LOC108209366

Resource Type: 
Gene
Name: 
LOC108209366
Identifier: 
LOC108209366
Cross Reference: 
NCBI GeneLoading content
Relationship: 
There are 4 relationships.
Relationships
The mRNA, XM_017380231.1, is a part of gene, LOC108209366.
The genetic_marker, MK009494 2_30760629, is located in gene, LOC108209366.
The mRNA, XM_017380230.1, is a part of gene, LOC108209366.
The mRNA, XM_017380232.1, is a part of gene, LOC108209366.
Loading content
Analysis: 
NameDescription

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
Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
These sequences can be viewed in JBrowse here.

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.

Loading content
Transcripts: 
Transcript NameIdentifierTypeLocation
XM_017380232.1XM_017380232.1mRNADCARv2_Chr2:30760143..30765685
XM_017380230.1XM_017380230.1mRNADCARv2_Chr2:30760143..30765685
XM_017380231.1XM_017380231.1mRNADCARv2_Chr2:30760143..30765685
Sequence: 
CTTTTAAACTTGAAGTTATAGATATGCATCAAAGGTTTCGTCCGTGAAAA
GGACTTGTGTGTCACTCTAACATCATCCCCATCACCATCAACTCTGTCTT
CTTCTTCATATTCTGCTGTATCTTCACTTACCCTTTTCTACTCCTTTCAT
GCATTCCCACTTTCTTTTATATTTCTGCCTCTTCACTTAACCTCCCCACC
AAAAGCTGCAAAAACCCAATAAAGCTGACAAGACACTATAAAGATTATTA
TTATTATTGCTCAAAGCTGCAATTTTTTTCATCATTCTCCTGGTACTTTA
CTCATTTTATCAATTTTGCTTTTGATATTGTGTTTATTTGGCTTTTACAG
ATTTTGGGTACATTTTTATTTGTGGTATAGTCTTGATTTGAGCTGTCTTT
TTGTTAAGTAGTCTTCTGGATCCTTGTTACTTGTATTTGATCTTGATTTT
CTTGATGGGGTTACTTGATTGATGTTCAAACTTGATTCTATTGTATTGAT
TTAAGGTTGTGTAATTGTATATTGAACTCGATATATTCTTAACTTGTCTC
TTAGTTTATTCTCTCCTGGTTCGATTAAGCTTAAAGTTGAGTTCTTTTTC
ATGCGTGTATGCCCATCAAGCATTGTTATACATGTTTGTATGTGTACTTG
TGTGTGCATATAGAATGATTATGGTTGCTTATGTGTGTTAGTGGCTTGGC
TGATGTGGAAGGGGGTCGATGCATCTATCTGTTTGCGTGTAGTATTGCTC
TAGTTGTGAGTGTATTAAATTAAGCTGATTCTGTGTTTGTGGTGTTAATC
AGCAGAAATTTCATTTTTGAAGGATGGTTCTCGGGCTTCGATCAAAGCAT
CGAAAAGATGCTTCTGTTCAAGTTGATTACGTTGTCTATGTAGGCGAGAT
AAATCCCTGGCCTCCATCTCAGTCTCTCAGATCGGTGCAGTCTGTATTGC
TTCAGTGGGAAAATGGTGATCAGAATTCTGGCTATCTCACTTCTAGTACT
GGGGATAGCAGTGTTCAATTTAATGAGGCATTTACACTTCCTGTGACTCT
ACGTAGAGAAAAAAGATCCAGTGAGAAGTATCAGAAGAACCTGTTGGAAT
TTTCCTTGTTTGAACCTAAAAAAGATAAGGTTACTAAAGGACAACTGCTA
GGAACAGCCATCATTAATCTTGCTGATTATGGCATTATCGAAGATATTGT
ATCTGTAAGCTCTCCAGTGAGCTGCAAGAAGAGTTCTAAGAACACAAAGC
AGCCTGTTCTCTTTCTTAGAATACAACAGGTTGATAAAAATAGCTCTAAT
