| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017380420.1, is a part of gene, LOC108209490. |
| The genetic_marker, MK009441 2_2488017, is located in gene, LOC108209490. |
| The mRNA, XM_017380419.1, is a part of gene, LOC108209490. |
| The mRNA, XM_017380421.1, is a part of gene, LOC108209490. |
| 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_017380421.1 | XM_017380421.1 | mRNA | DCARv2_Chr2:2484029..2488888 |
| XM_017380419.1 | XM_017380419.1 | mRNA | DCARv2_Chr2:2484029..2488888 |
| XM_017380420.1 | XM_017380420.1 | mRNA | DCARv2_Chr2:2484029..2488888 |
ATCCAGACACAAAATCCTAATCTTAAACTTCATTAGCTCTTGTCTGACCC
CTCTTTCCAAAACCCTAAATCTCATTTCTCATGGACTCCACTGAAACCCT
AATTCCTCCCCCAATTCCCACCTCACCAGACACCAACCCCAACACCACTC
TTGCAGAACACGAAAACACGACACGAACACGACGAAAGAGCCGATGGGAC
CCAGTAACAGAACCCAACAACCCAGAGAAGAAGAAAAAGTCAAGGTGGTC
AGAGGAGGAGCCAAAGCAAGCATTCCAGCTGCCTGACTTCATGAAGGACT
TCACTCAAGGTATGGACACTGACCCTGCTGTGCAAGCTCTCAATTCTCGA
TTACTCGAAATTAGTCAGATTTTACAAGCTAATGTTCAGTTAGATGATAG
GCCTGATAATGCTAGATCACCTTCACCTGAGCCATTGTATGATAATATGG
GAATTAGGATTAATACGCGAGAGTTTCGTGCTAGGGAGAGGCTTAATAGG
GAGAGACAGGAGATAATTGCGTTGATTATTAAGAGGAATCCTGCTTTTAA
GCCGCCTGCGGATTATAGGCCACCTAAGTTGTATAAGAAGTTGGGGATCC
CGATGAGGGAGTTTCCGGGGTATAATTTTATAGGGTTGATAATTGGGCCG
AGAGGGAATACGCAGAAGAGGATGGAGAAGGAGACTGGGGCGAAGATTGT
GATTAGGGGGAAGGGGAGTGTGAAGGAAGGTAGGTTTGGGCAGAAGAGGG
ATTTGAAGTTTGATTCGTCGGATAATGAGGATTTGCATGTTTTGGTTGAG
GCGGATAATCAGGAGTCGCTGGATGCGGCAGCGGGGATGGTGGAGAAGTT
GTTGAGGCCGGTTGATGAAGGGTTGAATGAGCATAAGAGGCAGCAGTTGA
AGGAGCTGGCGGCATTGAATGGGACGATTAGGGATGATGAGTTTTGTAGG
TTGTGTGGTGAGGCGGGGCATAGGCAGTATGCGTGTCCGTCGAGGTTGTC
GACTTTTAAGAGTGAGGTGTTGTGTAAGAATTGTGGCGATGGGGGGCATC
CGACTATTGATTGTCCTCTGAAAGGGACGGCGGGGAAGAAGATGGATGAT
GAGTATCAGAACTTTCTGGCAGAATTAGGTGGGAGTGTTCCGGAATCTAA
TACTAAGCATAGCACGCCGTTAGCTATTATGGGGTCTGAGAATTCTGGAA
GTAATCCTTCTCCTTGGGCAAATAATAGTACTGCTGGAAGTAATGGTAGC
