| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017367931.1, is a part of gene, LOC108199906. |
| The genetic_marker, MK001034 GSSR-035, is located in gene, LOC108199906. |
| 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_017367931.1 | XM_017367931.1 | mRNA | DCARv2_Chr8:20303242..20308511 |
AGAGCGAAGAGGATGTGGATGAAGAGAGAGAGAGAGTGAGAGAGAAGAAA
GGGCGTGGACCATCAGCCATTGGCTCCCCCTCTCCCCTTCTCCTGACGCT
GCGTTTTCGACGCTTCTTTTCAAACCTATACATACACCTATACATACAGC
AGTTGGATCGGCGCGTATGGTAAGTTATAAGATGGAGGATGAGTACATAA
GAAAGCATCACAAGCACCAGGTCAGAGAGAATCAGTGCACATCTTCGCTC
GTTAAACACGTCAAAGCTCCTGTTCATTTGGTCTCTCTCTCTCTCTCTCT
CTCTCCCTCCCTCTCTCCCTCTCTCCCTCTCTCTGCTCTATCTCTCTCTC
TGCAATTTCTTGTGCCTTTTAATTAATTTATCAATTAGTTAATTAGTTGT
GTTGATTAGTCTGGAGAGTCGGTGATTGTGAATTAGAGAAGGAATTAGAT
GTTTTGTTTTAGTCGTGTATGCTGCGGTGCTGAACATTTTAGTGAGCCTG
TTGAGAGAGAACATTTTCACGGACTGAACTGATTGGAATGGAATTGAACG
TTTCGAGTCTTGTGGTGATTAGGTTGTGTTTAAGTTCGCGGTAGTCAAGG
AGTTTTAGGAGAATCCGTGCCTCGGTTTGTAATATACATATTATTGCTAT
GTTTAGAGAGAACGTTTTCAGTTAACTTACCTGATTGGAATGTTACTAGT
GTGGTAACAAAGAGGTTTTGTTTGCGTAACTTTATTATGGCTAGTTACAA
GTAGTTAACAAGTTGATGAAGAGAACAGTTTCAGGTAGTTACCTGATTGG
AATGTTCCTAGTGTAACAGCAGATAGGTTTTTTTGCGCATCTTTAGAAAG
GGTAGTTTATTGGTACATTTTATGTTTTAAAGAATATCTGTTGGATATGA
TTTAGTTAAAATGTTCGGAAATTTGCGGAATAAGTTCTAGGAGAATTTAA
GTTGAGTTGGATATATATCAGCAATTGGAATTAATTGTAATAATTTTTTA
AAGCAAAATCATTTGTGTGATTACTGTTGATATTTGCGTGATTACTGTTG
ATATTTGCGTGATTACTGTTGACATTATAAGTTGGACATGTAAAGGGCAT
TGTTTCCTCTATATAGGTTAAACTTTTAAATCACATTGTATCTAAAGAAG
AATGTTTCTTTGTTTGTGTAACTATAGATTGATATGATCTCAATTCATTA
GTTCCATGTATGTATATCAGTAGAACAAGAAACAACTGAAGTTTAGTTGT
AATTCCTCAATGAGATATTTAATGTTTATGATAGATCGGGTTCTTGCAGG
TTTGGTCTCTGGTGAGAAGTTTTGATCAACCACAGAAGTACAAACCCTTT
GTGAGCGAGTGTGTTGCGCAGGGTAACTTTGAGATTGGGAGTGTTAGGGA
AGTCAATGTAAGATCTGGACTTCCGGCAACTACTAGCACCGAGAGGTTGG
AACTTTTGAATGACGAAGAGCATATCTTTGGCATGAAGATTGTTGGTGGT
GATCACAGGCTCAAGGTGTGATTTTTTACATTCCTCTTTCTATCATCACT
