACAGTAAAACAGTCAACGCGATGTATTCTGTAGACTGTGCTCGG
AAATGAGAATTTCTTGGATTTGCATAAGAAATTAGGCATGTGTCGCAATT
ATATTGTTCTGTGTGGGCAAATTAGAGGACAATCACCTGGACAGTTGGAA
TATAGATTTTCAGCCAAATGATTTCATAGTGCAAACTTTCATGACTACTA
TTAGCATCTGGGTAATTAGGCAATTGACCTGATAAGGCAAGAGGATGCTA
TGGAGCAACATTGCCTCGTACATGATGAAAATTTAATGCTGTCACTTATG
TTCATCTTTATAGCAGCATCAAGTACCTTATACTCAGTTATACTAGTTTG
TTTCTGTACTATGGGGGTTAGCTGGATAACTTGGCTCGATTTTTGTTTGT
TAATCATTCTTAAAGAGACGTTATATCTTTTATATTCAGAGTTAAGCATG
GTTGGAAGTTTGGAACAGTTGAATAAGGCATTTTATGTTTTACATATATA
TCTAATTAGAAATTGAATTTGGTATGCAATATTCACATCCAAAAGTCACT
GAAGTTGAAAGTTAATTGGCTGCTTTTGTTGTGCGTGTGGCGCGAACATG
ATTAAAGTCCGACTTGCATAATTCATAATTTTATTTGTTCTATTGTGTGT
TTTTGTTACTGATGAGATTATTATCTCTGACGGGACCTGTTAATATGTTC
TTGTTTTCAGTTTTTTACGACAGCGCCTCTTCCTTGTGATCCATCTAGCT
TACCTAAATATGCCCCGAGCAAAGAATATGATGCAAAGCTTCGAGAGGAG
AAAAAGAGGTATAATTGTGTAGGACTAATTCAGAGTTTGTTTAATGTCAC
CTTATATCATTTTTAAAAAATTATATGAGCTATATAACATTTTTATGTCT
GAAATTTATTTTAACTTGTGGAAGATGTAAGATGATATTCTACATTACAG
AATTCGTCATCATTTAGTATCACTTCTATGTAGAAGCCTGTGAAAGAGAT
TAAGTCGAAAACATACTTGCTTTTTTCAGTCCTAGCTTATATTTACGTAC
CGTTTGCATCTCTGTCATTTCTTCAGGCGAAAAGTAGAGTCTGTGAAAGG
ACGTGGGCCTGAATCTGTGAGGCGGGGTCACAGAGAATTGAAGGAAAATG
ATCCAACACCGGAATTCATGGCACACGGACAGGTGTTTACATGTATTACT
TATGGTTGGACTATGTATCAGTTTCTTGCATCAGATTCAATTTATAATAC
AATTGACTTGTGGTGCAGCAGGTACATTCTAACAAATGCGCTAGTGTAGC
GTACAAGCCTCATGGTGATGCTGGAGCTGGCTTCCCACTTGAGCCTTCTA
AAGGGTTGAAGAATACTGGGATAAATCATTCAACTTCAATGGTACATCCG
AGTGCAGCAGTCTCGTGGTCAGCTAAAGCAAAGGATGAGACTGGTGTGAC
AGTTTCAGGAAGGACAAACAGCTCTATTCACCGTGGTTCAAACTTAAGAA
GGCAGCATTCTCATAAAAATGAAAAGGCTTCCAGCAATGATAATATGGTA
AGTACTAATGATATGGCTCGCGTAATGCTCTCTTATATCATTCTTCTCAT
GCATACAGGTAAATTAAACTGAAACACTTATATATCATCCTCTTGTTCTG
TATTCCATTGGTTATCGAACATGTTAATGTGCTCTTACCATAAAGCAGAT
TGGATATGAACCAATAATATATAGCACTATTACTGGACAGAAGCAAGCCT
CAATTCTGTATCAACCAATCATTGATGATATATAACATCTCTAGGTATAT
TGTCTTTTGTGATCTAGGAACTGAATTAAATTGCTTCCCAATCTATGAAG
CAGGGAATCCTTTTGTGTAGAAAGTTATGTGGGTATACAGGGACAGCATG
CCTGGGTGACTCTAAGATTTACGGGTCAAAATCAGTTTTCGGGACCCTCA
TCTCTATTATACTATTTCATACATTTATATAAAAGATTCGACAATTATGG
ACCCCTTAACGTTAGGCGTCCTAGACGTAAGTCTTGTCCGCCTATAGCCA
GGGCCACTTCTGTACGCACGGGAGTGCGTAGGAATATCCCATGTAGCGTG
TCCCTTTGCACCCTAATACCCATATGTAAATAATGTGCTTATCCTCGTAC
TACCCACCCCCCACCCTTTATCTTGCTTTTAGCCCATAAGTTTATGCTTC
TAAGTTTAAACTCGGTGCTACAGCTTAGAACAGGCTTTCTCACGCAAGTC
ATGCATATACACAGTCTATACTTGTCTTGGATAAAGTTTTCTTCTGCATT
GATTCATTGAAACTTCTCAACTTTTGGCTTTATGCTAGGGCCAGATACGA
AAGAAAAGCAGAATCCTTTGTTCTGGACCATTAGTCCCCGCTGGGGGAAG
TATGGAAGACTTGCTAAAAGAACACGAAAAACATATTCAAGACGCAGTGC
GTAAAGCACGTCTTGACAAAGACAAGAGCAAGAAGAATCTGGGTGATTAA
CTAGAAACGTCCAATTTGGGCTATATTATCCAGGAGAGAGTGGAAGCCGA
ATTGTAATCTGCATCATTGATCCATTCAGGTGGGCTGATGGTATG