DCAR_001714

Resource Type: 
Gene
Name: 
DCAR_001714
Identifier: 
DCAR_001714.gene
Locus Tag: 
DCAR_001714
Publication: 
Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, Bowman M, Iovene M, Sanseverino W, Cavagnaro P, Yildiz M, Macko-Podgórni A, Moranska E, Grzebelus E, Grzebelus D, Ashrafi H, Zheng Z, Cheng S, Spooner D, Van Deynze A, Simon P. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.. Nature genetics. 2016 06; 48(6):657-66.
Relationship: 
There are 2 relationships.
Relationships
The mRNA, DCAR_001714, is a part of gene, DCAR_001714.
The genetic_marker, MK007959 1_19637328, is located in gene, DCAR_001714.
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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

For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins.

Data from this analysis can be viewed in JBrowse here.

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Transcripts: 
Transcript NameIdentifierTypeLocation
DCAR_001714DCAR_001714.mRNAmRNADCARv2_Chr1:19636710..19638153
Sequence: 
ATGCTTCCCTCATCCTTTAAAGGAGTTCTTGAACTTCGAACTATGAGGAA
CAAGAAAATGTATGACAATCTTCACTTTCTTGCTATTCTTGAAGAGTTTG
AAGATGAGTGCTCGGAAAATCACTGTTTCCTTTTTTCTCTAAAGACAACT
CGGTTAAGAAATGTTCAGTTTTCCGGCGGTTGGCCCGAAAATTACATCAA
AATTATGCTCAAACAACTTCTAACATGCCTATCTAAATTGGAAGAGAGTG
AAGAAGGAAGCTCTGTGGGAAAGTTGGATGTTGATCAAATTTCCGTGGAT
GCTGAAAAGAAGCTTGTCAAGATTGTTGTGGGAATGACTAGTTACAGGCC
TTTTGGTTCTCTTTCTTTCCAAATTACGGGGCCTCCTGAAGTGAAAATGT
ATGACGATCCCCACCATTTTGCTATTCTTGAAGAGTTTGAAGATGAGTGC
TTGAAAAATCACTATTTTCTTTTTTCTCTAAAAACAACTCGGTTAAGAAA
TGTTCAGTTTTCCGGCGGTTGGCCCAAAAATTACATCAAAATTGTGCTCA
AACAACTTCTAATATGCCTATCTGAATTGGAAGAGAGTGAAGAAGGAAGC
TCTGTGGGAAAGTTGGATGTTGACCAAATATCTGCGGATGCTGAAAAAAA
GCTTGTTAAGATTGCTATGGGAATGACTAGTTACATGCCTTTCGGTTCTC
CTTCTTTCCAAATTACGGGGCGTCCTGAAGTGGAAGAGCTACGATGTGGA
TACCAAGCTAAATCATATACCTGGATGGTAGGTGTCCAAGGACTCAAATT
GGGTTATGGGATCTCCGAAACGGATGATATTAACAGGAGGATACTCAGAG
GCGGATCCTGAAAGGGGCAAGAGGGGTCAGTCGACCCCCTTAAATTTTTT
CCTTAATTTTACATAATTACATAATGTCGTGGACCGGTAAAAACTCTAAA
TATTAAATTTTTTATCTATTTTATTATTTTGGTATTCACCATTCTAATCG
ATGTAGACATGACTTATTTATGTTATGTAACGGTAAAGAACTACATAATA
TGAATATTAAATTTTTTTTTTCATGTGTTTATTCCGATAGATCATCGTTA
CAAAATATTATTTACGACCTCCCTTACTTTCGAAGTTGGATCCTCCACTG
GGGATACTTTCTTGAATGTGGCAAGTTTCTTGGCAAGTTATAAGAGGTTA
TTGGACTCTTGGTCTGACATGATCAAACTACTGCCTGCTTTGTCCAAACA
GTTATGTAAAATGGGAACGTGTCAAAGGTTTTCCAAAGATTTCGGATCTT
TTGTTGGATTGTGCTTTCAAGATTTTAAAAAGCGCTTCATTCCTAGGCAA
GCCCTAAAACATGGGTTTCTGAAAGATGCAACAACTGAGAAAGAAATGAT
CAATAGCCTAATCAAAGAAGGAAGGGTTGGAAGAAGCGAATAG
Sequence Length: 
1443
Sequence Checksum: 
430435db84681244f232b5b1f5bd6634
View location in JBrowse: 
Cds: 
>DCAR_001714cds ATGCTTCCCTCATCCTTTAAAGGAGTTCTTGAACTTCGAACTATGAGGAA CAAGAAAATGTATGACAATCTTCACTTTCTTGCTATTCTTGAAGAGTTTG AAGATGAGTGCTCGGAAAATCACTGTTTCCTTTTTTCTCTAAAGACAACT CGGTTAAGAAATGTTCAGTTTTCCGGCGGTTGGCCCGAAAATTACATCAA AATTATGCTCAAACAACTTCTAACATGCCTATCTAAATTGGAAGAGAGTG AAGAAGGAAGCTCTGTGGGAAAGTTGGATGTTGATCAAATTTCCGTGGAT GCTGAAAAGAAGCTTGTCAAGATTGTTGTGGGAATGACTAGTTACAGGCC TTTTGGTTCTCTTTCTTTCCAAATTACGGGGCCTCCTGAAGTGAAAATGT ATGACGATCCCCACCATTTTGCTATTCTTGAAGAGTTTGAAGATGAGTGC TTGAAAAATCACTATTTTCTTTTTTCTCTAAAAACAACTCGGTTAAGAAA TGTTCAGTTTTCCGGCGGTTGGCCCAAAAATTACATCAAAATTGTGCTCA AACAACTTCTAATATGCCTATCTGAATTGGAAGAGAGTGAAGAAGGAAGC TCTGTGGGAAAGTTGGATGTTGACCAAATATCTGCGGATGCTGAAAAAAA GCTTGTTAAGATTGCTATGGGAATGACTAGTTACATGCCTTTCGGTTCTC CTTCTTTCCAAATTACGGGGCGTCCTGAAGTGGAAGAGCTACGATGTGGA TACCAAGCTAAATCATATACCTGGATGTTATGTAAAATGGGAACGTGTCA AAGGTTTTCCAAAGATTTCGGATCTTTTGTTGGATTGTGCTTTCAAGATT TTAAAAAGCGCTTCATTCCTAGGCAAGCCCTAAAACATGGGTTTCTGAAA GATGCAACAACTGAGAAAGAAATGATCAATAGCCTAATCAAAGAAGGAAG GGTTGGAAGAAGCGAATAG
Pep: 
>DCAR_001714pep MLPSSFKGVLELRTMRNKKMYDNLHFLAILEEFEDECSENHCFLFSLKTT RLRNVQFSGGWPENYIKIMLKQLLTCLSKLEESEEGSSVGKLDVDQISVD AEKKLVKIVVGMTSYRPFGSLSFQITGPPEVKMYDDPHHFAILEEFEDEC LKNHYFLFSLKTTRLRNVQFSGGWPKNYIKIVLKQLLICLSELEESEEGS SVGKLDVDQISADAEKKLVKIAMGMTSYMPFGSPSFQITGRPEVEELRCG YQAKSYTWMLCKMGTCQRFSKDFGSFVGLCFQDFKKRFIPRQALKHGFLK DATTEKEMINSLIKEGRVGRSE*