| NCBI Gene |  |
|---|
| Relationships |
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| The mRNA, XM_017386514.1, is a part of gene, LOC108214499. |
| The genetic_marker, MK002941 K0385, is located in gene, LOC108214499. |
| The genetic_marker, MK011008 3_50144167, is located in gene, LOC108214499. |
| The genetic_marker, MK010050 3_50144178, is located in gene, LOC108214499. |
| The genetic_marker, MK009550 3_50144206, is located in gene, LOC108214499. |
| 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_017386514.1 | XM_017386514.1 | mRNA | DCARv2_Chr3:50140145..50144383 |
AAATAGTTGAATTTCTTGTGCGAGAAATGAGAGAAAAAATAAAGAAAACA
CCTCGGATATGAGTGGTAGGAGTAGAAAGAATCTTAGCTGTATCCAAGTA
AAAACACACTAGCATTATATCATCATCTGCTGGTGAAAGATCTACTGTAG
TGCCCAGCAGTAGTAGTCGTTGCAGCACAAAGAAAGTTTTCACCATTTCA
CACCCTCTTCAACTCTTTCTCTCTAATCTCATCATTCAAATTAGTCACAG
GCAGGCAGCTCTATCCTAGTCCCCGTTTACACCAACACAGCAGTTAAAGA
AAAATGGCACATTCTTGGTTCTAGAGGGCGGCAGTCCCCACAGCTCAGAC
CACTGCATTTACTCTACCTCTCTCATCAACATCATCTCTCTCTCGTCTCT
CTCAAAATGCAAATGCAAATGCAAATGCAAACGCAAACCCACCTCATCTT
CCTCCTTCTCTTCCTTGTCCTCTCCTCCTCCACCACCACCGCCCACCCTC
AACAACACCGCCGTATTCTCCACCAGCCATTCTTCCCACAAGACTCCATC
CCACCATCGCAACCCCCTAACCTCCCTTCTACGACGACGACGACGACCAC
TCCTCCAGCTGACCAGCTCCCCTTCTTCCCAACCTACCCTTCACCCCCAC
CCCCACCGACACCAACCACCACCACCACATCCTCCTCCGTCCCGGCCAAC
GTCTCATCCCTCTCCCTCCCAAGACCCTCCTCTCCAAAACCCATCTCCAA
AAAACTCATCTTCACCGCCGTCGCCGCCGTCATTGCCGCCATCTCCGTGG
TGGCCGTCGTCATCCTCCTCCACATCCGTAAGCGTCAAAATCAAAACTTG
CCAAACACCCACCAAAAACCACAAACACCCAGTAATCTCAGCTCAGTTTC
AAGCATACCCACGAACCCAATCCCTAGAATACCTCCCCGGAAATCACCTC
AAACCAGCTCCGAGTTCCTCTACTTAGGCACTCTCGCAAACACCAACATC
TCGAATAACACCAACACTCAACACAGCAATGACACTAGTTCCAGAAAGAT
GGAATCACCGGACTTGCAACCACTGCCGCCACTCAAACTCAGCGGCCAAC
AACCCCAGCAACAGAACTTCCAAAATGCGGACTATTCAGGCCCTCTCATT
GCAGATGAAGAAGACGAAAACGATGAATTTTACTCTCCCAAAGGCTCAAT
CGGTACTGGATCAAGAAGGACGTTGTACGAGCCTAAGAGTTTCCAAGACG
AGAGAAGAGAAATTGAATCCACCACTTCATCTTCAACCTCTTATACCCCT
TCCGATTCGGGTGGTTCGCCGGTGAGGTCTGTTTCTTTGAGCATTTCTCC
TCCGGCAAGTTTAAGTCCTAAACACTTTTCAACAACCAAATCACCTGAAT
TGACTCCGCTTCAAATGAAGGATCTGAGTGATGTATCATCACAAGCTTCT
GAATTATCATCCGTAGATCGAGTGACCAGTACATTACATCCACAGCATCT
TGGTTTCACGGCTGCATCTTCACCAGTTTCTTCGTCACCCGAAAGATACA
TTAGTGAAAGTCAGGCTTCATCACCAACAGCATCTCATGTATCTTCACCA
GCTTCTTCTCATCGCCCTTCCTCCTCACCTGCTAGAATTCACAATTTTGC
GGATGCTCCATCATTGCCTCCACCACCACCACCACCCCTACCACCGACAA
GACAATCTGAAAGTCCGAAAACCCCTGGTACTAAAATGGCTCAGCCCGTG
TTGAGGCCACCGGTCCTGGCTGCCCCTTCTCGGCCTGTGACTTTAGCCAC
TCCAGCACTGATATCTCCCATAGAAATGCCCCCTCAAAGCACTGACAATG
