| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017398208.1, is a part of gene, LOC108223787. |
| The genetic_marker, MK004016 K1460, is located in gene, LOC108223787. |
| The genetic_marker, MK018308 5_5152015, is located in gene, LOC108223787. |
| The genetic_marker, MK018309 5_5152126, is located in gene, LOC108223787. |
| 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_017398208.1 | XM_017398208.1 | mRNA | DCARv2_Chr5:5150532..5155646 |
TAGCACAACATAATTATCCATCACATTCGAGAGTTGTTATATTTGTAGAG
TACTATCCAAGAAATAAAACCCCTCTTTCAGCTCACACACATCGAATCAA
ATCCCTCTTATTAATCTCCAAGCCAATTATTTTTCTCAATTTCACTAATT
CGCTTCATCAAAATGGTGCTCGAGGTTCGTATCGTCCATTTCTCATCGCT
TTTGTAAATTAGGGTTTTATTCACATCGCTGTGATTTTATTTATTTTGTG
CTGTGATTGATAATTGAATTGTGATGTTATCAGGCGACAATGATCTGCGT
TGATAACTCGGAGTGGATGCGCAACGGTGATTATTCGCCTTCCAGGTTTC
TAGCTCAAGCTGATGCTGTTAATCTCATTTGCGGTGCCAAAACTCAGGTC
TCGTTTCGATTCTGTATCTCTATGTGTGTCGATTGTGTTGGGAGTTTGTT
TAGATCAGTTGAGCTGTTGTCGATTTGTTGCGTCGTGTCGATAATTATTT
GATTTAGGGGAATTTGTAGTTTTTGTGAAATTGTTGGGGACTAGAATGTG
TTTGTGATGTTAAGAAGATTGGACTTTGTTTTGGTACAGTCTAATCCGGA
GAATACTGTGGGAGTGTTGACAATGGCGGGGAAAGGGGTTCGTGTTTTGG
TCACTCCTACTAGTGATCTTGGAAAGATCTTGGCGTGCATGCACGGTAAG
CTTTGATACTTTTTCTTGTTTGCTATATGTTTTAGGAATGCTGTATTGGG
TGAATGATGTTTTGGTTTTCTAATTTATGGTATTGTGAGTATGCCGCATG
TTTATAGTGTTGGCAATATGTTTGTAAATGGTTTGGTATAGTTGAAATTG
TTATTTTGCTTAGGTCTTGAAATTGGGGGTGAGATGAACTTGGCTGCGGG
AATTCAGATTGCTCAGTTGGCTCTTAAGCATCGCCAGAATAAGAAGCAGC
AACAGAGAATTATCGTGTTTGTTGGGGGGTAGGTACTTTTTGTACATATT
TGTTGGAGGAATTATATATCTGCCTGATGCGTTTTCCTAATATAATTTGA
TCTTGTGGTTTCCAGTCCAGTTAAGTATGATAAAAAGGTTCTTGAGATGA
TTGGAAGAAAGCTGAAAAAGAACAGTGTTGCACTTGATGTTGTTAACTTT
GGGGAGGAGGATGATGATAAAACAGAGAAGCTTCAGGCCTTAGTTTCTGC
TGTAAACAATAATGATAGTAGTCACATTGTTCATGTTCCTGCTGGTGCTA
ATGCTCTTTCGGATGTGCTTATAAGGTTGGTTTCTGCCAAACATCTTTTA
ATTGTTCAAATCATTTTCATCTGTTTGACTTGTGATATTGTTTTCTTTGA
CAGTACTCCTATATTTACTGGTGATGGAGAGGGGGGAAGTGGGTTTGCAG
