| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017403591.1, is a part of gene, LOC108228104. |
| The genetic_marker, MK011281 6_9360015, is located in gene, LOC108228104. |
| The genetic_marker, MK004721 K2165, is located in gene, LOC108228104. |
| 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_017403591.1 | XM_017403591.1 | mRNA | DCARv2_Chr6:9356734..9362822 |
TAAAAGAAAGAAACCTAGAAATATCTGAACGCAGAACAATATCGTTATCT
TTATATTTGCTCCCTCAGTCCCTCCCTTCGTCCTATCGCAGCAGCTCCTA
CAGCATTCTTTTGCTATATTTATCGATGATTATTCAGTATATACATGAAT
GACCTTTCCATGCCTTCATTAGGTCAGCTTCTATATCCCATTCTTGCTTT
TTCTGTTCATATACTATATAATTCTGTGTTTACTTCTGTTCATTTTTTGA
TTTATACTGCTCTTCTAAAACTTATGCTTCGTTTGGTCAAGGGAAAATGG
AATAATAATTGTTAACAAAACTAATCGGAGAATAGTGGAAAAAACGAGGG
AGTGTAATTTTTATCTAATCAGATTTGTGGAATAGTGAGTTAAATGGAGA
AGGGGAATGACCGAATTGGAGCAGTCGTTCTCGAGTGAAGCTGTGAGTTT
GGTTTAGATTGTTTCCAACGGGATGGAACGGAGGAAGGAATGAAAATTAA
GAATGTCGAGCCACCTGTTGGTGCAAAACTGCAAATGGATTCTCAACGAG
ACAGAATGTTAGTTTTTAGCTAGTAATTATCTTACCACCCGTACTTTTCT
GATAAATGCTCTCTCCGTGTCTATTAGGTTACTTACATTGTATTGTTTAC
AAAGTTTAATTTGATGAGATTCATAGATGATTAGTTTTTTGAAGAATCCG
AGAATGATGCCAAGCAAGGTATTAAAAGATAATTTTATATCTATTTATGA
GTGAAGTTAGTTGTTATATTTTATATGTAATTTGATTATATAAAATTAAT
AGATTATTAGGAATACTCGAGGTAATGGTAGACTTGTAGTAGAGCGTAGA
GCAATTGAGGACCCCCCCCTCCCCCCTCTCTACTTTACTTCTGTTAGTAG
TAGTACGTAAGTATTAATTTCATTATGCTAGTTGTACTATAATTAGAAAT
TTTTACTTGATTAAGTTTTAGGGTTGCGCTTAGTGTTGTTTAATGTGCAT
ATTCCTCGAAAGCGCAACATTTAATTTTGAAGTGTAAGCGCGCTGCTTTG
CCAAAAATGAAATATATGGAGAAGAGCACAAAAGAGAAGGCATATAGGTA
TTGAGAAGAAGACTATTTTGTAGATGGAGATGTGAGACGGTGAAAGACCT
TGAGATGTATATGTATATGAACCAGTATATGTGATGTGGTATGAAAAGTT
GAAAATAGGTTATCCTTATTCTTTTTGTCTTCACGTTTTTTTTTTCTAAT
TTAAAGATAAATTTTGGTTAAAGCATTTTCCTTCATTGTCAAAAGCAAAC
TAAATAGCAGATATTTGACTCGTGGACGTGTGCCCAGTGTAAAGCTCTAT
TGATCATGCACTTAAGCGTGCATTTAACAACACTGGTTGGGTTCCTATGG
AAGAAGTAATATATTCTATTGTATTCAAACTTTGATTAAGTACTGAAATT
GAGATTGAGATTCTAACATAATAGAATTGTATATAATTATACATGTATTA
TTTATCCAACTAAATTTTTTTTTAACATGTATTTATAAACTAGTTTAAGA
TTCTATGTATTATTTTCATTAAGTAATTTGGACCCCTGTTGTTTAAAATC
ATTGGTCTGCCATTTCGTACATGTGTATTTATGTATATATTACATTTTTA
AGACGAATGAATAATGCTTCAGCTAACTGCATCTGGCTGATGAGACTCTC
TACAACCTTCTTTATGTATTTGTGGCGCAGAGCTTACTTCTTCTCAGCAT
TTCTTCCAGCTTCATCGCATTTCATTTGGGTCTCAGAAGTTGTATCATTC
