LOC108195923

Resource Type: 
Gene
Name: 
LOC108195923
Identifier: 
LOC108195923
Cross Reference: 
NCBI GeneLoading content
Relationship: 
There are 2 relationships.
Relationships
The mRNA, XM_017362940.1, is a part of gene, LOC108195923.
The genetic_marker, MK001118 GSSR-119, is located in gene, LOC108195923.
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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_017362940.1XM_017362940.1mRNADCARv2_Chr7:18266848..18271152
Sequence: 
AAATTGTTATTACAAGAAAATGAATTTTAAGTAAAATATTGGTCTGAATC
TCATGGGCATTTATGAGTCGTCGGCAGCACTAGAGTAATACCAAGTGGAG
ATACAGTAGTAAGTCATACTAAGTCAAAGTGTCAAGAAAGCTAAAACCCT
CAAATCTCTGCACACTCACTTCACTTGCTAGGGTTTGCTGCTTCAGCTGC
TATTACTTACAACTTGTATGTATGTATGTATACTTGTCCGCCCACTTAAT
TCTTCAAATTGTTTGCATTTTTCTATGATCCCAACTTGCGCATTCTTGAT
CCTATTTTGGTCTGAATTACAGACTATACAATACCCAGATTTGGATTTGA
TGAATTTGTTTCAGATGTGTTGCTCCTTTTTACTTTGATAACTTCGAATT
GAGTCGTTGATATAGCCTGATCGTATATCGTTGATATGAATTTCTTGTCT
CGAATTAAATTAGTATTTCTCAGTGGGACAAGGAGATGGGTTTTTGTGGT
GGTTTTAGTAGCTGTAACTCATTTATTTTGTCAGTCCCTCATGCTTCCAT
ATACGAATTCTGTGCTCTCTCTGTTGCAACATGGCATGCTCCCACTGCAG
GGGCAACTCAACATCGTTAATGCTTCATCCGTCAGCAATGACTCCGAATC
TGCAGCTACTACTCTACGCCTGGACAAGGGATCTAAAAGCAGTGATAATT
CAGATATCAAAGTTCCCTTGGAGACGGATTTCGATATGGAAGGAATTCAG
GTGGAGAATGCTCGTCTTCAAGATGATGTCTACACATTGGAGACGAAGGC
CAGCCTTTCACTGAAACAGATTGCGGAACCGATTACTTCAGTTTTTGAGA
AAGATGTTCCACATATAAATGAAAGTCTTGCTTTAGATATTGCGAGTGCT
CTTCCATCTCCTCTTGTTCAATTAAGGGAAGGGACTTCTTTGATCAACAT
CACATTTCCAACTGATTCCACAACTGTAAGCATCGTTGACCATTCAACTC
CAAATATTTCCTTGCTTGACCGAGAAATGGAGGAATTCCCAACTGATGGA
GACCTTATACTTCTTCCAAGTCATAATTTGGTCAATGTTTCGGCAAACAT
GAGTAATCCTGTTAAGAAGAAAATGAGGTGTTTGACGCCGCCAAAGTCAA
TAACATCACTATATGAGATGAATCGTTTATTGCTCAGGCATCGTCGTGCA
ATGGTAAAAAGGACTTTTCTTTAAATATTGGAATCATTCATTCTCTGAAT
GCAGTTGTAAGATTTAATTTTTCTTCTTTGGATTGTTTGTAGAGGCCAAG
ATGGTCCTCAGAACGTGACCGCGAAATTTTAGCTGCAAAGTCACAAATTC
AAAATGCTCCAATTGTGAGAAACAATGCAGAACTGTTTTCTCCTCTCTTT
CGTAATGTTTCCACGTTTAAAAGGTTAGCATTCGTTTGTACAGAAGAATT
GAATTCATAGGATAATACTCAATTTTATATGTAGAGGATATTGTAAAAGT
CTGCAGTTTTCAATTTTCTGTTGAAGGCGACCTCTACTTATAGGAGTACA
TTGCTTAGATAGATAGTCATGTCAAAAAATAGATGTAATGGCCTAATGGG
TTATTATGCACTCCTTCAAATTGGAGGATAACAATACCATTTTCACTTGA
AGGTACTTTCTAGAAATGGACAATTCCAGTCATCTTAATATGTTCACTCC
CCCTTGTTGCACTTATTCGTCCTCAGTGTCTTATTTTGTGTCCCCCAAAG
TTATTGTCCATATTCAGTAAATATAATAAATTATGTCAATTTTATGGTAA
CTATTGGTTTTATATATTATGGTTAGATATTCTAATTATGGACAAAATTA
GTGTGGGGGGTAAAAGTTATTTGATTTATATATCTGAACTATAAATCGAG
TGCGCGTGTCACTTTTATAGTTATATGATGCTAAACTCACTAAAATCCTC
TAATACTTGCCCACTACAACTTTAGTTTTCCAGTGCTGCAACGTGGAACT