TGTCACGCTAATGACTGCTTTTGCTTCGAGTAATGCTGTTATACTCTTAT
TTTTCGTGATCATGATTTTAAATTAATTTTATGTCCTGCTAACTCCTTTG
TTTTTCACCTACTTTGTATGATATCTCCATATGCATTATCTTTTCATATA
GCTATAGCGTTTGCTCCTGAAATTGGTAGTACCAATAGCGAATTTCACAT
TACTACTGAACATAAAGTATTTCACTTATTAAAGTGCAAATACTTTATTG
AAGAAAGTTACCTATATTCAAAATTATTTTTTTGCTCATTAGTTAATGGT
TTGAGGACAAATCTCGGCATGTACGCTAGCTTATGGTTCGAGGACAAATG
GTCCTAGTCAGTTACAAAGGTCAGCATTTCGAGGTTGAATGACATTGCAC
AGTTTCTCTAACCAAAGCAAATCTATGACTGTCCCTATAGTGAGTACAAC
ACATGTTCTCATATTTTCCTTATCCTTCCTTGCACTTTTGACCTCACCGA
CCTCTAGCCCGACTTGTAAAAAGTTAAGAAGATAATGGCAAGCGTGAACA
ATTAAAATGCTAGTCAAGAATGATATCTTGCCATGATAAACTAACTTACA
TGGAAGTAAAATTTTAATGGGGTTCAAGCCTAAAGATTCGTATCAGACTT
TATAGACACGACAGTTTCCAAATTAAATGGAGTTCCTGAGGAACAAATAC
ATGTTTTTTCAAGATCTGGTATTTTTTATTACCATGTAATGTCTCTTTAA
CAATATCATCTTTTCGATCAAGTGATCCAAAAATCAAAATCATAATCTTA
AATTAATGGACTACAGGTACATTTTAGTAATAAGAAGTGATACCCTGTCA
TGCATTTCAACCGTCCTCCTACCGAAAGATTGCTCTTCCCTGACCTATAA
TAGCCATCAAAGCCAATAATATAGATATCAAGTTTATCTCAAATTTTAGA
TATTATTATTTTAAGGGTTATATAGTTGCAATAGTACTATTACTAACAAT
ATCAGTTGTCACGACTTTTTGGCCTACAAATCGTGTCTTTTTAGAGGATA
ATGCAGTAGTTGCAATTACAAGCTCAATTAACCTTAACCACCAGAGATTT
TACAATGTAATCAACTGGACAAACACACACACACACACAACAGTCTTTTA
CAGTAAGTCGTAATCAAATATGAGGTAATGCAAAGCCTCCCATGGGTAAA
GGTAATGCCACTGACTGATGGTGGAAGAGGTAAATTAACTGATTTTGATT
TCTTCAAATTCTCAGCCTCTAGATTAAGCTCATAATTCTCAAACTTATGT
TGAGGAGTCACAATATTGCAAGCAGCCACTCCTTGTTCTTTAATCTTGAC
TAAATGAGCAAGAACACAAGAGTAGGATGCAACCTACATCTTACTACAAT
AGTAGCATTATCACACTTCTCCCCCCTCTATCCTTAACGGTTGGCCGTAT
GAGTGTTAATAGGTCACGTGGCGGGTCGGACACATACTCAGCTGAGTCGC
TGATCGGAAACACATACGGAACCCATTTTGAAGAGTTTGTGCTCCCTTGC
TGATAAGCCAACATCTATGGCTGAGGGTAATAATGACTGCTATTGATATC
TAGTAAACTAGAACAATGTTGAAATTATGAGCTGTTGATGCATTAGATTG
GGATTTGGAGATAAATGTACCTATTACAACATAGGTTCTAGAGCATCCAA
ATTAATCATCACCTTGAAGTTTTTAAATTATTTTAATATTTTTATATAAT
TATTGTAATAAATTTAAATCAATTTGATGGGTTGTTCATTTGGATTATGA
TATACTCCCTTTGTTCCACTTATTTCATTACAGTTTTTTTAAATTGCTTG