TGGATGAAGACACTCCTAAATTGAAGTTAAAGCCATTGCATTGGGATAAA
GTCAGAGCAAGTTCTGATCGTGAAACTGTGTGGGATCACCTTAGATCAAG
TTCTTTCAAGTACAGTCCTCCACTTATTCCCTTTTCACCGTGTTGTTGTT
AGTTGCTTTAGCCGTATTATTTAATCGTATGATTGCTACAGGTTGAATGA
GGAAATGATGGAGACATTGTTTGTTGTGAATAAACCGACTCCTACTGTAA
CTCCCAATGAAACAACTTGGCGTCCAGTTCTTCCCTCATCAGGGCAAGAA
AATCGTGTACTGGATCCGAAGAAGTCCCAGAATGTTGCCATTTTGCTAAG
GGCCCTTAATGTCACAATAGAGGAAGTGTGTGAAGCTCTTCTGGAAGGTA
ACTCCAGCTTCCTACTGTTTGGGTTAACACCATCTTTTGCTTCATTATGA
TCTAGTGTATTCTGTCAGTTTTAGTCAATGTCTACAAAGCTTTTAAGGTG
AATAGAGGAATGAATGTAATGATATTTGACAAGAAGCTTTGATCAATTGG
CTGAAAAAGTGAAAAATTGTTAGTAATTAGAGAATTCAAGTATTATTATT
CGTAAACGATAGAAACATGTTTTTATGCAGGCAATGCTGATAACCTCGGA
ACTGAGCTTCTTGAAAGTCTATTGAAGATGGCTCCTACCAAGGAGGAAGA
ACGTAAGCTGAAAGAATATAAAGACGACTCGCCTTTCAAACTTGGTCCCG
CTGAGAAATTTTTGAAGTCAATGCTTGATATACCTTTCGCATTTAGAAGG
GTTGAGGCTATGCTTTACGTGTCCAATTTTGATTCTGAGGTCGAGTACCT
CAAAAAGTCATTTGAAACACTGGAGGTAAGCTATTATTTTACAAGACTTA
TCATGTTTGTTTTGTATATTCATTATATTGTTTATCTTGTTCGTATTGAC
TATGTAACTGGAACTTTTAAATTCAACTTCATGAGCTAAATAGGAATTTC
AAACAGAGCAAACACCTTTGCTACATTATATGTTATAAGTATCTAATTGC
CAAATAACTCATAGATCTTTTCTGATTCTCATTGAGCAAGTCAGATATAT
TAACTTGCAACATTTAGGTCCCAGTGCAAGCAAGTTAATTATTTTACAAT
ATTTTGTACGTATGTATAGAATTAGAATTATAAACAAAATCACGCACACT
GTCAATGGGTTCTGATGTTTACTAGTTCATTGACAAGAAGTACTCACTTT
TATGTAGTTTATTGGTAAAAATTCCTTGATCATCATATAGTAGTTTTATC
AATGCTGAGTAGTTTAAAAACAACAGGCCGCATGTGAAGAGCTTAGGACC
AGCAGGATGTTTCTAAAGCTTTTGGAAGCTGTTCTTAAAACCGGAAACCG
CATGAATGTTGGTACAAATCGTGGTGATGCCCAGGCTTTTAAGCTTGATA
CTCTCCTTAAGCTCGTCGATATAAAGGGTGCAGATGGAAAAACAACTCTT
TTGCATTTTGTGGTCCAGGAAATAATAAGAACTGAAGGTGCTCGACTTTC
TAATGCCAACCAAACTGTACAACCGACTTCTGCTGATGATGCCAAGTTGA
GGAAGCTTGGTCTGCAGGTCGTTTCAAGTATCAGCTTGGACCTTACAAAT
GTAAAGAAAGCTGCATCCATGGATTCTGAGGTGCTTAGCGGAGATGTCTT
GAAGCTTTCTAGAGGAATTGGAAAAATAGCAGAAATCGTCCGGATGATTC
AGGCTTTAGAATCTGATGAGAACAGTCGAGGATTTTCTAAATCAATGGGC
AATTTTGTAAAAATGGCAGAGGAGGAGATCATAAGAACTCAAGCTCAAGA
AAGTGTTGCACTTTCTTTGGTAAAAGAGATCACAGAATACTTCCATGGGA
ACTCCGCCAAGGAAGAAGCTCACCCTTTCAGAATATTCTTGGTCGTTAGG
GACTTTTTAACGATTCTTGATCGTGTTTGCAAGGAAGTAGGATTGATAAA
TGAGCGAACAATAGTCAGTTCTGCCCACAAATTCCCAGTACCCGTGAATC
CAACCATGCCTCCGGGTTTTGCCGGGTTTTCAGAAAGGAGGCAGTACGAT
TCTTCTTCTGACGAAAGTTCATCTCCTTAGTGGTTACAAGTCGTAGGATA
GGAGGAGCCTTTTTAGGATGGTCTCCTGCCAAAATATAGGTAAATGTAAT
CTTATTGCTTTGTTGTTTGTCTCCTTGTATTTATATAGATCCATATAAAA
GATTTTGAAAATTGTAGTTACCATCAATATATATAGAGGAAATTTGTTGC
TATGGAGATGACAAACACCAAATCTATTCTGAAGTCACGATAAATCAGAT
TTGGATGTGTAATGCTCTTTATTTCACAGTTATGATTA