CGGCGGCAGCAGCAGCTGCAGCTGGCGGTGTATCTGGCTTTGATTTTGAT
GTGGATCCCAATGTGGATCCTGAACTTGCTCTTGCCCTTAGAGTTTCAAT
GGAGGAAGAAAGGGCTAGGCAAGAAGAAGCTGCTAAGAAGGCTGCAGAAG
AAGGGGCACAGACAGAGAAGACAGGAGAACAAGCATCCACTTCGCAAGAT
GTAACCATGGCAGGAACTGCTGCTCCTACAGCTTCTGAAACTGAGAATAA
GGCGGTTAATTTAATGGTAACAATTACATATGCACCATGCTTCTATTTAT
TTTGCTTTGTGATGATGGTGTATAAAACCTTAACATGACTGCATATGTGG
TGAAATGATTTGTTCTACAAACAAAGTTTAAGCTATATATAGAGTATGCT
TATGGAAGAAAAACTAATATTGAAACTGTGTTGATATTTGAAGAATCAAA
TGCGTTAGGGAAATGAAAACTTTAATAACATTTAAAATATGTTCCCTATA
GTGTTGTTGACCCTTAGAATGGGAAATAGATCTAGTGCAAGTGTGCAACT
CAATTAATTGTTGGATAGCCAAAGTGGAGGTGGAATGAGTTTGTTAAGCT
TAGGAGGCATAAAGAAACCAAGTGAGAAATGTTATCTTGTTGATGCCCAG
TTGCTATGTACGGTTGTTCTGGTCATCTTGATAATGCTGGTGTATTGGAG
TACAAGATCTGGAATTTTTTCCATTGCTGGAATTGACTTGCGGATTTAAT
GATGTTTTAAATTCATATAAACTCTGGTCTTGTGTTTGTAAAATTTTAAT
TGTTGGAGGGTTTTCTTATGAAAAATTGTAATTGTGTTTGAATTCTAATG
CTATGTAATTAATTGTTCATTGAGTTAATATCATTTAACTGCTTGTTTGT
TTCATCGTGGCAAGATTGTGTGGCTATAATACATATGCCCCGGCTTTTTT
TTGATTGGTCAGTTTTACCTCCGAGCTTGTACAGTATAACCAATACTGAA
AGGCAACAATACTTGCAGGATGATGAGAACGCACTGCTACAGCAGGCACT
TGCAATGTCTATGGATGACCCTGCAGCTTCTGCTATTATGAGAGACACAG
ATATGTCAGAGGCTGCCGCTGATGATCAAGACTTGGCACTTGGTTAGTGT
ATTTTTGTTGGCAACATTATCTACTGACTGTTAAATAATCACAGGCATCT
ATTATACTATTTCAAATCCTAGATTGTATTCTGGTTTTATTTTACTTGAA
AAAATATCAAGAATGGCAAACATGTCTATGTATTCTGGATTTATTTTCCT
AGGCGTTGAATGTAATCTGGACATTATTAATCCTATTAACTTATGTAATT
TGTATTATCTTTATGATATTATAAGCAACTTCATCTGATCTAGTACGCAA
GCAAAACTATGTTTTTAAGAACCCTTTTCACTGAAGCTAGAATTATTTAC
TTTTACTACCAGTTTAGAACCCTCTTTCTTATGTGGATGTGTTTTCTACT
TTGTATGCGCAGTTTGATGTTTTTTCTTGGTTCTTTCTGGTTGCAGCTCT
TCAGTTATCTGTGCAGGGGGGTGCGGAAGATGGATCAAGTCATATGGACA
TGAGTAATGTGTTGGCGGACCAGACGTTTATGTCAACGATTCTTTCATCA
GTATGTTTGCTGCTTTGCAATGCTTTCCTCTGCTATCTATTCAAAGCATT
ACATCACCTTAATTTTAATGTGCATGGCCATTATTTAGGAGTCTTCCCCA
AGCAAAAGACCAACTTAAAATGATAATTTATCTTACGTTGGTTCGTTGTT
TGTTTTGTAGCTCCCAGGAGTTGATCCGAATGACCCGTCTGTTAAAGAGT
