| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017375203.1, is a part of gene, LOC108205300. |
| The genetic_marker, MK009423 1_50669719, is located in gene, LOC108205300. |
| The genetic_marker, MK009422 1_50669747, is located in gene, LOC108205300. |
| 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_017375203.1 | XM_017375203.1 | mRNA | DCARv2_Chr1:50667189..50671516 |
TTCCCACTACAGATTCCACTAAATTTCTGAGAAAAGATTCTGGTCTTACA
AAATTACAAGGCCCTTGTGTCTTCCGTCCACTACTCACAGACTTTCTATA
TACACACCTAATCTCTACATAAAATCTCTTCTTGTCCTTTTTCAGCTCTA
TATAGCCTTATTGCACATGTAAGAATAGTCATCAAAACCCACAGAGAATA
GAGAGATTAGAGAGAGAAAGATGGAGAGAGCTTTGAATAGACAGAAGGTT
TTGCTAGGACATCTATTGCCCTCTTCTTCATCATCTTCCCCAGATTCTTC
ACTATCTGTAAGTACCCTTTTCTTTGTATATGTATTTATTCGTTAATTTG
TTCTTTATGATCTTGATTCTTGTGTTTACAGTTTTTTGAATTAGCCCATT
TGTCAGTAGTGTGTTTTTATATGTTTTGTGTGTGTTTTATAGCCTGATCA
GGTTGAGGATGAGTTGTGAATTATGTATAGATAGGTCTTTAAACTAGATT
ATAAATTTCCTAGTGTAATTTGTGTGTGTTTTATAGCCTGATCATGTTGA
GGATGATTGTGATATAGATAGGCAGGCCTTTGAACTTGATTATAGATTTC
GTGTAAATGTTTTGTGTGTTTTATGAATTGCAGGCTGATCATTGGGGTAA
TTTATATGGATAGGCCTTGAGGCTTCTAACTAGATAAAAAATATTAAGAT
ATTGTATTGGTGTGTGTTAGTTTGAATAATAATTTCTGAACTGGACGGTC
ATTGAATTGGCCCATTTTGTTAGTATTGACTAGTGTTGTGTGTGTATTTT
GTGGCTGGACCAATTTGGGGATGAATTGAAATATTAATAAATAACCTTTC
AAACGGAATTATGACTACTAAGGGGGAGGTGATCTGTCATTGTATTCACA
TGGAAGAACTGTACATATTGATTTATAATTGGTTCAATCATTGAGTACGT
TCTTGGAAGGATTTGCTTTATATATATATAGAGTTGTATCCACTTTTTGT
TTCTTGACTTCAATTCGTAGTTCTGTTTTGTATCTTGTTGCGGGTTTAAA
TTGCTTGTGTCTGCTCTTCAGGCTTCGCTTTGTGTTGCCGGAGATAGTAG
TGCTTATCATAGACAGGCTGCTTTTGGAGATGATATTGTGATTGTGGCGT
AAGACAATTCATTTTGAACTTCTGACACATATAAACTGATTTGAATATCA
TTTTTGCGCTAAACAAACTGATTTGATTTTTAATTGATGTTAGATATGTT
TCCTTGATGTAATTGCATATTCATTTTCTCAGTGCATATCGAACTGCTAT
ATGCAAGGCAAAGCGTGGGGGTTTCAAGGATACTCTTCCAGATGATTTAC
TTGGAGCTGTTTTGAAGGTAGATATACCAAACAACCGAGAAAATCAGATA
CAAATGTATTTAATGCAAATAATTATTAATCTTCTGCTTCTCAGTAGAAG
TATGCTTAGTTTTCTATGATCTCATTTTATTATTATGTTGTAACAGGCAG
TGATAGACAAAACAAACTTGGATCCACGTGAAGTGGGGGATATAGTTGTT
GGCACTGTCTTAGCTCCTGGTTCACATAGAGCTATTGAGTGCAGGATGGC
AGCCTTCTATGCTGGTTTTCCTGGTACTTATCTTTACTTTATTGACCAAT
TTTTCCAAGTTTAATATATAACGTATATTTGAACAATATGGAAAAGTAAA
AATCATCTTTCAGTGGGATTTTCAAGTGTCTCTGAGATGAGAATGACTGG
ATCATAATCCTTAAGTCTTAACATAATCAACTACTGAACTAAAATGATAA
ACATGTGGAGTTTATTAGTCCAATAGTTTGGAAAGCTATGTCACGAATTT
GTTTTGACGCCATGTTTTTAGATTTCTCAATTTAGATAAGTCACTACGAT
TAGTTCGCACCAAGAGTTTTTATAAGACCAGTTTCACTTAGTGATGCATA