TCCACTCCTAAGACTGGCTTGTCAAAACAAGTCTCTCTAGATAAAGATAG
GCAAGATTCTGTTCCAGGATCGAGGAATGAAGAAAATGACGATGTATCCG
AGATAGCTTCTTTTACCGATGACGATGATGATATTTCTTCACATTCATCA
CGGACTTTTGCCTCCTCTGCTATTGACGCTGCAAATTCACCACACAGAAG
TGAGAAGGTAATTACTGCGCTCCTTGACCTATTAGTTATATAGTATTAGT
TATAGTAATTAAAGAATGCTCGAGTTGATAAGCTTTAGTTCAGTTTCAAA
TTTTGATATAGACCTGAATACATGTCCATTGGCGATAAATTAAGTTATAG
TAGACCCTTGATAAATTCATGATTTATAATCCATGATAGTTAATTACTTC
TAGTATATAGTATTGTTTCAGTTCCAGCATAATAAATACAGTATATATTT
AATCTTAATAAATTAATAATATTCATGGTTTTGAGGTTATTAATAATTTA
TAGAGGGTTAACTGTATATTGTTTAGTTTTGTATATGGTGATTGTTTGTC
GTCTTTGTTGTTTCCAGACTATAGCTTTGTGGAAATATATGGACGAGGAC
ATGAGGTTGTATAATTTTGACACAGCTTGATTAGGGATGAACCAAGTTAA
CTGCGAATAGTGTCTTTTACCTTGATGTAATTACTTGTAGTATGCCTTGG
TCTTGAGGTCAATTTTGTGCAATAGAATGTATGTGATGTTTATCACTCTG
AGAAATGCAGGTTGGATCGAATATAGCTGCAGAAAACACAGGCAGGATAA
AACCAGAGCCTGCTCTACCTGTGGTGGTATATCCTTCAACAACAAAAGTT
AATCCAGAGACAGAAGCATTTAAACGTCCAAGTGGAACTTCACACACTTT
ATTATCAAAAGACTTGGTCCCTGGTGTGGAGAGGCCAGCAAATGATCATG
TTTCTTTTCCTGAGTTTCCAGAGAGGAACATCACATCAATCAAGAAAGAA
TGTGATCCTCCAGTTCAATATTCTTCCTCATTTCCTCAGTTTCTGGACTC
GAGTAAGGACTCTATGGGCATCATGAATAGCTTAGAACAAGAAAACACAA
GTGACAGCCTTTATGAAAATGTTGCTAGCAGCGTAGACGGAACTAAAGCA
AGTACTTTGCCACTTGCTGAAGAAATTTTTGACAAATTTGGAGTCAGGGT
TGTAGCCGGCAATGCATATACAGATAGCCCGTCCAATCAAAAAAGTGGCC
AAGTGGAGGCAACCATTGTTACTAACTTAGATATTGATATGACAGAGGGC
AAATTGGAAATAGAACAGCAAGAAATTTCACATGATGAACAAAGATCAGA
TGAAAAGATACAAGGTTTAGGAAACAAAGTTGCTAGTAAAGTTTATCAAA
ATGCTGCCAGAAAGCAAGGCACATTAAGGAGTACTACTTTGGCATCCAAT
GGGAAAGTGGTTGGAGGTCAGGGAACTCCTTTTACCGATAGCAAACTAAA
ACATGTGAATTCTGTGCAGTTGCCACTAGAACCAGCTAAAGCCAAAATGT
ATAATGAGAATGAGAAGAAGATTAATAAAGTCGGTGGCGTTAATGATGCT
CAAAGTAATCTTACAAATACTGCAACGTTTGGAAGAAAAGAACTAGTGAA
TGGCTCTGACCAAAAAAATGAGTGGAAATCTAAAGCTGAGATACTTGAAG
AAGAATTGAGGGAAGCAGCAGCCCTTGAGGTTTCCCTTTATTCTGTTGTT
GCGGAGCATGGTGGTTCAATAAACAAGGTCCATGCTCCTGCCCGGCGCCT
CTCTAGATTCTATCTTCATGCTTGCAGAGCAAGGTTTTCAGATAAAAGAG
CTAGTGCAGCAAGGGCCGCTGTGTCAGGATTAGTTTTGGTTGCCAAAGCA
TGTGGAAATGATGTTCCAAGGTATGTATCAATTACATAGTTAAATGTTCT
ATTTAGACAGAAAATGAGAATGTGACTGTATGGGGCACTTTGTTATATTG
CCAGTTTCACCAGGTATAATTCACATGTCTGCAGGTTAACTTTCTGGTTG
TCCAATTCAATTATGTTAAGAGCAATTGTCAGAAAGACTGCCGGGGAATT
GCGACTTTCCAGCGAACCATGCATTAAAAGTTGTATTGGTAAAAATGAAT
CTAATGGAAAAGTTAAAACAACTGAAGAATTTGGTGACTGGGAGGACCCA
