| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017377540.1, is a part of gene, LOC108207075. |
| The genetic_marker, MK016958 2_1719224, is located in gene, LOC108207075. |
| The genetic_marker, MK009430 2_1719242, is located in gene, LOC108207075. |
| The genetic_marker, MK009431 2_1719263, is located in gene, LOC108207075. |
| The genetic_marker, MK016959 2_1719272, is located in gene, LOC108207075. |
| The genetic_marker, MK009429 2_1719278, is located in gene, LOC108207075. |
| 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_017377540.1 | XM_017377540.1 | mRNA | DCARv2_Chr2:1715405..1720712 |
ATGCAAGTATGTGTATAATTCACATTTATTGAAATATTTTGTAATACTCC
CTCCATCCCAAATTAGATGGCCCCGTTGACTTTGGGCACACAATTTAAGG
TTCATTGACCGCATAGATACGTGATTTATTTTTAAAATTTTATTTTTTCA
AATAAAAATTAAAATATGAAATTTTCATTTATAAAAGAAAAAATAAAAAA
ATAAATTTCGGAAGTAGACGGTCAATACACCTAACGTTACGTGCCCAAAG
TCAACGGGGACATATAATTTGGGATGGAGGTAGTATTATATAAATTTAAA
CTGAAATTTTAAAAATTCATTATACCTAGGCGACTTATATATCTGTATCT
TGGCTTATATTTAACTGAAAAATATGTCACATCTTATAAACGATCTAAAT
ATGATGAAAAGACAAAACTCACCGCATTAATACGATCTTGAATATAATTA
CTCATATACCCATACAAATTATGCTCCATATTATTTTTTAACAAAATAAT
TCTAATAATATATGTGAACATGATTATGATTCATGATCCATATTCGACTA
AAATCATATATTTTAATACATTTACAAGTAATTGTCATTTTAAACACAAT
TTACAAGTAATTTTGACCGAGTTGAGAGATGGAATAAGAAGGGAGATCGC
ATCTGTTTCAAATATAAGTTGTTTGATTTTTGAAATATACTTTTAATTAT
ATTTACCGTATCAAAATGTTTTTTTAATAAAAATATATGATCAATATTTT
AATTTAGAACATAAATATATTAAAAAAATAATAATTTTAAAAATGTCAAA
CCATCATCCATACTAATTTTTAAAAAAACGGGTGTATAAGGTGACAGAAC
AAGAGGGGGCGCGTGTGCTGATTCTGACCAGTCATCCACCATCTCTCAGA
ATCTTCACTCTTTTATCCATTTCAGATATACTCAACAAAATCCAACAGAC
CCTTTAAAAATGGCACTCACTTCAATCTCTCTTCTTCCGATAAAGNTCCG
ATCAAGCCCATAAACAACAACCCTACGTGCTGTTATTCTTGTTGCTCTAA
TAATACTAGGTCTAGCACTATACTTTCCAAGTCCACTGCTGCACTTTCCA
AATTGCAACCTCAAAAACATGCAACAGGTAAATCATATTACTATGTTGCA
GCATCATTTTTTTTATTTTACTTGTTTATTTTCGGCGGACTTTCATGTGA
CATCTTAAAATTTTAGACTAGATGGTTACTTGACATGGTATCAGAGCGTT
ATCTATGTTGGTTATCTATGTTGAAGAGTATAAGATTCTATTAGGGTCTT
TACGGGTATTTATCAGCTTTTTCAAATTATACTAAAGCTTTGACAAGTTG
