| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017371728.1, is a part of gene, LOC108203037. |
| The genetic_marker, MK004277 K1721, is located in gene, LOC108203037. |
| The mRNA, XM_017371729.1, is a part of gene, LOC108203037. |
| The mRNA, XM_017371731.1, is a part of gene, LOC108203037. |
| The mRNA, XM_017371730.1, is a part of gene, LOC108203037. |
| 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_017371730.1 | XM_017371730.1 | mRNA | DCARv2_Chr9:1460986..1465361 |
| XM_017371731.1 | XM_017371731.1 | mRNA | DCARv2_Chr9:1460986..1465344 |
| XM_017371729.1 | XM_017371729.1 | mRNA | DCARv2_Chr9:1460986..1465253 |
| XM_017371728.1 | XM_017371728.1 | mRNA | DCARv2_Chr9:1460986..1465253 |
CCGACTTTGGTATTTACCACATGAGGTTGATTGTCGGTGGGTTGGAGAGG
GTGAAATGTGATCTCACTTGACAAGTGGTTTATGTCTCTGAGGTTGAGGG
GGGTCAGTACACCTACTAGTGTAATTGTAATCTTTCCCATTATACACATT
CATACGCTACATTCACAGCTTTCTTTGTATTTATCTGTGTCTGTTCTGCC
ATAAATTGCTTCATTTAGCTCTTCATCTTCTTGGCTAGTGGCTACAATGG
TGTCTAAGCTAGACATAGTTACCAACCCTTCTTCACTTCTCCACTAAGCT
AGGTGATCATCTCTGTTTAGCCCCTTCAGACACAAAATAACTTGTACTTT
TTATCTGTTCCAATATAAACTTCGGAGTGAGCGTGAATCGAACTCAGAAT
CTACTACGATAAGCCTTTATCACTAGGTTATCTCATCACGCTGATGACTT
CACTTAATTTTTAGAAGTTGTTTACTTGTTGTCATGCATCATTTTACTTT
AGTGTTTATGTAACATCCCACGCTGGTTAGATAAAGAGTATTTAGACCCT
TTATTAACACAAGCAAATTATTAATGTATATTAATTTGTTAGTACTTTTG
GGCCGACCTGTGGTGGATTGTTGAGTCTGGTATACATATAGTTGTGGACG
CAATTTTATTCGTGTTCTAGCATTTTGTGTTTGTTGTTCCTTGATTGTGA
GAGTCTGCAGATATGGCATTATGTTCTTGTGTATCTTTTATCTGTGAAAT
TGTGTGTGTGAATTTGGTCACTTCTGGTTGGGGAAAGCCTGATTAGGTGT
TATTGTTATCGATTACGGAGATTGTGCATATCTGTAAATTTGGTGCAGAC
ATTGTGTAAATTTCTTAGATTTTTTTTTGAATAATTGTTTGCTTGTCACT
ATTTAGCTGTGAAAGTGTTTTCTCTTTTGATATCCTGATATTATTAGTAG
TTCATGCAGCCTAGTAACTTGTCCTTAAGTAAATAGTGTTAGAGTTCTTG
ATCCAAGATTGCGTATGCAGTTCTTGTTAACTTCCTTCAAGTTGGTTTCA
ATTTTTGTTTTGTAACATTTCTGTAACCTAACCTTACTCTTGAATATGTA
TGGATGGTTGTTATTCAGAAAGAAATTGAGGTGCACCTAGTTTTCGGACC
AGATACTTGATAACATGGATCATAAGACATGGCTTTGGAGGAAAAAGCCT
TCGGAGAAAACAATTCTTGCAACAGATAAAACCGACCAAAATGAAGAAGA
GGTAACAGATTTTCTATTTTCTGTTACTAGTGAAAGAAAAGTATTATTAA
AATTTCGACTGCTATTTATTTCTTCTTACATGACGATTATGTGCTCACTT
TCTTCTCAGAAAGAAGTTCATCTGGAGAGTCTAGTGAAAAACCTAAACGA
GACGTTAACATCTGTTCTTCGCGATTCTAACACCAAAGATGATTTGGTGG
CAAAACATGAGAAGAGAGCTCAAGATGCTATTGCAGGTGATTATAGTTTT
TTTTTTGTCTCGGTAAGTGATTAATCAACATATTTTATAGCAGTGTAATA
TATTAATTGAGCTTGTGCCTCTCGATGAGAATATTTAGGCCAGAAGAAGG
CGGAGATGGAGGCAGTTTTTCTAAAGCAAGAACTTGATGAGGCTTTGTTG
CAGAATGTATCAGCAAATGAAACGATCACTTATCTAACTTCTGCATTGAA
GGAATCTATACAAAAAATTGCTTCTGCACGAGAGGATCATGAGAAAAGTT
TGCATGATGCTGTTATGAGTACATCAAGAGAATTCGAGAAGGTACAAAAG
AAATTAGAGGATAGGTTTACGGAAACAACTAAAAGATTAGAAAATCTGAT
