LOC108216932

Resource Type: 
Gene
Name: 
LOC108216932
Identifier: 
LOC108216932
Cross Reference: 
NCBI GeneLoading content
Relationship: 
There are 5 relationships.
Relationships
The mRNA, XM_017389815.1, is a part of gene, LOC108216932.
The genetic_marker, MK010713 1_36938287, is located in gene, LOC108216932.
The genetic_marker, MK016769 1_36938332, is located in gene, LOC108216932.
The genetic_marker, MK010725 1_36938350, is located in gene, LOC108216932.
The mRNA, XM_017389862.1, is a part of gene, LOC108216932.
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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.

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Transcripts: 
Transcript NameIdentifierTypeLocation
XM_017389815.1XM_017389815.1mRNADCARv2_Chr1:36933718..36939873
XM_017389862.1XM_017389862.1mRNADCARv2_Chr1:36933865..36939873
Sequence: 
TACTCAGTTTTGTCTCTAAAGTGCACACATGTGCGCCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCTCAGTGTGAACTAGAGGCAACTTCTTTCAAATT
ATTTCTATCTCACCTTTCTTCTGCTTTCCATTTCAGGTTCTTTCTCTTCT
CCTTTCTTTATAGTTTATTGCTCATGGGAGTAGTCAGTTGTGAGGCTTAC
TTGATGTCTGTTACCTCAGTTCTTATCTCTTTGTACTTCATCATATCTCA
ACAATGTTAGGTAGATTCATGAGTTTGCAAGACTTTTTTCATGTATATAT
TCACAATTATTAGTAACATGGTGCTTCAAAATATAGACAAGTTTTTGTCA
TTATGGTTTTAATTTGTGTTCAGATGCCCTTTTTGTCTTTTGGCATTTTA
CTGAAAGCTTTTCTGCTTATGCTAATTACCTCAATAATGATAATTACCGA
GTAATGAGGAGCTTCAGACCTTTAATTCCTCTTTCCTGATAAACATTTTG
TTATATGTGATTTGCTTGTCCAGACTCCAGAGTGTTAAGTGTTAACTAGA
ACTAAACAAACTATGTTGACATTGACTGCCACTTGCTACAAGAAGTATAA
TTGACTTAAGATGCCAATCTACTAGGGCCCCTTAGCACCAATCAAAATGC
AGATGTCATCTTACTTTCTAGATTCTAGTTCTATGTTTTCGTAGCGTAGG
TCTATGCCTGTGGCATCTTCCTTGAGGCTCTCCACCCCCTGGTGAAAATA
GAAAAAATAGGTAAACTGGGTTTAGATAAGAGAAAGAGCAATATTGTATT
AGCCTCTTAGCTGAATAGTGTGAGCGGATATTACTGCTGATAATTTGGTG
ATTCAGTGTGATTAATCATGCTAATATTCATTGTCTATTGATGTTTTGAC
ATCACACTACAATCGACATGTCTAACTCAACTTGAACCATTCCTTTCTCT
ATGTGTCATTCTACTTCGGTAAATTCTTATCACTATGCCCAACTGTCTCA
GTGTACTCCAAACAAACTGACTATGTTTAGGCTATTGCATAATTATCTGT
CTTTTACTTTTTACTGAAGTTGTAATGAAGTTTGCTGCTTATATATTGCA
GCAATGCTTATCGTAGTTCCTCACGCGAATTATTGAGTGGTCAGCTCATT
CATTTTCATATACCTTGTACCTTATATCTACTTCAATTCTAAGATAATAG
TCCTAAGATTAAGTTACTACCATCTGATGAGGAAGTGTGTCACCTCTAAA
CTAGCTCAGCATTATCAGATCCTAACTAGTGAACTAAAATGTAGTTCAAA
ACCAAAAGTAGGATTGCCTCCCAATTTAGCCCTTCAAGTTCTGTTCCTTC
TGTTGAAAATGACACATTAAATCAAAACCTTAATTTGCCGATTTGGACCA
GCTTGATTATCTCACTCAATCGTTCTCCTTTCTGCCTATTTGCTGAACTC
GACAAGCTAACACATAATAGATAATGTACTAGTGGATGTCTAGACCTTAT