TGTTTGTGTGTGTGCAGAACCAAAGAAATGGAGAGGTCTGGTTTCGACTG
CATTGGCGGCTGCTGTGATTGCATTTAGCTCTGATTTTTCGGCTTTGGCA
GATCTTAATAAGTTTGAAGCTGATATACGAGGGGAATTCGGGATAGGGTC
TGCTGCACAATATGGTTCTGCTGATCTCAGGTAAATAGTGTCTTCAAGTC
TGCTGTTGTATGGTTTCTATAGTTTTGTGATTCCGAAATAATTTCTGGTG
ACCATTCGTAATTTTTTAATGCAGGAAGGCTGTGCACACAAATGAAAATT
TCAGGTGAACAAATGCAAATTGAAGTAGAAATGTAAAAGGATTGTATTTT
GGATGTTTCCTTAAGAAAACACGATTTCTTCAACAAATTATCAGTACTCT
GTGAATTTATCGATGAATTTTCCCTGAATATGAAATTCAGGAGTAGATAT
ATGGTAGCATACTTTTAATTTTAGTGTGAATTGTTGAGGATAGTGGCTTC
GGAGGATTTAATTTGAATTTGTGTCCTCAACCTTTTGATATTATGAGTTT
GTAACTTAACACGATCATGCATCAGTCATATAAGAGTTGAAGTTATTTTC
TGCAGTCATCATAATTCTTCCGCCATTTAGGTGCTTTCCAAGGACGACAA
GAGATATGGGTAGCATTACACTTGTCCAATGGAAGTTCTAAAAATCCGAT
GTCTTTCTGCAATTCCGTGTTTGAAAATCTAGTTCTTACTGGATTAGTGT
TTAAATAGAAGTTCACAATCAAATTTTAATGTGTTGAATTTTTGTAGGCA
ACTTATATATTTATTGTTCTGCCTATCTGTACTTCTGTGTTGCAGCTTCA
CTGTAATACCTAAGACATGTTTCAGGAAGCTTAAGACGAAAACATAATGA
TTATGATGGTGTTTTAGATATGAAATTTCATCAAGGGTAAAGGCATAGTA
AACCAAACTGATTGTCATGATCTCACCATTACAAACTCTGATAACATGGG
CACTGACATATGAAAAGCACGTGTTTTCTTAGACTTGCTTTGTCATAATA
CTAAATTTAAATTGCTGAAACAGGAGAGCAAATTTTACATCTGCTGATAT
GAGGGAATCAGATTTCAGTGGATCAACATTCAATGGTGCATATATGGAAA
AGGCTGTTGCATATAAAGCAAATTTCAGCGGTAAAGATTCAATTCAGTAT
TGTATAAATTTAAAAATGCGAAGTCTTGAACTGAGGGAGTAAACATTATC
CAAAAACAAATAATATATACATTATGTCGACATAGGTGGAGGCAGCGACC
CTGCACATACATGTCTCCAGAAAGAATTGCTTTAGTTTTAGTATTCGTGT
AGTGAAGATGCCTCATTTCCCCTTCTTAATTGGAACATCAGCAGATACAC
CTAGAATAACTATCTTGATATATTGACCGGCAATAATCTATTTTTACATC
GGTTAGATTACCTATACCAGATTATGAATTGTAGTGTTCTCCTTACTGCT
TTAATTTGTGTGCAGAGCATCAAACTTTTTTTACCTCCTCTCATTCAAAA
TTCGAATTTTCTTTCAGACCTTGACCGCTTACTGTTTTATGTCATTCTTG
ACTACCCCCCTCGAAATCTATCATCTTTTCTAGTGGACACTTATTCTTTG
AGGACTTGGACTTTGATGCCCGTTCCCTTACTGAACATTATTTCATTGCT
TAGATGACCTGAAGGGTTTTATGCAATAACTGACATCAGTATATTTTCGG
TGAATGGATTTCAGGTATCAGAACCCTCTGTAAGACTAATTAGCATTTCT
ACCTGTATTGGTTGGGCTTCAATTTCTGGAACAGAGAATGCGTGCATTTC
TTTAAACAGTTCTGCTTCTTTTGCCATAAACTTTGAATATATCACTTGAA
TTCTTTTTCATTAAAAAAAAAGAAGCTGAGAATTTTTCATCATGAGAGGA
ATATCTGTTTCAAGCCGCAGGAATTTGAGTCAGAATTTCCCACAAAGGTG
