| Relationships |
|---|
| The mRNA, DCAR_016127, is a part of gene, DCAR_016127. |
| The genetic_marker, MK008759 85036.705, is located in gene, DCAR_016127. |
| 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 | |
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. |
| Transcript Name | Identifier | Type | Location |
|---|---|---|---|
| DCAR_016127 | DCAR_016127.mRNA | mRNA | DCARv2_Chr5:486451..493889 |
ATGGACCCGAACATCATTCCTCAACAACAAAACCAAACTCAAATTACATC
CGCTTCAAACCTTAACAACAACAACAACAACATTAACTCAATTGATCTCC
CTCAACTCACACCCTCAAATCAACAGCAACAACAATTCAATTTACAACAA
CAGCATAGTAATAATAACATGATGGGGCCCACTTCAAGTTTTCAGATGCA
GAGATCACCGTCAATGTCTAGGCTACAGCAACAACAGCAGTACAGCCTCG
CCGCCGCGGCCCGGCAGCAGGCCGCCGTCGCCGGAATTTACGGGCAGATG
AGCTTCGGTGGCAATGCTTCTCAGCAACAACAGAATAGTAATAATTTAAA
TAACAATAATCAACAGCAGCAAATGGGTCAAATGGGTCAAGTGGGTAATG
CTAATTTATCGCGGTCCGGGTTAATGGGTGCTCAAGGTGGAAACTTGCCG
ATGTTACCTGCTCAGGCAGCTGCTCAGCTCAATTTGCAGTCACAACTTTT
AGCTTCGGTATAAATTGCTTTGTTTTACGGTTTTCTTTAATTTTTTCGAG
TAAAGTCTGTGCCTTTTTTGCTGAGAATTCACTTGTTTATTACTCGGGAT
TGTATGATGTTCTATTATTTCCACACCAAATCTGCCCGAATTTTGTTGAT
TTAAGAACTGTGCAGTTATGTCTTTGATTTGAAGATACTTGGTTGAATTT
CAAGTTTCCTGCTATTTTTTTTATTCCAGCAGGCTCATGTTTTTTGTAAA
TTGATTTTCCCACTAGTTTTGCCTTCCATGTGATATTTTCCGGTGTAACT
TTTACACCTTGGCAATCATCTTGATATTCATATTTTTAGTCTTAAAATGT
GTTGTTTGTACCGAGAATTGTGGCGGCATAACTAGATTTTGAAAAGGAAA
AGAAAAGATCACGCTCAGCCTACTTTTTAGTTGTTTGTCGTCACTGTTTC
TAGATATTACTGAATTCGTCACAATAGACTTATATTGCAGTTATATTCTC
TGTTATATTATTATATTGAGACTTTGATTGGAAATGTATTGTCTCAGACA
CGTGGAAGATCTGGATTTAGTATAAACTATTCGTCAGTTGTGTAGCTTAT
ATAGCGGTTGCATTTAATCAATTGAGATTTCAGTTGTTTTTGTCGTGGTC
ATAAATTTGCAAAATTCTTTATTTTGACGTTCTGTTTCTGAGACTATGGA
GTTTCAATGCAGCCAAGGCAGAAAACTGGGTTAGCACAAGCAGGGACACA
ATTCCATCCGGGAAATTCTCCTGCACAGTCTTTGCAGGGAATGCAAGCAA
TGGGAATGATGGGAAATTTTAACATAGGCTCACAAATCAGAGGGAACGGA
TCAATAGCATACACACAACAGCGTCTGAACCAAGGACAAATGAGGCAACA
GTTGTCCCAGCAAAATCAACTTAACTCAACACAGGTGTCTTTTTTGACCT
ACTATTTTGTTATTTTTTATATATCATAAACTCTCGCGATCTTCAGTGGA
GAAAATGAATAATCATCTTGGCTAAACCGGCATCTATCTGAATTTCCTAT
