| Relationships |
|---|
| The mRNA, DCAR_027490, is a part of gene, DCAR_027490. |
| The genetic_marker, MK004249 K1693, is located in gene, DCAR_027490. |
| The genetic_marker, MK018889 8_22593995, is located in gene, DCAR_027490. |
| 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_027490 | DCAR_027490.mRNA | mRNA | DCARv2_Chr8:22587530..22596601 |
ATGGCTGCTTCATTCGCCGGTTGTATTCAAAAATCTCCTCTTTCAGTTGC
CCATAAATTACCCCATAAGCCACTGTCCTTCGCTCCTGTCTCGCTCATTT
CTTACAAATCTTCGTCACACTTGGTTTGCTCTTCTGTCTCATTATCTTCT
CCTGCTAACTCAGGTAATTTTCTTCACTTTTTAGCACTACCCATTTCGTT
TATGTTCTTAAATTTAGTGTAATTTACTGCTTTGCCCAGGTGGGGTTTCA
TGATTTTTTGGGTTTATAAGTTAGCCTTGTTTTTTTAGGAGAGATTTTGC
GTATTTCTTGAGTCTTTGGCATGACCCATTTGATTTATTTTCATAAATGT
GTGTAGTTTTTGTGAAGTTTGCTTGATTCTTGAGTTTTTAGTATTGCCCT
ATCTCGGATTCTTTATGATAATGTAGTTAGTTTACAAATTGTGTTTTTAA
TGCCAAGGGGCTGGAGTACCACTGTTTGGTGGGGTTAGGGATGAGAAGAA
TTTGAAAGATAGGTCAGCATTTGCTCAGACGGAAGCTGTTCGACACTTGA
CTGGCTCCCTCACTTCTGCTGCTGGTTTTCGCTTTGCTGTTGTATGTACT
TCTGCACCTATTCCCTGCACATTGATACATGGACACCTGCATACACTTGC
ATACATAGATAAAACTAAATGACTGCTACCCGGTATGTTTTGCAAGCCTA
TATCCTGCTCATAAGGGTAGAGTCGTAGAGCGGCAGTTTCTTTAAAATTC
CTTTGCTTTGGCCGTGCTAGTAATTTCATATGAATAAAAGACGAGAGATG
ATATATATCAAGCAGTAAAATATTATAGCTCAACTTCCAGGTAACAAACA
TTCAGTACAATAACCAAACTAGTATATAGGTGCAGAACATGTGGACATAG
ATGTATAGAGCAGATCTTGTAACTTTAAATTACACAGCTTTCAGGACCAA
TCCCCATCATTTTATTTTCTTATATACAGACATCAATGATAGTCTCAGTT
CTGTTTTGCTGTATATGAGAAATGTGGCTGCTTCATTTTTCACCTAAATC
TAGCCGTCGATATTAAGATTACATCTAATAGTCACCCCAGATAACTCTTT
AGTAACAGCTGACCGCACCTTGTTGCTTCTTTTGGCTAGTGTAAATAATT
TATTTCTTTAAACTATCACTAATTTTCTAGCTGCCATTCTTTTCTTATTA
TTGTTATTGCAAAAGGTGGTAGCTCGGTTCAATGAGATTGTTACCAGGCC
ACTGTTGAATGGAGCTCTGGAGACGTTCAGCAGATATTCAGTTAAAGATG
AGGATATTGATGTACGTAACATTGTATATACCTGACATATCCTTATTGAT
TTACCTGTATATGTCGGTCCACTCCATACTTTCACATTCCTGTTAAATTA
CCTCGCGAAACAAGTGATGCAACAACTTAAAGATGAAGTAACATAGACAT
ACTGATTCCGTATTCGAAATGGTATTCAATAAGTATGCAATGGATAATCT
AATATTTCTTTGGACCTTTACTATGTTAAAAAATGATTTATGTTGGACAG
TGTTGTGATCTGCTAATGAGCTCATCATTTTAGTTGCCTCATGTTGCACC
CTTTGATTACATCACTTCTGACATTAGCGCATCATTGTTGTTATTATCAA
CCAGGTCGTGTGGGTTCCTGGTAGTTTTGAGATTGGTGTTGTTGCAGAGA
GGCTTGGGAAGTCTAAAAAGTATGATGCAATATTGTGTATTGGGGCTGTG
GTATGATTTCATCTCCCTAATCACAACTCAATATGTTCTTATAAAACCAC
CCAATAATTAAATTTGTTCAGATTTCTTAAAGCCCCATGAACTGTTATAT
CAAGCAGGTACTTTTGTTGTTGTAATGTTTGTCTGCATAATCTTGTATAT
TGGACATTTTCATTCAGTAAATAATTATAAAATTAAGTATATAGTGGAAC
CTAGTTGTAAGATCTGTAAATTTATTGTTTTTTTAGGTAAGAGGTGATAC
GACCCACTATGATGCTGTGTCTAATTCAGCAGCTTCTGGAATACTCTCAG
CTAGTCTGAATTCTGGTAGGTTTGAATGTTTTATTGTCTTTTTAACTTTA
TCTTTAATTAGATCATAACTTATATTTTGTTATTATAAGATTGTAAATAC
TTTCTTACAAGATTTTTCAATAAAAACAGTAACCAAATGTTTTTATTGCT
GTATAGAGACATTCCTAAAATCAAATAAAATACTATACAGACACCTAGGA
GGAGTCTTGCTAAAAAAACAACTCGTGGTAGACTAAGCAGCCACTTTACA