GGTTGAGAATTCCCATTTAAGTGAAGCACTGTTGTTGAAAGAGAATATGA
TTCAATCTCTGAATAGACTCAAAGCTCAGACAGAGACAGAGTTCGAGACA
CTTATGGCTAGGCTAGATAAGATGGAAAAAGAAAATGGTTTCTTGAAGTA
TGAGTTTCGGATTCTTGAGAAGGAGCTTGAGATTCGAAATGAGGAGTTGG
AATTCAATCGTCGGTCTGCTGATGCATCACATAAGCAACATTTGGAGAGC
ATGAAGAAGGTTTCAAAGTTGGAGGCAGAATGTCAGAGATTAAGAGTCTT
GATGCGGAAAAGACTTCCAGGTCCAGCTGCTTTTGCAGAGATGAGGAATG
AAGTAGAAATTCATGGAAGAAAACACACAGAGACTACGAGAAGAAATATG
AATAATGCGACAGGATTAACTATTGAAAGATCTTCCGAGACTTATGGTAA
AAATTCAAGCTTTCTAATAGGAAGGCTGTCCATAGTCGAGGAAGAAAACA
AAATTCTGAAAGAACTTCTAATCAAGAAAGATGATGAAATCCATTCTTCA
AGAACCTCATTTTCTCAAACAGCTTCCAAATTATCACATGTCGAGGCTCA
GCTAAGAGATCTCTTAAAAGATCCAAAACATGTAAAGAAGTCCATGTACG
GTCATTCATCCAATAGGTCTCTGTCATCTAGTTTTGATCTTGCATATGAT
GATGAACTAGTTCATTCTAGATCATTGGCTTTGATCTCACAGGAGGAAGC
AAAAAGTACACCTGACTGCAAAATGACTGGAGTTTCAGACATGAGCCTTA
TGGATGATTTTGTTGAGATGGAGAAATTAGCAATTGTTGCAGTTCATTCC
CCGTCAGGAAGTTCTCAAGTTTCTTCAGATGTGAGTAAAACCTTCTCTAA
TCGCTTGATGAGCGATTCAAGAGAACATGATTTAGAAATTAGTGGCAAGG
AACTAGTTCCAGTAGAGCCTCTTGTTGAAATTAGTGATGCTTGTTGGCCT
CAGGATGTGTTGAAGGTAATTTTGGATCAGAAGCGGATTTCAAATAAAAG
CCTTGATGAACTTCTGGAGGAGATAAAAGTAGCTTTATCTAACAAGATAC
GTACGAGTTCCAAGGATTTTGATCAGGCTGCTCTACTTCCTGTTAGTGGT
TACATCACTTGGAAAACTCCTACTAGTTCTCCACTGAAGGATTGTCTTAA
AAAAATGTCCGATATAGGCATTTTAGTAGACGAACGTGAATCCTCAAGAA
ATGAACCAAAGATTGTAAAAGCCCAGGACGAGGACTTGGAGGCATTGCTG
AAAGTGGCAAATGAGAAGAATGATAAACTGATGTTACAACTTGCAGAAAC
AGAAGAAAGAATCGGAAGCCTACAAACTGAGCTCGGGACACTAAAAGAAT
CAAAAAGTATTATTGCGGAGCAACTAGAACATCAGAAGTTGTTAAATGAG
GATCTACATATGCAACTTACAGTTTCCAAACTAGAACTCGATAAACTTTA
TGAAAAGTTATCATATCTTGAAGTGGAACTCGAGGAAAGAAGTAGATGCT
GTGAAGAATTCGAAGCAACTTGTCTGGAGCTTGGACTGCAACTAGAGAGG
TACCATCTTTTCCTGTTAACTATAGAGTCCTTGTAATTTTTCATGAAGGA
AAAGAAAGGATCTAAATTCAGAGCCCTTGATTTGCAGTGTTACGAACAAG
GACCGTACAAAGAAAGACCTGGATCCAGATAAAAAGCTACTCCAAACTGT
AAGTTCAATATCTACAAGAGGAGCATTGGTTTTTTCACTTATTTGTTGCG
AAAATGTTATTATTTTACAACTGACCATTTCCAGGACTCCGAGATCAATG
CTGCTTCTGCAAAATTAGCAGAGTGCCAAGAAACCATCTTTAACCTCGGA
AAACAGTTAAAAGCACTGTCTTCTCGGAAGGAATCATCTGAATTTGAAAA
GGTTGTCTCTACTCCAAACACCACCGAGTCCAAAAGTAAGCTAAACCAGC
GTTCATCTCTGCGCGACATGCTAGATGAGCACAGTGGCGAGCCTACAACT
CTCGAGTCTCCAAAAACAAAAGAGATCATAAGCACTTCAGAAAAAAAGAT
ATCATCCACTATTCACTACAAGAATCAGGATGTTTTAATATCACCTAAAG
TTCATTTCCTTGGCGGAAAGCATGAGGCCTTAACTCCGGTTAGGACTATG
GCCATTATCCCGAGTAAAAAACAGGAAGGAAGTAGTTTGTTGAAGAAACT
ATTCCTTAGGAGGAAGAGGGGAACGAAGGTGAAGAGATCTCTGTCATTTC
GCACATAGACCATATGCAGGTTGAAGTTTTCATTTTCGGAGTTTTGAAGA
TTGGCTAGTTAGAATTTGAGTTTATGCGGTTTGGTTTGTGGTATGTGATC
TAAGACGTTATGTTTGTTAACTTAATTTCCTAAATGTTTTGCACTTTTGT
GACCTTTTGCGCCTGTAGATATAGTTGACACTTGAATAATAACTTGGTTT
TACTATAGTTTAGCAGTTTCAGATC