CATTCCAACTTAATATTGGAATATGGTAGATATATAACTGTGACACTATT
TTCTGTTAGAAGGTGTTTATTTTTTCAGGCAAGACATTATATTCGGCTCG
CTTATCTTCTTGACACTCTTAGGATATGAACTTAATAATTGTCTTATGAG
CTATTTTATTTCAATGTTGATGTTTGTACTAATGGCACTTGTAAGCACAT
GAAATTCTGAAGGGTTCCACTTCATGTATTTTGGTGGACTTAACAATCAA
AAACTCAGTTCTGTGGGGAGACAAAGTGGTCACTAACAACACTTTTACTT
CTTAATTTCCTATTTCTTTGTATCTGAACATGGTTTTAAAAAGCTGACAG
GATATATTATGATTTAACATCCTGATATTGGTGATACGGTTGTGCAGATA
ATTGTGGTGATATATATTTCAGCGTTCAATGAGAGGATAACATAATAAGA
CACTTCTCGAGGAATTGCCGCATCTGTTATTATCGTGATAATACTTAGTT
TTTCTATTGAGAATATCTAGAATGGTATTAGGTTAAGTTTCAAGAAGTCT
TGATTAGTAATCTGTTTGAACAAAAGTTTTATCCTCCAAACAACCCTCAG
AACAAATTCCTTCTCATTTTGGGATCACTAATCTTAAATATTTTGGTGGT
GCCTATGAGTTTGTGTATCAAAGGATTGTTGATTTCCAGTCTCGGGTAGT
TAATAGGTTAGGATGATGCCTGCCTTATTTATTATTTATTGGTGTAGATT
TCTTCGAACCCCTCACATATTCTTATTCCTAGTTTTGGTCTTGTAAATAT
ATATGGTATTCTCTTTTATATATATTCATTCATCTTGCACTAGATATTAA
GAGTTTGTATATAATGACCAACTTACCCAATAGGGGTGGCAATATCAGAC
ACGACCCGAAACCCGACACGAACCCGACCCAACCCGAAACCCGATTTACT
GAGACAGAAACCCGAAAGTGACCCGAAAATCACCCGACAGACCCGAAATG
GACCCGAAATGACCCGAAACTAGAATTTCATTTGTAATAACTTCAATTTT
TGGTTTTATTCAATTTTAAGTGATTTTAGGTTGACCCGAAATCGACCCGA
TTGCTGACACGAACACGACCCGTTACCCGAAATTGCCACCCCTATAATAC
CCAAGTAATAAATAAATGCATTAATGCTCTACAACTGGAATATAAGTGAA
GATCTTTCGTTAAAAAAAAAAGCAGAATTCTTTAGTTTTTTTTTTTTGTG
TGTGTGTGTGTGTGTGTAAATAGGTAGGAAAGTCATATGCGGGAATTTAA
GATGCAAATATCACAAAGTAGTTTCTTGTTAATTGATTGTGGTGGTTACG
CCCAATATCAAAAGGCGAAACGGTACTGTTTTTGCTGACTACTTCCTACG
CGTATCATGCTTTTTTTTCAAAGTTGTAATAAATGCTATTCTTATCAACG
GAATAAAATCTTTATGTAACGCTTATCTGCAGAAACTACAGGCACAAAGT
CTTGGGAGGACATCCTTTATAAACCCTCAGTTATCCGGGTTGGCTCAGAA
TGGGCAACCAGCTTTGATTCAGAATACGCTGTCACAACAACAGTGGTTGA
AACAGGTTCCGGCAATGTCTGCACCTAACTCACCTTCATACCGTCTCCAG
CATCAGAGGCAGCAACAAGCACTTCTGCAGCAGCAGCTGGCTTCATCTTC
TCAGATGCAGCAAAATTCTAGTGCGTTAAATCCACAGCAGTTGTCCCAAA
TGGTACAACAACAGCAACAGCAATCAGCGGGACAGCTGCAGCTGCAGCAA
CAGCAGCAACCAGTACCACCAACACAACAGCAAATTTTGCATCATCAACA
GCAGTCTCCTAGGATGGCAACACCTGCTGGTCAAAAATCTTTAAGCCTTA