AGTTTACATCCAGGTCTTGGAAGTATTGTACCCAAGATTGGAAAAGAAAT
TGATCATACAAATTTGTATATTGGTTACTTGCCTCCTACTATGGAAGATG
ATGAACTAATAAGATTGTTTCAGCCTTTTGGAGATATCGTAATGGCCAAG
GTTATCAAAGATAGAATGACTGGACAGACTAAAGGTTATGGTTTCGTTAA
GTTTTCGGATGTTGAGCAAGCCAATCAGGCAACTGCTAGCATGAATGGTC
ATCGACTGAATGGAAGAGCAATTGCAGTACGAGTTGCAGGGATACAACCC
CAGCCTGTTGTCCCCCCTGGACCTCCTGCTCCACCTGCGCCTATGTACCC
TGGTCCCAACCACGGGTATGGTGGATACCCATCTCAACAGATGCAGTCAG
GTGGTTCTCTTGGGATTGCACCACCAGGTAGCTACATGGGTCCTCCTCCT
CCTTGGAGGCCTCCACCACCTCCTTATGGAGGTTACCCTCCTCCCCCTCC
TCCGGGGTCAAACATGTATGGCCCTTACCAGGGTCAATCCATGCCCCCTT
ATGCCATGCAATATCCCCCACCGGGACAAACAGCCACACCGGATCAGAAC
TTGGCAAATGCTGAACCACAGCAAATTTATTCTGCTGGAATGCAATCTCA
AAGTAACACATCTGCATCTAACAATATATATGGCAACTCGGCAGCAGGAA
TGGCCCCAAACTCGCAACCAACTTATCCTCCATCTTCAGGGGGTTATGCT
TCTTATTATGGAGTAAATCCCCCACCTCCGGCTGTACCGCAATCTTCAGC
TGAACAACAGAGTTTTGCAAGTGCTCCATGGGCTGTGAATCCGCCATTGC
CTCCATCAGTCCCATCTGCAGATCAAAATCAGCAGACTACATATGGAGCG
GACCCGGAGTACGAGAAGTTCATGGCTGAGATGAAATGAAACAGTATGTT
GGCAAGGATCAATGGATCATAACTCAAATGTAAGTATGCACATTATTTTT
GTAAATATTATGGAGTCTCTGAAGCTGGGATCTTCTTGAGGACCATATTT
TACACAAATTTTTTATCGGCATCTGTATTCTTGTAAAATTTTTGGTGTAC
CCAGCTCAATTGATCTGTTACGAAACAATATTCGCTTGTTATTACTTTCA
GCTTCTGGTTTTTGTTCAAATAAAGAAAATAGATTATTGAAGATGCAAAT
TGTCTGAAAAGTGAATATGTAACTAATACATGTTAACATTTTTATGGAAT
GTTTTGTGCAATTATATTTTAATTTAATTCTTCAGTAATAGTTGGTCAGT
GCTGTTCAACAAATGAGTGCTCAAAAGTTAATAATATATTTACTTTTTTC
TTGTACAAGAAATAGTGATTGAAGTATTACAAATAACTTCATTTTATATG
TTTAAAGAGTTAACAGGAATTTGGGTGGTAAGATATGTGATTGTATGTGC
TAATAAATACCCTATCAATTTTCAGTATGAGCTACTAGCGCGTTTGGTAT
ATAAAACAGGTCTGAGTTTTGAGCTTTATATATCCATGATTTCCACCTCT
TGTACTGTGATTCTGGAGTTCTCTTGCTTTATCTAAGTTATTTGTCTTGT
TCATGGTCGTAATCTTTGGCAGGGTGTGGTTTCTTGGAGCTCTTGTCAGC
CTTATTACTTTCGTGTTGCATTTCACTTCAACTTGTTGGAAGTTTCAGAC
TCACATCTTTACTCTTGCTGTGCTATTGTTACTATTGCAGAAATCTTTAA
GTCAATCCGGTTGATTTCTTGCTCCAGCTGGAAGTCTTTTGAGGGCTTTT
