| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017386475.1, is a part of gene, LOC108214464. |
| The genetic_marker, MK003396 K0840, is located in gene, LOC108214464. |
| The mRNA, XM_017386474.1, is a part of gene, LOC108214464. |
| The mRNA, XM_017386472.1, is a part of gene, LOC108214464. |
| The mRNA, XM_017386473.1, is a part of gene, LOC108214464. |
| The mRNA, XM_017386471.1, is a part of gene, LOC108214464. |
| 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_017386471.1 | XM_017386471.1 | mRNA | DCARv2_Chr3:9637052..9641921 |
| XM_017386473.1 | XM_017386473.1 | mRNA | DCARv2_Chr3:9637052..9641386 |
| XM_017386472.1 | XM_017386472.1 | mRNA | DCARv2_Chr3:9637052..9641368 |
| XM_017386474.1 | XM_017386474.1 | mRNA | DCARv2_Chr3:9637052..9641282 |
| XM_017386475.1 | XM_017386475.1 | mRNA | DCARv2_Chr3:9637052..9640104 |
CTACATAACCAAAGACAGGTACAGCTGTATCTGATTTGAATCATCATCGC
TTTGTTGATTCTGGTTTAAAATTTGTTGAGGGTGCTCCTTTATAACCTGT
CATGCATGTTATGGGTTCATATAAAATTTCAATTGAAGATATATGCGTGC
ACACACGTCAGTTCGATAAACAACCAACTGAACAAGCTGATTACAAACTC
ATCGTCAAGATGATGTAGAGGAAAATAAAAAGTATATAAATAAAGCCAGG
CCATTATGATTGACCATAGCCCCAATTTTACTTAACGAGACTCGCAACGA
GAGAAATATGTGTCAAAATTATTAATGATTTTTTGAGGTTTCAGGTTGCT
GTTTTGTCGCACGATAAAAGCGCCGTACATAGTACGTTATAATTTATATT
TATACTAATTCAAAACTTTTTAGATAAATATAAGATAAGATTTTTTTTGA
TAATAAGATTTTATTTTTATTTAAAATTAGTTTAAAATTATAATTTATAT
TATACTAATTCTAAAAATATAAATATTAATTTTAGTTCAAATTCAGGTAA
AAATTAAAATGGTGTATAAATGTTCCAGAGCCCCGATTTTCTCTCTCTGT
GACTCTTCTCTCTCTGCCCTTCTCTCTTCTCCGGTACGTATCTCTCTCCT
TTATCTGCTCTCTATGCTCAACTATTGTCGAATTCTACACTCATCTCCAT
CAATCTTTTCTACCCATCCCCTCCCTTCCCCATCTGGTATGTATATATAA
CAACTGTATCTGTGTCTACATGTAACCTCAACTGTATTGATACGTGTTAG
TTTGTGTTCTTACATCTGTTTATACATATTGATTGCTCATATTTAGTCTA
GTTCGGGCCGGTTCCGAGTTATGGGTCACATAGCTACTTACAGTTTGTTA
AAAGATGCTTTAATTACAGACCCACGTAGCGTTCGACGAAATTCCCCTGA
AATGAAAAAAGTCATTACGAGTTTGTTAATTAGTATGTTCTCGAAGTATG
GAACTTGGGTCTGGTTTAAAAGAGAAATTAGGAAATGGAAATGCTCTTGT