CTATGACAGGGGACTGTCATTTTTGTGGAGATCTTTCAAGATCTCCACGA
CACAAAGAGCGTTTAGTGTCAGTCATTTTAAAATGCGATGTGACAGAGTA
CTGATTAATGCAGTTGCTACTCTTGAACCCAAAATTGTAAATGAGAAGAA
TGCACATGATGGGCACTGTACATTACATATTCATAGTGATTCAGAAACAC
TACAACGGGCTGAGCACCAATCTACAAGTGATGATGAGTTGGATGATAGA
GAGAAGTTGAGAAGGAAGAGAATCTCTAAAGCAAATAAAGGGAAATCACC
TTGGAATAAAGGCAGGAAGCATAGTCCAGGTAGTTAACTAACATCATGCT
TGTTGTGGTGCTCTTAAAATTACATGGAATCTTTATCTCTCTTTTTATTC
CTTTCAGAAACCCGACAAAGGATTAAAGAAAAGACAAGGCTTGCCATGCA
GGATCCTAAGGTGAGGTCATGTGATACAAAAACTGCAAATAATTTGGAAA
TTAAAAAAAAAAAATCCCAAGTACCGATCCCAAGTAGCAATGATGTAGCA
AATTTTTAAATGAATAGTTAAAGATTTGGGGTTAGAATTAGTTTTGTTTT
TCCGTTTAAATGTCAAATCGTTATTTGCACAAAAAAGTATTGGTATAATT
ACTCTAGAGCTGCTGACAATATCTACCATCTTGTCAGCTCGGTCTGACCA
GTTTATTTACTTATAATCATCTAGCTTACTTGGAACAATTCTGAATAACC
ACATTTTGAGTCTATAATCTGAACTCTGGTTTCTGTAAAAATAAGTTTAT
TTATGACACAAAAACTAGCTCACTGCATGATGCCTCACTTGGTATCCAAC
AGGTGCACTTAGTATTTGACAAACAGGCATTGAAAGGAATTGAAAGGCAC
CCTTTTAGCATCTGTTAGATCACAATCGGGCTATTAGTTTTCTCAATAAT
GGACCACCTAGGTAATTGGAACTTATGCATCTTGATTTGCAGGAACATCC
TCACTTCCTAATTGGTATCTGCATTATATTCTAATGTTCAAATAACAAGC
TGTTGTCATGCAGGTAAGGATGAAGTTGATTAATCTGGGACATACTCAGA
GGTAGAGTATTCTTCTAGTCTCAAAATTACCTCTTTGCCTCATTTTCCTT
AGTCCTGGACATGTGTCAATGGGGTGAAAGAGACTTCTAGATTACTGAAT
ACTGGCAAACCATACAGACCAAGTAACTTTCTATTCCACTTGAGCCACTA
TTAAGACTGAAACATTGAAATTATATTTCCCTGGACTTCTATCGTTTCCT
TTCTTGCCTTGTACTTACCCTTGCCATTTACAAATACTATTGGAGTACCT
TTTTTTATTTTGTTTTATAGACATGCTCTAACAAATTTCGTTTATTAGCT
TAAACCAGTTATTTCGTCCAATTTATATTAAAACTGTATGTATTGTGCAG
CAAAGAAACAAGGGTAAAAATAGGGGTTGCGGTGCGAATCGGGTGGAAGA
AACGTCGTGAGAAGCTGATGCTGCAGGAAACATGTCATGTTGATTGGCAA
AACCTGATAGCTGAGGCCTCAAGAAGGGGATTAACTGGTGAGGAAGAACT
ACAATGGGACTCCTACAATATCTTGGATGAACAGCTTGAGAAGGAATGGG
TGGAAAGTGTTCAACAAAGGAAGAGAGCTCCCAGGCCCAAAGGTAGCAAG
AGAGCACCCAAATCAGCAGAGCAGAGAAAAAGAATTTCGGAGGCGATTGC
TGCCAAGTGGGCCGATCCTGTAAGAAGTTATAGCATTAATACTTTTGATG
TTTAAATATTCTGTTCCGCCATCAGAAGTAATCAATACCTGGAGTTCATA
AGTATGTTTCTAACTGGATCCACACTTTTAAACTACAAGGTGTATCCTTC
TCTTGACCTTGGAAGGTTTAGTTGATATGGAGCAATCTTAGAGTCATCCT
TTTTCCATTGTGGAAATAGAGTGTAGTTATTACTCTACCAGTTGATACTT
TTTCTATGTATGAATTTTTTCATTAAAGTATTCTTGGCTCCAGGCTTACC
GTGATCGTGTATATACTGGTCTATCCAAATATCATGGCACCCCAATCGGT
GCTGACAATCCGAGAAGAAGGCAAAAAAGAGCAAGCACAAGCACAAGCAT