GTGACATTTACTACAGCACTGGAAAGAGTTGAAGCTTGGATATTCTCTCG
AATTGTCGAGTCTGTGTGGTGGCAGGTCATTTTACTGGTTCTCTTTGACC
TGCTAACATTCGAGTTCTTATAATCGAAATTTTAATTTAACTAGAAGTGT
TCACTTATTAAATTAATTTACTTGCCCTTTGCAGACTCTGACTCCGCATA
TGCAGCCTGCAGCTGCAAAGAGTAGTAGAACAATCAGTTCAGGTTCAAGA
AAAACAACTGGAAGTAAGCATATCTTGCGAGATCAAGAGCAAGGAAATAA
CTCCATAGAACTTTGGAAAAGGGCTTTTAAAGATGCTTGTGAAAGGCTTT
GCCCAATTCGAGCTGGAGGGCACGAGTGTGGCTGCTTACCTGTATTGGCT
AGATTGGTATGATGTTGTCTTACTTGATGTAGTATAGTTTTTAACATCTG
AAACTTATCAGTTGATACTTTTCCTTTATGAAAGTGTGCCGGTTTGCCGT
CTATTGGGACACAAAAGTGTCGTATCTAACAGTACATTGCGATATGATTA
TATAGGGCCCTAAATCAGCATAATGACTGCATTGTAGGTAATGGAGCAGT
TGGTGAGTAGACTAGATGTGGCGATGTTTAATGCTATTCTTCGTGAATCA
GCTGAAGAAATGCCAACAGATCCTGTATCTGATCCCATAGCTGATTCTAA
GGTCCTACCAGTACCTTCTGGTCGATCAAGCTTTGGTGCTGGAGCACAAT
TGAAAAATGCTGTGAGTATTATCACATCATTGTGGTGGTTGTGTATTGTT
TTATCTATTTATCGTCATGCTGGTAAAATTGTGTTATGGGGTAACTTAAT
TTTGCTGCAAGTGGAAGTTATTGAGCCTGTAATGAGATTCTCTCTCTCGG
TTAGCCATAAGAACTGATAGTTTCTATCTCAAGTCCTAACATCTATTTCG
TACGACACTAGATTGGCAACTGGTCAAGATGGCTGACAGACCTCTTCGGC
ATTGAGGATAACGATTCTCATGAAGATACTGACAGACTTGGTGATTACGA
GGAAGTAGAAACTGATACATCTTTCAAGCCCTTCCGTCTCCTCAATGCAT
TGAGTGATCTTATGATGCTTCCATTTGAAATGCTTGCTGATGCCCCGACA
AGAAGAGAAGTTGGTCCTTCCAACTCTAGAGCATTTGATTCAAATACTTC
AAATATTCTTCAATATTTCTTAAATACTGATTGCTTGCGTACTCTATTTT
TTCAAGGTTTGCCCAACATTTTCTGCACCACTTATCAGAAGGGTTTTCAT
CAATTTTGTTCCAGACGAGTTCTGTCCAGAACCAATTCCAGATTCTGTTA
TAGATTCTTTGGATTCTGAGGTAAGTATGTCTGTTATAACTATTAGACCT
TCAGTCTTGGAAAATCTAACGCAGGCTATTTTATTGCTTGTTCAGTATCT
AAGTGATAGAATGCATGTTAAAACATGTTTTCCTTGTGTCTTCTTTTTTC
ATGAAGGATGCTGCAGCAACTGTGGAAGAATCCCTCACAGTTTTTCCATG
CAATGCAAATCCTACAGTCTACCACCCACCTGCAGCAGCAGCATTTTCAA
GCATTGTTGGAGAAATGGGCAGCCATGAACTGCGCAGAAGCGGATCATCA
GTGCGTCGAAAAGCATATGCTAGCGACGATGAACTCGATGAGCTGGAGTC
TCCATTGACTTCAATCCTCAGCGATAACCTGCTTGTCTCACAACCTTCAA
CCAGACCTAACATAAAGTTGAACGAAAAGGGTGGTCGAAATGTTGCCAGA
TATCAGCTCCTTCGGGAGGTATGGAGAGATGGTGAATAGGCCTGCTGTAG
ATTTCTTCTTATATCCCATCCATGTACATTAGCAAAATGATGGTTCTTTT
TCCTCTTTTGAGCTTGGAAGAGTTTATTTTTATGTAATAAGTACGAATAT
GAATTTTTGAGCTCCTGTATCACTTGTAAACCGATTAAGCCCTCTGGATT
TGTTATTATGAAATAATACTAGAATTTCTCTAGGACTAAAAA
Sequence Length: 
5542
Sequence Checksum: 
313110b794fb6c83634769e7887aaeae
View location in JBrowse: 
Gene: 
LOC108209366
Gene Biotype: 
protein_coding
Gbkey: 
Gene