TGCTTGCTTCCATGCAAAATGCAAGTGAGGTCAGTTTTTGTTTTTGCTTT
TTTAATTGAGTGGTTCTCTCTTGTAGTCTTGTTTGTCTTTGTTAAGAGCA
TCTGTTTGATCGGCGGATCATTTGCATTCGTTTACAGATTTCTTTTAGTT
TCATTTGAAATGCATGCAGACAGAGATACTGAATGTTTCTATGAGAGTGT
TCACATTACATTTTCTACTGCTCGCAATTCTGCACAGTGCATGATTTTAT
GATAATTTATTAGGATAAATGATCATATCTATTTGTTGTTCCTTTTATTT
TTTAATTTTTATATGTCCAACTTATCTGATAGGAATTATGAAGTGTACAT
CTAAAGCAAGTCCAATGGCGGTGTTAAAAGTGATGTTATCCTTATAATAC
AGCATCTAAAGAAAAAATCCACTCTAATGCAATGGTAAACATCGATGTAC
AACAGCAAAAATCTTATACTTGGCGCTCAATATAGAACCAAGTATAGATG
TTGATTGTAATTGCCATGTAAGCATACAAGTGGAAAGTGGAAAAATGTAG
TATAACAGAATAGTGAGAAATATAATTAGTCGTGCAGTCAAAGGTTAGGC
GGTTGCAATATAGCCAAATTTGTATCTACTTGGTGTCATTTTAGAGTTAT
GCATTGGACTACGAGTTCTATTTTGACATCGAAAATCACTTTTTGATTCC
TTAATTTAGCAATAGCTATATGTCTATTAGCTCACAACTGGACATGCTCT
GATAGTGTCTATATGGTGCCATATAGCATGTTTAATGTAATGCTATATCT
ATAATACAACACCAAAATTAGAAAACACCTCTCCATGCAATGCTAAACAT
GGATGCAAACTAGCAACATGCTATATTTGGTGCTAAACATATAATGAAGT
AGACGTTGCTATAATTGCCATGTAGGCATGCAAGAGGGAAAATGGAGTGA
AGCACATAACAGTGACAAATATAATTGTGCATTGAAAGATTAGGCGCCTA
AAATATAGCTAAATCTGGATATTTTGTGTCATTTAAAACTATGCATCGGA
CTACTAGTTGTATTTTAAAATTAAAATTTCAAAATGTAGCCCTAGCAATA
TGTATTTTAGCTCTGCCAGTGGACATAGCTCTTAACTGATTTAGGCTGTC
CAATATGTAGCTTTTGTATATCGTCATACAGCTCATTTTCTTGAAGTGAT
GGTTTGAAAACTACCATTCGTTTAACATACTTTTAAATATGATTTTTTTA
ATGTCCTAAACTCCCGTCTGTTGAGGAGAAAATCTGAGTGTCATGTTTGT
TCATGTTTTGTTTTTTGTGAAGCTTTCTCCTATGCTTAGTATATACTTTT
AATGTATATTGCCGCCGTGTCTGATATATTATAGGGCTATTTGTATTTTT
CTCTTCCATTTCTTTATGGTAATGGTCATTAAGTGATTCGTTTTATTTCT
TTAGCCTGAGCATAAAAAAGATGAGGACAACAAACCAGGAGAAGAGAAGT
AAAATCCTGTAGCATATGCCTGACCACAGGTACAAAATATAGAACACATA
TTACCCTTGTATCTTTGTTTGACAACCAAATTATTAATCTGACATCATTC
TGTTTTGCAGGTCTCAGTTAAGCTACAGTGCCGCCTCTAGAAAAGGAATG
CTTGTTACTGCCGTTAATGAACAATAATAGAGACTAAAAGCCGATTCTTG
TATTTTCTAGTGTTACTCTGTTGATGTAATTTGGGATCATGAATCTATTT
TAATTTGTGGTGCTGATATGTGATCTTTGTTGCTATAAACGGTCTGGTAA
CAAGAGCCAGAAAAGTGTATCTCGTCCTAGATTGAAGAATTTTATTGCAT
TTCACGAGCACAAA