ATTGAAGAAGAAAAAGAACAATGTAACAGATAACCCTGCAGGCAATGAAA
GAAAAGCCTCAACTCCACGGTCAAGAATAAAAAGGAGTAATGCGCCCATC
TATAAAGATCCTCTGGCGAGTTCAAAGTTGCAGATGATAAAAACTATCAG
AGCTGATAGAGAAAATAAAAAAGCCGAAGCCGTGAGAAGAGCAAAGTAAG
TTTCATTTCCCTTTTTGCCAGAAATCTGAGTAATATAGTTTCTACTTTCT
CTACATATGGAGCTACAAGAAAAGTAACATGTAAAGAGATTATGTGGTTT
GGCTGCAAATGCACCGTAAAACAGAGAAAATTAAATTTCTACACAGATAG
CAATAAAACCTCTTAGGCTCATCGTTTTTTTGCAATGATAAAGTTTCATT
GATGAGACAAATGAATGATTTTATGTCAAATGATGCTGTTCTGCACAGTA
GATCAAGCAATTTGTCGCCTTAAAATTAAGTTACTGTCCCACCTCTGCCG
TGTGTCTGGTTAATGATATATTGTTTTCTGTAACTACTGTTGTCTATGCC
ACGTTTGGGCCGACCTTTCTGTTTATACAACCTAGGTTTACAAGTAAAGG
GGAGTGGTGTGAAGTGAAACTTGGGTTTGGTTGTCATCAAGCAGCCCTTA
ATTTTCAATCATTTCATCTTCATCCCTATATGATATTTCTTTTGCCTTGC
ACTCAACTTCTTCTGTGAAACAACCTGAAGATTTCAGTTGTAGGAGCAAA
TGATATCGAGTCCCTTCTCTCTTGCCTACATTTTGTTCAAACTTCAAACT
GAACCGTGACGCTTTGTTTTTCTTTTGATTCTTAGATAATAGATTCCAAA
AATCCCCTTAGCCAGGCCTCTATATTTTGGTCTATAGAACCTCAACGTGG
TTGTTATCATGCAGGTTGTTAATTGCTGAAGCAGAGAACGCAGCGAAGGC
CCTTGAATTGGCTGCAAGCAAGAGCCCTCTTGCTCAAGCTTCCCTCATTG
AAACTAGGAAGCTCATAGATGAGGCAATTCAGTCTATTGAATCAATAGAG
GGTAGTTTTGACGAGAATGAGCCAGACAGCCCTTTAAGTCTCAGCGATGT
CGAGGACCTTAAATCTAGAGGATTTGTGACAAAGGATCAGATAGAAGTAA
ATGGAGCCTCACTGTCGAATTTTGATGACATTTCAGACTCTGCTATTGGA
AAGTTCAATCTGCAACAATTACTGAACCACGAGGATGAAAATCTACCTAG
CAGCTCGTACGATGTAGATTTTATGAATGATATGGACTACTTGAAAGGAT
TGCTTGATAATGAAACTGATTTGTCTCAGTTGGAACCACTAAACAAGCCC
TCTAGCTTAACCCATCAATTGGATCTCCTGGCACCCAATGGTACTACCGC
CAAACATGGAAACCCAGTACCAAATGGAGCAAAGTCTGAGTTATTGGAAT
TAAAGAAACCTCCTAAATCAATAAATTCAAGCAAAGAGAAGCCACCTAAA
TCAACAAATACAGTCAAAAAGTGGGTTCGCGGAAAGCTGGTTGAAGTGAC
GGAAGGAGATTAGAGAAAACAACCCTATTTTGAACCAGGCAGGCTAGCTG
GCTTTTGTCTCATTCAGCTTTGGTAAGATTAAGGCATTTGAAGCTATGGT
CTACATGTTATAATCTGCCAACACTCACCACAAACTGATAGCTTAGTTCG
GTGCTGAATAAGTTAGTGTTCTGTAGTTTTGACATTGTTGGCGAAAACGA
CGTGATCTATGTGATGTCGTATATTAGCAGAAAGAGTAATTGTTGGCCAA
AGACTGCTAGTCGTGGTTAAATATGTCCATATTGTTGTCAGTATGCTTGT
ACTAAGATTGTAGCATGGACGACTTGGTTGTTTGGTGTTTGCCATGATGT
GCATTGTGCTGTGTAGCCTTCATCTTCCAAAGCTCCAGGTAGCTGATTAG
TAGAGCAAGGATGATATTAAGATAGAGGTGGTTAGGTGACAGTGAAATCA
TTTAGAATTTCTCTTATTTTATGTAATTTGAACGATTAAGATATGCACCT
TGGGCCTCGCTTTTGTACCATATAAACCTGGTCGGCTAGTTTGGTTACTA
TGTGCTCAGAGGAATAAGACTGGTTAATATTCACAAGA