CTGGATCACAACCAGATGCTACTGCATCTGGAACAACTACGCCAGGTGGG
AGTTCAAGCCAAGGGACAGAGGCTAGCAATCAACTTCTTGGGAAGAGGAG
AATACAAGATCTGGTTTCACAGGTTGCCTTTATATGCCTCTGTGTCTTTT
GCCATGTTAGACAAAGCAAAACTACAGTTTTTAGATATTAATTTATTTTT
TTGGCTATGTTAAAAAAAATGAAACATCTTAAAATTAATCTCCACTCATC
AAGTTTAGACTCTTCTAGCAATTACATCGATTGACCTTTCCTTTATTCGG
GATACGTCCATCTTGACTTGGGAGCGATGAAAGTTGAAGCTGCAAAGTTT
CAAGACTGATTTATAAAGCTTCTATCGTCTTTGATTTTCTTATAATTGAT
TTCGGATGTCATTTGCGTGTAGGTGGACCCACAAGCAAAGTTGGACCCTG
TTGTGGAAGATATGCTTTTGGAGATTGCGGATAACTTTATTGATTCGGTA
AAGGCTTGATTAATTTTACTTTAGACTTTATCTTACACTTGTTTATCTAT
CGTTGGGGGTGTAAATGAGTCCAATTGTTCGTGAGTTACTCGAATTGGGC
TTGGTAGGTATTCATTTTGGCTCAACAATAATCGAGCCGATCTCAAGCTC
GAGCATTCGAATACTTTTTCGAGCCACTCTCGAGTTTCAAATTACTCAGC
TCATGAGGCTTGTGAGCCTTCGTTTATTTTACTTTTTATATATTATACAT
ATTAATATATAAGTTATTGAATATTTTAATAAATTTTACATATTAAGTCT
TGTCGAACTCTACTTTAATTTTTCAGTAGAATCACATTGGAGGCTTTGTC
AACATCTGGGAAAATCAATTCGAGCTTTTGTGTCAAGTTCGAACCTCTCG
AACTTTTGTCAAGCCAAATTCCAATCTTAAAATTTGTGGCTCAATTGATC
TCGAACTAATTAGACAAGCTAGAATTTGAGGCTCGGCTTGTTAAATCTAT
CCCATTTGTAGTGTCATCTATCCCATTTTTAGTGACAAGATCTGCAATTT
TTGTGAAGTGGGAACTGACAAGTCGTGCAGAGGACTAGAGGAGGATGAAA
CTTGTTTACTATTAACACTTAAGAACTAGCAACTCGACTAATAAATTTTA
TATTTAGTATTATTATGTTCAAGGGCTCTACTGTTACTGTTAATATGTAA
TTGTACTTTTAACTGTGGTCCTCTAATAAATTACAATATATGTCCACTAG
CTTAAACTTATTGGAGGCAATATTTGTGGTTTGTATAAAAAGTCGAGAAC
AAATATCCGGTCCACAAAATTCTTGGGGACTCTAATTGGATTTATCAAAT
ATTTTATTTTATTTTAAATAATTAAACACACACGCACCCGCCTTGTCTTT
GACAAGGTTCATGCCTTGACATCCTGTAAAGGGAGCGAGAGAGATACAGT
TGAACCAAGAGTTCGTTGGTGGATTTATTAGAATTACTGCTGTGATATGG
TATTATAGAAAGTGCTTTTCTTCAATGGACAGCTGCACATCTGTATTTGA
TTAATATTATTTTGCAAGTATAGTCCATCTGAAGGTCCAGAAAAACCAAA
ATACATACCAATTTTGTTCTGATTTGTTTTATGCATGCTTCTGCTTAAAC
AAAGTTGTGATAAAAAGTGCATTCCAGCCCCAACAGGACAGTCAAAAAAC
TTAAGTTCACATGTTTTTCATTATTGTGGCTTTTGCAGGTTACTTCATAT
GCATGCAGTTTGGCAAAGCATCGTAATTCTTCTACAGTGGAGTCCAAAGA
TGTATTGCTACACTTGGGTAGGTGCTGATTATATACATCTATGTGTGTAT
GCTGAGTAGTATTTGACTACTAGATGTCGTTCTCAATTCAGAATGGTTAT
TTCATAGTGTCACTTATATGAAATGTCTCCACCTTTTCTTTTGTTTTTTT
TTTTGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNGGGGGGTTAATGTATCATTTTATGGTTTTACAATTTATTCTG
CTGCAATCTGAGATGAATTAATTTTTTTTCTTAGTAACTGTCTCTTTAGA
TTTATATCTAAAGTGTCTGCACAAACATTTATACTGAGGGTGATCTCATA
TATATAGTGCTGCTTTTCTGTGTTGTAGTTTTATCTTTCACATTTCTTGC
ATTTTTCTTATTGGTGATTTTACTTCCAGATCTACTCTAGTTTTTGTCCT
TGACTCTAAAAAATCTTTAAATTTTATTTGTATTTACCATTTATCTACTA
ACACATTGGGAATGATGGTTGTCTTGCTCTTGCTCTACAAATGTGAGTGG
GTGTCTGTTGTGTGTATGAGAGAGAGAGAGAGGGAGAGATAAAATGTTTG
TTTTTATCATGCAGTTCTTTTTGTTTTGCGTTTTTATAATGAATTTTGAA
TATATTTTACTCTAGCTTATTGTGGTATGTACTTCCATAAATATATTCTC
ATCCTTAACTTTGGCGGTAGTATTGTTTTATTGATATTGGGCCTGTAGCC
TTTTAATGTCTCAGAGGTATCTCTAAGATCTCAGTATTTTTAATGAAAAT
CACATGCTTCTAGACTGAAGTTGGGTTATGCAACTATTCCATATACTGAT
GACAACTTGAATACATATCCCATCATTTTTTATGATTTCGAAATTACTTG
TAAAAAGTAGGAAGTCAACTTGTCCCTCTATCCCCACTTGGTACAATACA
TGCGGATATATCCCATAGAGTAAAAGGTTTGTTTAGTAAATAATAATACA
GGTCTTGCATATATTTAGTTGTAAGTATGTTTGCTGACTGCAGTTATTGG
TAAGAAAGCCTGGATCGCATATACTCTCATGTGGACTGACCCTTCATTTT
TTACTGTGCAGAAAAGAACTTAGGTTTGTCTATTCCAGGGTACTCAAGTG
AAGAGCGGAAGCACCAAGAAAATGATGTAAGACTTGAGTTTACTTTAGAG
TATCTTTTAGTGGTGCAATAGTGTGCACTGTGCAATAGTTAGTTTTTTCA
TCACCATGTAGGAACACTAAAAATTCAAAAGATTTAGGCAACTACCTTCT
GCATATACTTTGGTGCTAATGTTTATACTTTCAAACTTTTGTCGGAGAAG
TAGTTATCGTAATTGATTGTAAATATTATTTTGCTTCGTTGATTGACTAA
TATAAAAGGTAAACTTGCTTGTAAACTGTGTGCAATTCTGCTGTATTCAT
TATGCTTCTTTTGACATGCTCTTTTTGCATCTCATTTCTAATTCCTTTAT
TGAGTCACTATATTAGAATGTTAGGCAATTCCATTTGGACACTGTATGCA
ATTTAGTGTGAGTTCAAAAAGATTATAGCAAGGAAGCAGTATTGATTTTA
TGCTTGATTATACTTGCAGTCATCAAGTCATGCCCACAAAACTCGACTCG
ATAAGGTAAACAGGATATCTTTTTATCTTCACACTGCTATTTAACTGTTT
TATTCTCTCTTTTGAATATATTACTTGCTGCAAAACTATTAACCCAGATA
TGCTCTATTACTCAGATACGCTCGTTAATGGAATCCTCAAACTCCGACAC
AATCAATGCTAACGAGGTGACTGGACAGGGGACTGGCAACTCTGTGGGTG
CCAACCACCTGATGAGGCCTTCTAGTTCAGATCAGCTGGTTTCTCAAGTG
CAGCATCAGATAAAAAGGTTCAATTTTAACACATCTGTTTTCATAGTCAT
ATTCTTATAGTAAATAACTAGATTTTCTAATGTTACATTAGAAGGGGTAA
TTGAGCTTCTTATTCTCTTAGAGCTATTATTTTTTATACGTTTTAAGTGT
TGAATATCTGTTGCAGGTTCGGTTCGGTTGACGAGTGA