TCAAAAATTTGCTTCATGTAATAATCTTCCTCATAGACTGTATCTTATTG
TTATTGTGTACCTTCAGAAGAGAATAAAATCCAAGTTGCTAAAGTAATAT
AAGTGATAATGAAAAGTAACTAGGGAGAGTACTTCTGTGAAAAGTTTTTC
GACTTAATATTATTTTGTTGGCAGGAGCTATGAAATCATGGAACGCGTAT
TGAAAGTTTATGTATACAAGGATGGGGAAAAGCCTATCTTCCATCAACCC
GTTCTCAAGGGCTTGTATGCATCTGAGGGATGGTTTATGAAACTGATGGA
GGGAAATGGACAATTTTCTGTGAAGGATCCCCGAAAAGCACACTTGTTTT
ATATGCCCTTCAGTTCTCGCATATTAGGGAGCATGCTATATGTACCAAAC
TCTCACAATCGAACAGGTCTGCGTGGGTATTTGAAGAATTACGCTGAGAA
GCTTGCAGCAAAATATCCCTTTTGGAACAGGACTGGTGGCGCAGATCACT
TCCTTGTTGCTTGCCATGATTGGGTATGCTTCCTATCTGTCATGATTTCA
TGAATCTGCCTCAGTTCCTTGATTGTGCTGAATGCCTGTTGAGATACCCA
GAGTCCCAGACATACATAAAAGTTTTGTGTTTAAACTACATCTTACTTGT
CAAATGCTGGGATTAGGAACATTAATGGAACTTCTCCACAAATTTAGAGG
TATATTATACACTAATACAAGCATAAATGATAAGGGCGCACAGATATAAG
AGCCAGAAGCATGAAGAAGCTATTGAGATATTTTATATCACAGTTGCATA
GTCAGTCAAGTTATAACTTCTCAATCACCTTACAATTGCTTAGTCTATTC
TAGTTAGTTTCGAGAGCAAGGGGAGCTTCTTTGATTAAGACATCCTAAGT
GCCACTGTTGTTGGCTTTAAAACTTAAATTAGTCTCAGCATCTTTCATCA
ACAGCAACATGGTTCCCCAGATGGTACACGAGGCTTCCAATCAATATCCA
GTTATTTCATTGAGCCCTACAGATTTTACTCCCCTATTTAGTCTCTTTTG
AAAGTGGTTCTCTTCAATCAGATGGTACACGAGGCTTCCAATCATATGCT
TCTTTGATCGATGATTCTCTTCAATCAGCCACATACTTTGAGCAATTATG
TATTCAAATAAATGGATGCTAAAGTGATGAAATATCATTTGAAAATAATA
ATGTGCCAAGTTTTAAAATATAAGTGTAATATTCAAATGCCTTCTCTGCC
TATTAAATGCATTGATAGATAGGAAAGTCTGCTATTAAATGCATTGATAC
ATACCTTGCATTTTTTACAGGCTCCGTATGAGACAAGGCATCATATGGAA
CACTGCATTAAAGCTCTCTGCAATACAGATGTAACTGAGGGCTTCAAAAT
CGGAACAGATGTTTCCCTGCCAGAAACATATGTGCGATCTGCAAGAAATC
CTCAAAGAGACCTCGGAGGAAAGCCACCTTCTCAAAGACATGTACTTGCC
TTCTATGCTGGTAACATGCATGGATATTTGCGTCCTATATTGCTCAAGCA
TTGGAAGGATAAAGATCCCGACATGAAGATATTCGGTCCAATGCCTCCTG
GTGTTGCAAGTAAAATGAATTACATTCAGCATATGAAGAGCAGCAAGTAC
TGCCTTTGCCCTAAAGGGTATGAGGTCGCCAGCCCTAGGATTGTTGAAGC
CTTCTTTTACGAGTGCGTACCTGTGATTATATCTGACAACTTTGTGCCGC
CATTTTTTGAGGTTTTGAATTGGGATGCATTTGCGATAATTCTAGCAGAG
AAAGACATTCCGAACTTGAAAAATATACTTCTATCCATCTCTCAAGAGAA
GTACCTAGAAATGCAGCTTGCAGTTCGGAAGGTGCAGAGGCATTTTATAT
GGCATGCTAAACCGACAAAGTATGATCTCTTTCACATGACTCTTCATTCC
ATCTGGTACAACAGAGTGTTTCAGTTCAAACCGAGATAATAACCTGAGAT
ATATTTCTTCGAGCATCTAGGCTAGTAAAAAATAAAACAAGGCTTAGTTC
CGAGGAATTTTCATGCGATTGAGATGCCTATAAAGGGGTGCAACATTTTG
AGATTTTCGGGGGTTTTCCTGTAACTAGCTATAGTGAGAGTGGACCTATA
CCTGATATTTTAAGCTGTTGAATTGTAACTAGCTTTTGTACATATGCTGT
AACATTTCCTATTAAAACAGATTTACCACAGATACGGACCTCGCCTTGTG
TATGTATGTTACTGGTTTATACTTTATATTAAGAAAAACCCGAATCTTAT
AATA
Sequence Length: 
4304
Sequence Checksum: 
aa472a901666a182e351f340de6d8bfb
View location in JBrowse: 
Gene: 
LOC108195923
Gene Biotype: 
protein_coding
Gbkey: 
Gene