GCACTCATTTTAAGGTGCATATAATATATAGTTTCATGACTTATTTTTGA
AATTTCTTTATTGTATCAATATTTAAACTTTAAATTTTTATTCAGAAGAA
AAAAGGTTTAAAATAATTTGTGAAACTACATTTCAAAGGAGGCTTAAAAT
GCGTGCCAAGCTCCCGTCCCCCAAAGTAAACTACCTGGAGGGACAGAGGG
AGTAAACTTTTATTATTCAAAACCAAAAAAATAAAATAAGTTGTTAAAAA
TAGTTGCTTCTACTAATTTCCGGCTTTAAGCTTCTTTTTATTTTATTTTT
ACTTTTAGTCACTTTCTGATAATCCAGAGACATATCTCAACTTAAAGTCT
GAAATCACTTTAAGCCTCTAACGTAAATCCATCCCAAACAGGCTCTAGGT
CAAATAGGCGGACGTCTTGGGTCTCGAAATATGTAAGGTCTTTAAAGTAC
CATGTCTTTCTACATTCTCTATAATAAAATACTTAACTTTATTAATGTCA
TGCTGAAGAGCACATTAATGATAACCTAGTTTTTGGTGGACAAATATTAA
TGGGGTGCAATGGTGCCTGCTGTGTCATATATACAAATATTAATGGGGTG
CAATGGTGCCTGCTGTGTCATATATATTTTTGTTTAGGTTACGTTCACTG
TGTTGTAATGTTTGCAGAGAATAATAAAGCTTGTAGAGTACAATATACAT
TAGTCAGGTTATAGTTGAGCAGGATAGGCTAGAGGACTGGTTACTAAGAT
GAGCTGTATATGCAAGGGCATTTGAATCATACCACATTGTGATATATGAC
ATTTCAGACGTTAAGCAACCTAGAGATTTGTGATAATTATATTGCTTTGT
CTTCTTCAAAAAACCCTATGTTTAGAGATTTATTAATATCCTGCGCTCCA
ATCTCTAACTTATTGATTTGTTATGCAAGTGCACAAGCATATTCGCTCGT
AGGTCCTTCTAATCTTATTGCTTACAGGTCCTTCTAGTCTTATTGCTTAC
GTATATTACACACATGTTTTATGTGAAGCTGTAATGTGCTAGCTGGTTAA
ATGCAGCTGCTTGCAGACGCATTTATAGACTTATCTTCTGACCTAGGCCC
CTGGATCTGAAAGTAAAAGTATTATTATCAGGATGAAATAAAAATATGCT
TTTAAGTTGAGTAGGATCATGATAGGACTACCAGATTTATATAATAAATA
TGATATGCTATATTCTATTTGTAGTTTTGGATATCTCTGTTTTTATTAGC
TTTTATTACTTTAGTTATCACAACTGTGTGCATCCTTTTTTTTTTTTTTT
TTTTGCAGAATTACTCTTCAGTAATTACTGTTCATCCTGAGATCGTAGAT
GGTAGACCAGGCACAGTTGTGATTGAATCATTTGTGGTGGATGTACCTGA
TGGAAACACGAAAGATGAAACATGCTACTTTGTTGAGGCCTTGATAAAGT
GCAATTTAAAATCGCTGGCTGATGTCTCTGAGCGTTTGGCTGTGCAAGAC
CGAACTGAGCCCATTGACAGAATTTGAGAAACTTGTTTGAGGTTCTGATT
AGAAGTTCCAGTCGTTTTGGGTAAATGATGTTCTGTCTGAACTATGTAAG
GAAGCTCTCTTTGATATTTGGAAGTACAAATGTGGTTCAATGCTTCAATT
ATCTGGAGATGGTATTAAATTGTTGCGTCAGCAAACTGTTTACTGGCTCA
TTATTAGGTGTCATTCTGCTTCCACTTTGTAAACAAATCTCTATGTTTGT
TTTATTCACTAGACACTGGACCGGACTTGTGTTGTAAATATCTATGCTTG
AGAAAATTTGACGATTATGTGTTCGATTTTGTTGTTAACACGTGTTGTAT
AAAACCTTTTTTTAAATCA