| NCBI Gene |  |
|---|
| Relationships |
|---|
| The mRNA, XM_017401870.1, is a part of gene, LOC108226844. |
| The genetic_marker, MK010763 1_43545468, is located in gene, LOC108226844. |
| The genetic_marker, MK016860 1_43545508, is located in gene, LOC108226844. |
| The genetic_marker, MK010760 1_43545519, is located in gene, LOC108226844. |
| The genetic_marker, MK010767 1_43545533, is located in gene, LOC108226844. |
| The genetic_marker, MK016854 1_43545762, is located in gene, LOC108226844. |
| The genetic_marker, MK010762 1_43545837, is located in gene, LOC108226844. |
| The genetic_marker, MK010761 1_43546761, is located in gene, LOC108226844. |
| The genetic_marker, MK016858 1_43546812, is located in gene, LOC108226844. |
| The genetic_marker, MK016864 1_43546863, is located in gene, LOC108226844. |
| 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_017401870.1 | XM_017401870.1 | mRNA | DCARv2_Chr1:43544858..43549360 |
GTACACTTCGACTATAAAACTGCAGAGAAATAACCTAAATTTTCATGTTT
AATTCTTTAGTCTTTAATATGAAGCAAGTTTTGTTTGTGCCATTATTACT
ATTACTTCCTCTCTTAGCTTTCTCTGCTGACACAAAGGTATTATTACATA
TGTTGTGAGTTAATGAAGTGTGTGTTTTTGTGACATGGTGTAATAATTGA
TGGGCTTGTACATGATGTTATGATTCAGGTGTACATAGTTTATTTTGGTG
AGCATAGTGGAGAGAAAGCTCTGCATGAGATTGAGGAAGACCATCACTCA
TACTTGTTTTCTGTGAAGAAAACTGAGGAAGAAGCCAGAGCTTCTCTTCT
CTATAGCTACAAGAACATCTTCAATGGTTTCGCGGCTTCGCTTACTCCTG
AAGAAGCCGCCAAGTTATCCGGTATATATGCATTGCACATAAGGCATTCT
TTTTAGTCCCTGCTGTTTCGAGATCCTGGTTCTGTCATGGACTCATGGGG
GTAACTGTGATATATGTTTGTTGTTGAACAGAAAAAGAAGAAGTGGTATT
GGTGATTGAGAGCCAGCCAGACAAGTACTCACTGCAGACTACAAGGTCAT
GGGAGTTTTCAGGGGTAGAAGAAACAAAAGCATGGAGCTTTGTGAAGAAC
AAGGGAGACAACTTGCTATTAAAATCCAAATATGGGAAAGATGTTATTAT
TGGGATTTTGGATTCTGGTATATATTTTATCTGTTATTCTGATAATATTA
TAAATTCCCAATCATTGAGTTTAGTATTATGACACTATAGTTCATTATAT
ATGAGCTGCATGTTGTGATAATTTGCTGGTTGAAACTTTTTGTGTGTGTT
TGTGTGTGGTGAGCAATGAATTGACATTGAGGAACTATAACTATGGGAGA
TGATGAGTGTGTTATTAATCATTATCAGGTGTGTGGCCTGAGTCAAAGAG
CTTTAGTGATGAAGCAATGGGACCTATTCCAGAGTCTTGGAAAGGAATCT
GCCAAACTGGTGATAATTTTACCACCAAACATTGTAATAGGTGACTCTCT
TGCTCTCTTAATCCTCATTATTGGTTATTAATAATTTGCATGTTGAATAT
AGATAATGTTTTAGGGGTCCGGGTCCTTGACGTGTGTATGTTAATAGCAT
ACATTCAGTAATCAGGGTAAAATTGTCTCATGTTTAACGTTTAATGCTCT
TTTTCCCATTGAACGTATGCTACTATCATTCGTATGTTCTGGACCAGCTA
CAATATTTTAGTAGCGCAAGTTACAACAACCTCTATTATTCTACCATTGT
TCATGAATTTAGGATTAGTAATGTATTCTCTAGAAACCTCGTTTGTTCTT
ACCTTGGACTTAGAAAAATGTCGGGATTGAAATTATCAAAGGAAACAATT
TTCATTTGATCAATTAGTCAGTCAGGGTGTCCTACATAGGCAGCTCCTAG
TTGGGTGATGAGTTTGTCTATTTCATCAAAAACAAAGATATGAGCTGACC
CATTGTGTTATTGATTTTGGCCTTTTATCATCTTGTGACCTTTATTTATT
ATCTCTTCCAAGTTTCCAACTTTGTTTACACTCTGTACCCTGCTGTGTGA
TTACTGTTCACTCTCTGCACTATATCCTTGCATCCTTTTCAAGGTTTTGG
AAATGATAACTATTATATTTTATTTTATTTTTTTAAATCTAGGGTATATT
GTGTTGATTTACAGATAGTGTGCCTGATAAAGATGATTCACTTTTATATG
TATGCAATTCTGTCAGTAACACTTTCTTTTTTGATGGTTGGTTCTTGGTT