TTCTAATCAACAGAGCAATTCCTCATCTTTATAATACTCTATTCTGTAGT
GACAGAGCAATTTCTCATCTTTGTTCCTCAGTAGTAAAGATATGTACTCT
AAGTCTCTAATATTCTGACATCAGTTAGAAATTTTCTCATAAGTCATGGA
CAACTTACTTGCATAAATCCTTTTCCCAGAAGACAGAATAAAACATTTTA
TTGAAAATAACTAAACTTATGTATTAAACTCTCTAGATGACTTGAGCACT
CCATTGAGCAATTACATCTGCCTCATTCAGACTGTCAAGCCGTTTTCTGT
TCATCCGAAAAACTCCCTGCTAAATAAAAGCATAATTTTGCTATTGATTT
CGCATTTTAGATACTAGGTGAGACTTGCTTCTTGACAACTTTACAGGTTA
GATATGACCAAAATTTCCATCAATTCTGGCATGACATCATGAGAATTGAT
TAATTGAACACCACATTTTGTTTACCATATGCTGCTTAAACACATAGGTC
ATAACTCCTACAGTTCCGTATCACGCTCTCTATCATGAGCGGTTACACAA
CACACTTTCTAAGTTCTATCTTCTAATAGCTTCGGCTTCCCTTTCAGTTT
CACACCATCATAAGCATTGTAACCATAACGAATAGGAAAACGTGCATATA
TACCATTTGGGTTGAAGTCACATATTTCATGGGAGATGGTCCCTGACAAG
TGACAAGTGATTGTTGGCAACAATCTTTTCACGTTTATTTTATAGCTAAA
AGAAACTCTAGAACGGGTGTCTAAAGCACAAATAAGCCACGTGGCCCCCT
ACATTCACATAAAAAAATAGGTATTATGTCTTTCAGCTATAAAAAAAATA
GCCGCTAGATTGCTGCAACAACCGATTGTCAGGGACCCAGACCCATATTT
TATTTGGTTATAAAATAATATACAGACTAAATTTGTGCATGTTGTCGCTG
TACAGGTGCAGATTTGAGTGATACATTGATGGATCGCATGGTAAGACTAC
ACCTGATCCGTAGACACACGATCATTTCAATTGCAGCAAATTCTAGCATA
TGTTTTATGTACATGACAGAGTACTTGTGTTACTTTCTAAGAGCAGTGTT
TGATCTTAATTCTTAAACGATGCTGTCAGAAGACTACTTTCTCTGTGAAT
AGAGGGGGTTGTACCCATATCACGAATCTGCGTTGTAGTGTTGTACTGCT
ATTTACCATTAATTTGATATATTTCTGTTCATGCATATAAATACTATTTA
TACTTCTATAAAACTTCTTGTTCATGTACACATTTACAGGTTCTTAATGA
AGCTAATCTAAAAGATGCGGTACTTGTTAGATCTGTTCTCACTCGTAGTG
ACCTCGGAGGTGCTCTTATTGAAGGTGCAGACTTTAGTGACGCTGTTTTG
GACCTGCTTCAGAAACAGGTATGCAGAGTCACATATTTCAGTAGCATAGA
TTTTACGAAGATTAAGAGTAAAACTGAGAGCATTGCAACTCAATATGACA
ATATCTACCTTAACGAAAGAAGATAGAACAATATTTATTTTGAAGAATAT
TTTTAAAAATTGCACTCTCGTTTGGTAAGTGGAGCGGTTCATATTGTGCA
GGCACTCTGCAAGTACGCGAGTGGGACAAATCCAACAACAGGAGTTAGCA
CCAGAACAAGTTTAGGGTGTGGAAACAGTCGACGTAATGCTTATGGAACC
CCATCTTCTCCTCTGCTAAGTGCTCCAGCTCCTAAGCTGCTTGACCGAGA
TGGATTCTGCGATCCTGCTAGTGGTCTTTGTGATGCGAAATGAGTGGCTT
GCAGAAGATAAACATGACATACATCTTTAAGCTCTAGTTATAAATATTAT
GCTTGTAAAGACTGGACTTATGTAACATGAAATGTAATGTTGCGGAATGA
GGAATGGATACAAAGAGTTTGATACATGAAAACAGTCGGAATGGGGTCAT
ACGAGCA