CTTTTATTATTTAATTGTAGTAATTAGGTTTTAAACTTTTAGTGCTTTAT
TTGCCAGTATGATACCATACCACTATACACTACGATACACTTTGTTTTAG
TCAATAACGCCTCAAATATTGTTTCGTTGGCAACAGACCATATCCATCTT
ACTGACTGAAGTTAAAAATGTTAGATATTATTAGGTCCACCACCCGGAAA
CCAACCAAAATTTCTCCTGAAAATTAATTGTTTTCCTTATTCTCTATTTG
GTGTTTTCTCTATATTTATTTGTTAGATAAGTTATGAAATCCCTGACTGA
TAGTTGACTTGTTTAGCTGGATATTGTGTCAGTGACTGTAAATATGTTAC
CTAATGTTTTAGTGTTCTCTCTCGATCGTCATGCAAAGTCCACCTTAGTT
AGGACTTGCAATTTAGATCCTTTAACCTAATTACTTTTTCTTCCTTTTGT
TTCGCCTAAGTACAGCAGAAATGACATATTAATGAGTATTACTTTTACTT
TACAAACCAAGGAAACTTTTATGAAGTTTTGCTCAGTATCTGATCTAATA
TTTTGAGATTACTATTCATAATTCGAATGCATGGGCATCTACAGATAAAA
AGTTTCCAATACCTTCATATTGCATAATTAAGATTACTTGCTCAAACTTT
GTAGGCTTTTGAGGTAATAACTAAAAAACAAAGTCCATATTGGAGTGGAT
GATGCTCGAGCTATGGATTAGAAGCGTGCTACTTATGTTTGGCATGTTAT
CCAGCACAATAGGTAACTCATTGAACTTGTTCCTTTTTTTATTAGCTTAA
AATATATTCTCACATGTTCACAATTTCACATGGAACTTTCAAGACCATGA
CAGCCTCTGACAAATTATTTTTCCTTGGTCATTTAGTTATGAAGGATCAC
ACTGGAGTTAATTCTTGTTTCTGCGATACTCGTGAAATTCACATAGAAAG
AAAACTACATTTTAACCAAATAATATTGAGTCATTGACAGTATGATGTAT
GTCACAGTATGTTGCTCCTATATTTTTTCTTTTGTTGCCTTTTCTTTAAA
TCAAATTTTCACCTTCCATCTGCTCAGTATTTAAATGTTTGATGCATTGT
ATCATCTAAAATCTTTTCAATTATCTTCAACATACATTTTTCTGAGATTT
AATTGTTTCCGTAAAATTTCTACATCTTCTGAAACTTGTAGTTTTTTCTT
AAAAGGGGCGAGAGGGGATCCATTTCTAAATAATAACACAAGATATATGC
CGCTTAATATCTCAGTTCCTTCTTCTGCATCCTGCTTAATTTGGTTTGTA
AATGCCATACTTTAGCTAGAGTTGCAGAATTTATGTATTAGTTTTATAAA
ATGACAGTCTTTTGTGATTATCACTAAGAAAAAGACTGTGCTGATGTAAA
CTTCTCAGGCTTCCTTTCTACTTGGGGGGTTAAGGGCTTCTAGTGACATT
GAATATATTACAAATTTAGTTGTTATGTAAAATATTATTGATATCTCAGT
AAAAGATGCGGAAAGATATAATGATTCGCTAATGGTGTCTGTGAAGTGCA
GGTGGATATGTTGGAATAAATATTGGAACTGATCTTTCCAATTTACCCTC
CACGTCTGACGTGGTTGCAATTATTAAAGCCAACCAGATAACTCATGTAC
GCCTTTTCGATGCTGACGCTCACATGCTAACTGCTCTGTCAGACACTGGA
ATCGAAGTTATAGTTGGTGTCACTAACGAGGAAGTACTGGGAATTGGTGA
ATCTGCTGCAGTAGCGGCAGCGTGGATAAATAATAATGTTGCAGCTTATT
TGCCATCAACCAATATTACAGCCATCGCTGTTGGGAGTGAAGTACTTAGT
TCGATTCCGAATGCTGCCCCTGTTTTGGTTCCTGCCATGAATAATCTTCA
CAAAGCATTGGTTGCATCAAATCTAAATAATCACATTAAAGTTTCAGCCC
CCCAATCGATGGATATAATCCCTAAGCCTTTTCCTCCTTCCACGGCCATG
TTCAATTCAACATGGAACTCCACCATTTCCCAGATGCTTCAATTTTTAAA
AACCACAGATTCGTACTTCATGCTAAATGCTTATCCATACTATGGATATA
TAAATAATGGTGGTATCTTTCCTATTGATTATGCACTATTCCGACCAATG
TCATCAGTGAAGCAGATAGTTGACCCAAATACTCTTTTTCATTATGACAG
CATGTTTGATGCTATGGTGGATGCTACCTATAACTCTATATCAGCATTTA
ATTCGTCTATTATTCCTGTTGTTGTGACAGAATCTGGGTGGCCTTGGTTT
GGTGGTGCTAACGAGCCTGATGCTACTATGGACAATGCAGAAACTTTTAA
TAATAATTTGATCCAACGTGTCTCGAATGATTCTGGTCCACCTAGTCAAC