CTTTTCGGACACTACAAGACCTAGGCTTAATGGTCTAAGAGTGGGGGTGT
GTGGCAATGTGTATTTTATGATTATCTTTATTGCAGATACTGTTCCTCTT
AGAACGGTCAACAGGCAATGTTCATCTGGCCTCCAGGCAGTTGCTGATGT
AGCTTCAGCCATAAATACAGGATTTTATGATATAGGTGAGTTTTGTACTT
TGGTTTGTGGTACTAGTTACTTTATTTGTGAGTTTAGCCCCACTTTATTC
GATGTTTTCTTAAAGGTATTGCGGCTGGACTGGAGTCCATGACAGTTGAT
CAAATGGGCATAAATTGGAAAATTAACCCAAAAGTGAGTTTATGACTTTG
AATTTACCAGCAATTGTTTGGTTAGTTCTGAGCAAGTTGTCTTTCACACT
GTATAATAATTATCAATATATCTTCTCTCAACAGGTTGAAATGTTCCAAC
AAGCTAGGGAATGTCTTCTTCCGATGGGAATTACATCTGAGAATGTTGCA
ATGCGTTATGGCGTAACACGTGAAGAACAAGATCAAGCAGCAGTGAGTTT
TTAAAAATCTTTTTGTGGAAGAAATTCTCCAAGCAGGGTTTACAGTTTAC
ACCCCTTGTTTCTGGCTCCATAGGTTATATCTCATAAGCGTGCTGCTGCT
GCAAATGCATCTGGAAGATTTAAGGATGAAATTATTCCGGTTAATACAAA
GGTAATGCGGTGGTCTTATCTCCTTCATTTAAAATTTTCTGCCACTTTCA
ACAATAGACCATATTTTATCATAGCACTGTACATCTAGTATACTACTCTC
CCCTTTGCCTTTACATGTATTTAGACATACTGATGGTTTTGCAAATGGCA
AATTCAATTGGCAGATTGTGGACCCGAAGACCGGAGAGGAGAAATCTGTA
ACAATATCTGTAGATGATGGCATTCGACCTGGCACAACTATGGAAGCTCT
GTCAAAGCTGAAACCCTCATTTAAGAAGGATGGGACCACAACTGCTGGTA
AGCACTGGTGGTGTTATTTTAATATTGTCATTTATAACTATATGATTGAC
ACCTGAAGGTATGCAATCTGCTATTCCAGGTAATGCTAGCCAAGTAAGTG
ACGGTGCTGGGGCAGTCCTCCTCATGAAAAGAAGTGTAGCTGTTAAAAAG
GGACTTCCCATTCTTGGTGTATTCAGGTATTGTTATCTTCTCAAGAAGTG
ATTTCTGGTCAAACATTAAAAGTTTGGGTATTAACTTGTGTTCTTGTTGA
AATTCCTAAATTTTGTTACGGTCTTGGACCTCTGAGGTTTATTGCTAAAA
TTATTTGCAAGACATAAGATATTACTCCTAAGGGTGCTATCATGTTTTTT
CATGCAGGAGTTTTGCCGCTGTTGGAGTTGATCCTGCTGTCATGGGAGTC
GGGCCAGCAGTAGCAATTCCAGCTGCTTTGAAGTCCGCAGGTCTTCAAGT
TGATGATATTGATTTGTTTGAAATAAACGAGGTGATTTGTCTGCTTGATT
TTTGTTTTCTTTTACTTTATAATAAGTTGGTGATAAACTTGGACTAATTC
GTTATAAATTTTTACAGGCTTTTGCATCGCAGTACGTATATTGCTGTAAG
AAGCTAGAGCTTGATCCAGAAAAGGTCAATGTCAATGGAGGAGCACTTGC
TCTTGGGCACCCTTTGGGTGCTACAGGTAGACTTCCAAAGTTGTATAAGG
ACTCGTGAAATGGATTATATAGTTGCTTCTGCTAAGTTGTTTCCACACAA
GTCTATTAAATAAAACTTAGGACCATGCTAAGTCTCGAAGTAGAAGTAAA
ACTAATAATTTATTGTTTTAGGTGCTCGTTGTGTTGCAACTCTACTGAAT
GAGATGAAGCGTAGGGGTAAAGACTCTCGTTATGGTGTGATTTCAATGTG
CATAGGTATCTATCACTTCATCTCCAGCAATGTTTAGCAATCAGTCTTGT
TTCTTTGAACTTGAAAACATCATTGTTATAAGCTATTAACATGTAATGTC
CTAATTACAGGATCAGGCATGGGGGCTGCAGCTGTTTTTGAGAGAGGGGA
CTGTGTCGATGAGCTGTCCAATGCTAGAATTGCGGGAACCAGCAGTTCGT
GATCAAAGGATGCCCAATAGATCGATGTCTTCAAAACCATTGTGGAAGTT
AAGATGTTATAGGACAATCTTATATATATTGTAATTTCAAATTTCGGTCA
AAGTATTTATATTAGAATAGAGTTGGGCTCCGTAAAGACCCACATATACG
GAGATCGTGGAGACCTATGTTATGGCCCTTGGATCGATTTTCTTTGTGTT
TCTGGGAATAAAGAGATTATAAGTACATTTTTTAAAATTTGTTTTTTCAT
TAAGGGTAATGATTTGCCATATTTAAA