CAAGTCTGAATGGTGCTAAATGCTAATATTTCTCATTGACAGTTGCCTCC
ATTGAATTATTTTGAGACTTATATTTCAATTTCAGGGAACAGATGCTAAC
ATTTCTGTCTGTTTTATTTTGATATAACCGTTGATTACTGCTTTTAAATG
TTTTGTTCAATTCATAATAATCTTGGTTTGTAAACTTTTATTTGTTTCTT
TTAACGCAAGACATAAATTGGTTCTTCTCTGTGTTTCTTTTTTTGTACTG
CTATACTTGGCAAGGATTCAGTGTGAACCTCACTTTGGGGTGGATGTACA
TTCAAGGTAGTACAGTTATTGATCATTTTGTTGCATCTCATCTGCCTTGT
GAGGGTGTTGAATCTCATCTGCCTCCCAAGGGTGTTGAGATCCCAAATAC
TATTTCGCAGCTGGTAACTCTGGTAAGTAGAAGACTTCTTTTTATTTTGA
CAACTAAAAAGAACTTACCGTTCTTTTAGTAGGAATCAATCTCTATCTCC
TTGATGAAATAGTAGAGTTTGAAGCTACAAAAATTAGGTTTGTGAATTAA
GTTTGTACTTCCATTTGTCAAATATCTGAACATGGAACTGCAGGGTTGTC
CTAAGTCTAACTAAGCTAAATCTGATAGTTGACAAGTAGAGCATAACGTG
TTATACCAATTTTATGGCATATTGTACCCGTCAAATTATTACTTTAATAG
ATTATAATTTGACTTGAAATTATCCAGCAAGTCACCAGTTATGGTAATGC
CACTGACAACCTGTAGAAGATCTACATTATGATTGAATAATCATTTGTAA
GAAGGTAGACACGTAATAAATAAATTGCTTGATTAATATTATATATAATA
ACGGGCTAGCTTATTAGCTCAAGACACTTAAACAGATTTAGTTCGGGTGG
CATTTTTGTCTTTTTGTGCTGTAATTTCTTCTTCCCTCTTCTCTCTTCAC
ATGTATTGAATTTTAAAACAGTCATTTTGATTATTTTAGATCAAATTAAT
CTGAGTTGGTTTATAGACATATGCTGCTAGTTGCCAAATGCTTGACTAAT
TGCTAAAGGAGACAACAAAAGTATCTTCATCTACTAAATCTATAGGAAGG
ATATTCCTTTTATCTGCCTAGATGATTTTTACAAGATTTGGAAACTTAAA
AATTTTAATCCATCCCACTAGAGCTGTCCATGAAGCTTCTTTTGTCCCAT
GGCATAGATGCAGGTTGGTGTTAGGAATCTGTTTCAGAAGTTATTGCAGA
GGATTTGGATTTATTGATATGCTTAGACGGCTTGACCTGTCCGAAAAATA
GTTCACCCACTTGAGAAGTGAAAACATGCCTTCACATTAGTCTTTTAATT
ATTGCCAGTTACAGCCTGAAAAGTAATGAAGCGTTTTCACTACTGACATG
CTGTATTTTGTGGTAGGTAACCGATTTTTTTGGCCAAAAACATATGACCT
GTATTTTCCTGCAGTTTAAGGTTACATTGTGGTCATTTCAGTTAGTTTGA
ACTTTAGATGGCATCAGATCGGTAAGTGATACAATCTTTAGCAGTCATTA
AAGGACTGTGCAACCCATTTTTGGAAGTAAAGCTAGCAGTCAAGGTCCTC
AAGGATGAGTTCAAGCCAGATTGGTCGTATACCTCCCACTTGCTGTTTGG
AAGTAGGAAGGAAATTAGGAGGCAGCTTTGCTCTTCATTGTGGTAGCTAA
ATAGTAGCAGCACTTGTATCTTATTTGTGAATGTTCCCATATCCTATCTG
GTGTATATACTTTTTAAATATATTGGACTCTTCTCCTCTTGAAGGATAAG
CTCTCGTCA