TAGTTTCTATGCAAAATGTGGCAATTTGGAATTTCCGGAGTGTTTTTGCG
GGTTGTTGATAGAGACACATTGGCTTGGAACTCGTCAGTGCATTCGAGAC
CGGGAATGGTGGAAGATATTGTGTGTTCTTTTGGGCCAATGTGGAATTGT
GGGGTGGTGCCTGATCAGTTCACTTTTGCTATTGTTTTTCCTAGTTGCGG
TAGAGTGAATGTGGAGTTGGGGAAGCAAGTGCATTGTTTTTATTGACTAG
GCATACTGTGTTCCGATTGTTTGTTGTCTGTTAGCAGTGATCAAGCCATG
GTTTTTTGTTAATGCTTATTTGAATTAATGATATTTTTGATGTAGTTTGA
TTACTTTGAAATTAAATTGCGAAAAAACATGCTAGTAATAATTATGGAGA
AATTTGGATATTGTCATGTAAGTTTAATTGTTTGATGAGTTTGTTGTTAT
AAAAAATAATTTTTTGTTTTTGGATTTAATTTGAAATTTCCAAAATGTCA
AACAAACACCGGAAATTATTTTCTGGTACAGGAAAATATTCTCTAGGAAA
ACATTTTCCACAATCAAGTTATTTTCAGCAAACAAATGGAGCCTTAATTC
GTCATTATTCCAAGGTTGCAATAAAATTAACGACAAAAACACCTGCTAAT
ACAGTGTTAATTTTGATTTATATCATATTCACTAATATAACTCATGCACA
TCTACCTATCTGTGTAGCAGCAGCCATTCTTTTCTGTTTTTGCTGGAGTT
GAGTTGTATTAGTAGAAGATTTAGTAATGTCAGAAAGCACTAGTATTCCT
GAGGCCCAGAGATTAGCTCCGTCGCTGTTGAATCCTTCATCACGTATTAT
TTGTCGAGTGTACGTTCTAAACCTTTACTTCTCGGTAACTGATTTTGATT
GTAGTATGTAAATGTAGTTTCTATTGATGCCGCCTGGTTTTTAAGCTTGT
ATCTCTTTATATGCAGATGTGAAAAGCAGTTTTCACAGTATACTTGTCCA
CGATGCAACACGAGGTACTGCTCTCTTCATTGCTACAAGGTTAGTAGATT
TCATTACAGTACCTGGTGTTATTGCTTCTGCTAATTTTGAAATTTTTCTA
AATGTTTTGATTAGTTACGGGATTCACTAGCTATCCATTTCGATAAATAT
ATAATTGGACATTTGGTCTTGTGGGCGTTGACTTGTCATAGTTCTGATCA
TCGTAATGAGTTGTATTGTTGTTGCAGTCTCATAGTCGATCTTGCACTGA
ATCTTTTATGAGAGATAATGTAGTTGAGGAGCTCAAACAGTTGGAACCTA
ATGATGCAACTAAACAAAAAATGATGGCGATCCTCCAACGGTTTCATACA
CAAGAAGAGATAGACAACTCAGATGAGCTGTTGGATAGCACACCGGGGGA
TGGTATGTTGTTTCTAGTCTGTTAATTTATGCTGCTCTAAAATGTATCAT
TGAAGTTTGCTAGTTTTGATAGGAATTAGATAGGTTTTTGCTAGTATGTG
TAATGCTTTACAAGTAACTTTGGAACTTGTCTACCCTTTTATGATCAATT
TAGGAACTTAGTACTTCCATATTTTGGAATGGTTATTAGTGTTTGTTTAT
CATTTGATATTTTGTTCTAGATAGGCTGAGAATTTAATAAAGGGATCTTC
TAGGATAGTTACATCCAGCCCTAGGTGACAACCTGACCTTATAAGAAACA
GCACTGGACCCTACCAGGATAAACTAAGGGCATAAAACCCTAAAATTGTT
CCTATCTCCTAGAAAGAGAAAACTGTTGCGTATTCCTTTCATATTAATTA
GGTCGCTTAATTCTTTTAGATAACACTTTGAGAGTAATATCATGGCGGTA
TTGACTAAGCTAATTGGCAGATAATCGAAAGCTGAACTTATTTTAGATGT