CCACTATTCCCATCAATGCATACATTTACGAATTGTTTAATGAAGACAAA
AAATCTGGACCCATATCAGAAAGAAACTGGGGTTTATTTTTTTCCAATGG
GACTTCTGTATATCCCCTTAGTCTGACTACATCAAACAATAGTGTTGGAA
ATTCTTCAGTAGCTTTCTGTGTGGCAAGAGAAGGGGCAGATTCCAGTAAG
TTGCAGAGTGGAGTTAGTTGGGCTTGTGGACAAGGCCAGGCGAACTGCAC
GGCCATTCAGTCTGGGAACCCATGTTACCTTCCTGATACTCTACAAAACC
ATGCTTCCTTTGCTTACAATGATTATTATCAGAAAATGAAAAGCATAGGT
GGAACCTGCGACTTCGATGGTACTGCCATGACAACTAAAAATGATCCCAG
TAAGTCCCTTTTCAATTCAATTTTGTTATTTTCTCAACTTATGGTTGGCA
GGTGCATACGTCTTTCACATGCCAGGTTCCTACTAGTTCTATATATTGTA
TGTTCCTAAAGCTTGCTTTTTCTGGTGTAGTCAGACACCTGTAAACTGAA
ATAGATAGTCCATAGAGTGTCTGGTGGTAAAAGTGTATGTTTTTATTATG
GATAGCTTTAAGTGAAGTTTGAAGCATGAATTGTTACTGAATATGTGACT
TAAAGCAGCTCAAGATTTAAACATGTAGGAATTGTTTATATTTTTGCCTG
TGAAAATCGAGTTGTTTACTAATACTAGACTGTAGCCCAATGAATTATTA
GGCTGCCAATCCATCCTTGGAGACATTTATTCTTGAACATTTGTGGTTTA
ATACACATTTTTGAAACTTCTTAATTGGACATCTTATGTACTCATGCATG
GCTTCTTTATGATTCGTCATGAATTTGCAATACATTACCTGAACCTCTTT
AGTCACAGTAAGATTACGAATGCATGCTATCATCCTCAACTTTTTCAACC
ACTATATCTTTTGTCCACACTGGGCTGCGAGCAACTATGGCTCTAGTCTG
CATAAGAATTAGAACAAAACCTTGATACTAGACTTATTTAATCCAGTGTA
TCGATTTTGTGGATGAAGTATAATTTCAGTTGACGTAACAGCCTAATATT
AGGCTAAGTAGCACTAATGTTTTTTCTAGTATATTCAGATGTCTAGGATT
TTAATAAAACTCTGGCTTGTATATAAGTTTTTGTAGTGCTCAAGCTAGGA
ACTTGATCTAGGGCATGGACTAAAGGATATGACATTTCACAAATCAAGAT
AATAAAACATTAAAAAAATTATGATAGTACTGGTTAATTTTATTTATAGT
AGATGTCTTCCCCAAACGATTTGTTCAAATTTGCTGCACCAACTTTGTAT
AAATTTTTTACTGACAATCACTAATTTTTTTTACTCTATAAACCACTGAA
TAGGAAAATAGTGAAATTGTAATTCAAAAAAAAAAATTAAATAAACACAG
GGGTAGTTATAATAGATAGGGTCCTTGTGTCTTCATGTTCTGTTAATGTT
CCTTTTGTCCTGGTTTATTGGTAATTGTTTTTTCTGTGGTGGAATATATA
TCCTTTCACATTGCATTCACCATCCTTGACCTTAGTTTTACTTATTAATA
TTTTTTGTTAATATTGCTCTCTACTCTGCAAAGACTTTCCATGTTTCATT
GTAATGACAAGTAATCATTGATTCCGGTTAACTAAGTCTGTCTTTATCGT
GGGATTATGGTTTTTATATAACCCCATAACATCTAAAATTGTTAATTCCT
TGTCAGGTTATGGATCTTGCATATTTACTGGAAGGTGAGAACTGAAAGCA
TCAGTACAAAATTAAAATTTATCGACTTGTTGCTTATTATGACATCTAAT
ATGTGCTTGTTCATATGACAGTTCAAACTCGAGTTCATTCGGCTTTAGCA
CACCTGCATTTGCACCTATTAGCCCTCAGGGGAAGAGTTCCAAACTCCAA
ATTCATGTGGTTTGGTCTTTAGCTTTGACACTGTTTATTACTTTCCTAGT
GGTCGATGTTCATATTCACCCCTTCTGCAATTGAGATCTATTGCCAAGTC
TTAGGAAATTCCTAGATGCATCTGATTTTTGGTTGCTAAAATGTTATTTG
TAGTAGATACCAATATTTATTTATTCTCATCTTGTGTCTAAGATTTATTC
CAGAAAAATAATCTCAAGTTAGGATGTCACGTATCAGTAATTTTTTTAGT
AACTTGTTATGCATGAAGAATGTTAAGAACATTGGCTAAGTGATTTTTTT
TTTAA
Sequence Length: 
6155
Sequence Checksum: 
7611cc6567858a3e090d4112506291b4
View location in JBrowse: 
Gene: 
LOC108216932
Gene Biotype: 
protein_coding
Gbkey: 
Gene