GGTCCTCAAGGTTTACATCAAGCCTGTCAGTCAAAGTTTACAATTATCAC
CTAGCAAGGTGCTTCTCCAATGCCCATATGATGGTGGGGTATTTGTAAAT
TGAAAAAAAACACACTGTATTCTGAGGAAACAAATTGCAGAGCACTGTAA
AACTGTTTACATCTTCTTGACAGCTTTGAATTGTGTCCTTGATTGTTTCA
CAATTAGAAAATATAAATCAGATTAATACATGTGAATAAACCTTAGCAAT
TAGGACTACCTAATTGTTTTAAATTGAGTTGTTAATCTTGTTTGTTTTTT
TTTTTTGCAGGAAAATAATTGGAGCTAGGTACTACCTGAAAGGCTATCAG
AAGTTCTATGGCACTCTGAACAGGACCCTGGATTATCAATCACCGCGTGA
CAAGGATGGCCATGGAAGTCATACAGCATCGACTGCAGCAGGGCGGGTTG
TCCCTAAAGTCTCTGCGCTTGGTGGCTTTGCCTATGGCACAGCCTCAGGA
GGTGCACCACTTGCCCGTTTAGCAATCTACAAAGTTTGCTGGCCAATACC
TAAGAAGGGAAAAGAAGAAGGAAACACATGCACGGAGATAGACATGCTAG
CAGCCATGGATGATGCAGTGGCTGATGGCGTTCATGTTATAAGTCTTTCC
ATTGGTACACAAAAACCTGTGGCATATGATCAAGATGCTCTAGCCATCGG
AGCGCTTCATGCTGCTAAAAAGAACATTGTGGTGTCCTGCAGTGCTGGCA
ATTCTGGTCCTTCCCCAGCAACATTGTCTAATCCAGCTCCTTGGGTTATT
ACAGTTGGTGCAAGCAGCTTGGATCGCTCTTTCATTGCCCCGGTTATACT
TGGAAATGGCATGAAAGTTGAGGTAAATTTGTAAAACAAGATATAGCTAA
CAGTTTAATAATTGCTGTATTGAGAGAGTCTTGTCCAGGATGTGGATATT
TAAAACCTAATTCTCTGTACCAAAATAACCAGGGACAAACAGTGACTCCA
TACAAGCTGAAAAGAAAGATGTACCCACTAGTTCATGCAGCACAAGTACT
TGATCATAGCTTTGACCCGAAAAATTCTACAGCAATGTAATTCTCAGTAT
TTACTTCCTACAATTCATACTAGAACATACATATCTTAAGAGATGAATTG
ATCATACATAGATTAAATCTTGCAGGCAATGCTTACCAGGATCTCTATCA
CCTCAGAAGGCCAGAGGGAAAATTGTCTTTTGCTTGAGAGGAAATGGAAC
AAGAATTGGAAAAGGCCTGGAGGTGAAAAGGGTTGGTGCTGCTGGTTATA
TCTTGGGGAACAGCCCTGCAAACGGAGCAGAGTTGGCTGTTGATTGTCAT
GTTCTCCCTGCGACAGCAGTCACTTCAGAAGACGCCATAAAAATTTCCAA
GTACATTAATTCTACAAAGAATCCAACGGCGTATATTGTGCGTGCAGTCA
CAAAATTATATAGTAAACCTGCACCTTACATGGCTGCCTTCACCAGCAGG
GGGCCAAACGTGATTTCACCTGACATTCTCAAGGTTATTAGCAAGTATTT
CTTCAACTATAATTTTTTTTGCCACAATAGTTGCAGTCGAGTCAATTCCA
TGTTCTGATAAGTTAGAGATCTCAGGCCTGTTTTTTTTTCTGGATTACAT
GGCAGCCTGATATCACAGCTCCAGGTCTGAATATATTGGCAGCATGGACT
GAAGGAAATTCGCCTACCAAGCTGGAAAGTGATACTCGAGTTGTCAAGTA
TAACATACTCTCTGGAACTTCTATGTCTTGCCCTCATGTGGCTGGCGTCG
CTGCATTACTTAGAGCTGCCCATCCTAGTTGGAGCAATGCTGCCATAAGA
TCTGCTATTATGACCTCAGGTATGCACACTCTCAGAGAACAACATAAGCA
GAATACCATCTCAAACACAAAATCAATAATTGTTCTTGATTCTCTAATGT
CCATGCGCTAAATTCTCCAATGTTTTACACATCTAACTTGCAGCTGGACT
ACTGAACAACGAAGGTAGGCTCATAACTGATGCATCCCAAATAACCTTAG
CAGATCCCTTCCAGTATGGCTCCGGCCATTTCAGGCCAGAACTGGCAGCA
GATCCTGGACTGGTATACGATGCTACACATAAAGATTATCTTCTCTTCCT
CTGCGCTTCTGGACTAAAAGTCGTCGATCCAGTCTACAAGTGTCCAAAAA
ATCCACCTGCCACATACAATCTCAACTATCCTTCCCTGGCAATTCCAAAC
CTCAATGGCACCAAAATTGTCAAGAGAACAGTCACCAATGTTGGCGGCAG
CAAGGGCGTCTACTTTGTCAGGGTTAACCCGCCTATCGGATACTCTGTAA
AGGTCTTTCCACCTGTGTTGGTTTTTAGTCATGTTGGCCAGCAGAAGAGT
TTCACCATAACAGTGAAAGCAAATAAAAAGAAGGCTGAAAAGAGTGGTGA
CTACTCATTTGGATGGTATACATGGACTGATGGATTCCACATTGTGAGAA
GTCCCATGGCTGTGTCATCTGCATAGTTCTCATCAACATGATATAATTTT
CTCATGAATTTATCGAGTAGTTTGTTATCCTTATAATTACAATACAAAGA
AGGATTTGAGATTTAGGCGAAATAGAAATTTCTGACACTTGTGCTATAAT
GTTCTTCCTATTTTTTGGACACATTTGGATCATGACTTCTCAAATCTTGC
CA