CTAGGGAATTAAAACTAAAATGAATAATTTATAACAGACAGTGAGTAGCA
GTAATCATGAAATTTCTACTAATTAAAGAAAAATTCTCTTTGATAATCTC
CCAAACTGCGTTGATATATATAAGCACTATTGAGGCCGTTGGGGCTTGGC
GCTTTTGTTGATTCGTATTATGATAAAGCTAAGGAAATTCCCTCGATCTT
AATGTGTTTTGTTGACGTAGACGAGTCAAAATGATCCAATTTGATGAATG
ATTATAAGAATGAATATTGGTACAATTTCACATTGGATTATTGGTTCCAT
TTCATTTAAGAAGACACAAGGCATAAAAGAAAAAATAAATAAAAATGACA
GCTATGTTGTGTAATGTCGGAAATTGGATCTCAAGGAATAAGCTGTTTCT
AGTATTCAAACCAATTATATGTTAGATAACAAAGACATATTTGACCATCA
TGACAAACACGACCTTGAACACAAAATTTAAAATTTTGATATATATATTA
TATATGAGTACCGAAGTAGCTAAGCTGCTTTTGCAGACCTTTGTTTTAAT
TAGGGCATACCCCTCTTAATTTTGCAGTTGCTTCCTTTGCAATGAATTTT
TTTCATCTATCAGAAAAAACATGTCAACATGTATCTTGCCATTATTTGCA
TACTACTATAACTGTTTTGATGGATTTTTATTGTATGATATTTTTCTCCT
TTCAGTTACCGATTCAAATTTCTCAGAGGTGGTTATTCAAAAGATTTTAT
CTGGTAATTAGGATCCTTTACTCTTTCATTTTGTGCTAAATTATCTACCC
TGGAATTTTGCTTGCTGTCATAGTACTGCTTCATTTTTAATCTAATTGCC
TCTACAGGAGGAGAAATCCAAGTTGAAGATTTGTCTGAGGATGAAAAGAA
AAGATTTCAAAGAGCAGTGGTTTCTGGAGAGCTAAGCAGGATGATTGAGC
CATGGGAACCTTGGTGGTTGAAGCCTTCTGCGAAAACAATCCATCTCAGC
GAACAAGGTAGCCGACTTGTGCAACCAATTGTGAGACACGAGAGCATAGC
ATCAAAGAGCGAAATTGTTGAAAATGATCAGTCACTCCACATTCCGCCTG
GACCAGAAACCCCACTGCCTCCAGTTAGCAAGCTTAGCGCTACTGCACCT
TCCCCGCTTCTAGCAGTTCACCTAGTAGACATCATCTATAGTTACTGTTT
CACCCTTCGCCTTTATAATGGAGAGTGGCTAACAGATCCGATAGGATCAG
TTATGCATGCTCTGAGTGTATCTTTAGTTCTTGGTCAAGGGGGGAAGCCA
GAAACTGTTTCGGAAGCTGTATCTCATTGTTTGGAGCAAACATGTTCCCC
AGTTTTGAGGCACGTGGGTGGCTTGCAATTTGGATTGGGCCTCTTAGATG
ATGTAGTATGCCTACTTTCTATTGGTGGAACAGCTTTGGTTTGTCTGCTT
TGTGATTTTCAGAGGATGATTCAGGCTGCAGAGAAGGAGCTCAAATCGGA
GAAACCACGCAAGTCAAGAAGAGTAGAGGCTAAGGGCAATCTCAAGTCTG
CTGAGAGGAAAGTATATTTTATGATGTGTTGGGTCCATGAACAGCATGAA
GACACTTGGTTTTCTATAGCAAGCATGGTAGAAGCAGAAAAAAGCGCAAA
TTTGGCTTGCACAGGTAATAGAAAGGATACCTTGAGTGTACAAGAGAGAG
CCCGACCTCGAGGCAAGATGTTGATTGAGGAGGTTTAAGGACCTTTTTGG
CAACATTATGAAGACACTTAAAATACAGTCTTGAATGGTGCTTGGTAGTT
GTAATATTGAGAACTAGTCTAGTCTTCTAATTTTGGTAATGCTAGTTTGG
AGTATCGAATTGTCACACATCTATGGGTATGCAGGTTCTTTCAGTTATTA
ATTCCTATTCTATTTTCTA