TAAATAATTTTTACAATGGAAAAAGCAACCAACTGTCTTTTGTTTGTTAA
AGTTATCAATGGAAATCGAAGATTTATAGCAGACACACTTATGATAGCCC
TATTAAAATTTACTAATATTTATAAGAACCTAACTATCTAAACTAATGCA
GCCACTAGACTTCACACCTTGTAAGCATAAAACAGTATATTAACCCAAGC
ACGGTCAGTCTTGCCTTACAAAATCCCTCCATGACCAAGGTTGGCGACCA
ATTTGTCCATCTGGTCCTGTCTTGAAGCTTGCTCATTCTAGCTTAACTTG
GATTTTTGTTAATATTGTTTTATTTATAAATTTCTAATATCGGTTTCATC
ACAGGTGTTCCTTGCATATTTGGCGTCTTGACGACTGAAAATATGGATCA
GGTAATGCTTTGCATAGCTTTTACTTATATGCAATCATTACTTAGGATTA
TCTTTCTTTTATGCTGTATATAGCTTTGTACTGTTCAAAGTTAGCACCAA
TAGAAAAAGAAAAACCATGTTAACCCCTTTTTTGCTGCTAAGGTTTAGCT
GAGTAAAAAAGACAGCAATTTTGATCTTATTTTATTGCTGCCAGAATGTT
AATTCCCTTACCTACACTGCATTGCAGGCTATGAACCGAGCTGGTGGTAA
ATCAGGAAATAAGGGTGCGGAAGCAGCTCTAACAGCTGTAAGTTAAACTA
TATTTGTTCATTGGTTGCAAGGGGAGACGGACAAAATATACCTGGATGTC
TGTAAAAATACGTTAAGCAGAATTGTTAATTATTTATTTCTTTCTTATCT
GTTGAACATGACCTTTTGCAATTGAGCCGTTAACACAAAATTTCAATGCT
GCTTTTGCAAATTCCATTAAAGCTTTGGTTGTTTCTCCTGTTAAAATGAT
AATTAAGTGCTAATATCATCTAATTTCTATATACAGATAGAGATGGCATC
CTTGTTCGAGCACCACTTAAAGGAGCAGTAATGCAGTTTGTTCGGGAAGG
GATCATATCATTTTCCCTGATTCACCATTTACTTTGGAAAAGGGTCGCTA
TAGTATTTTATCTTTGGAAGCACGAGGCTATATTGTTTCATTATAGAGTT
TAGAGGAACTGCAGAATTGCAATTGTAAGGGTTTGGTGGCATGAAGATTC
AAATACTGTTGAAATAAACATGAACAGTATGTTCAATGTATGAAATAAAG
ACCCTTTTTTTATTTTAATTTTAATTTTTTTGATAAGAAAATAAACAATT
TCCTGTTTTGAAATGTGGTGTTTGGTGGTGTTTCCTCTTTTTTGTCTCTG
AAGATATATTCTTTAAACCATGGCCATAGTAGTAATCAGTTATAATCATA
ACTAGTTATTACTATAATTTCTAAGTTTTAGTCAAATTATAAACCACATC
AAGTTGATCTCTAAATTTTAATCGAATTAGAGCATCTCCAACCATCGAAA
GCCCTTTGCTAAAAAGTGAGTTGGTATACTTAAAATAAAAAAAATTTAGC
CAACAGCTCGAAAAACTCAACTCCAACCATACTCAGCTGTTGTCTATAAA
TTTAGTCAAGGCTAAATTTGTCGAACCTCTGCAGGTCTGTAAGAAATCTG
TAGGAAGATTGCACATCATTTATTACCATATGACCTGATATATTCTATTT
TAACAATTTAAAATATTAATAACATACTATTTTTAAATTATAACCAACCA
ATATAGTCAATACCATTGAAGCAATTTTTATATAATGTATTACAGATCTC
ATTTAGCTGACGATTATAGTCAACGCGGTTGGAGATGCTCTTGTAAACTT
GATAAAGTTGGATCGTGAGTAGTTGAAGTTATATAGAACCACACATATCA
CATATAAACAAAACACACCTGGAGGCATACAGTCAAAATACACCAGGAGG
CATATAAAATTTGTTTGCACGATGAATAAAAATTTTCTAAATTATTCCGG
ATTTTTTCCAGTATCAATATTTAATTTGTACGAATATATTCTGGAAATAT
TTTTGGATAATTACATATGAGTAAGATGTTTTAGTATAATAGAAACATGT
TTATACACTACTCCCTCCGTTTCAATTTATATGTCCACTTTGAAGAAAAT
CTTTTATTTCAAATTACTTGTCCACTTCAACTTTCAATGCAAAATCATAT
TTCCAAAGTCAACTTTATTCCACGTATGACTTATTTATATTTCCTAGATC
AATCTCACTCCACATATTTTGATCATTTAATGCAATTAATGTGTGAACAT
CCATTTTTCTTAAACTGTGTGATTTTTTTAAAATAGACATCTAATTTGAA
ACGGAGGGAGTAATATTTAATTTATCTTAAACAAATTTGACATATTTTAT
ATTATTTTAATCAGGTTTTTGTGAACATACTAAATTAATAAGATAGAGCG
GAGTGTATCTTATCTCTCTGCAGGAGTGAGGAGCTGTAAACCTCTAGACC
CAGAAGAACAAAGATTGGAGCTTCAAGGGTGGTAATTAATATATAATATA
TTGTTTGATATAGATTACATATTTTTATATATATATATATATCAACCATT
CAATCAAATCCCATACAAACAAGGAAGCTTGCTAGACTCAGGTTTTTCCC
TTATGTTATCATAAAGTTTGGTTCTTGAAATTTAATGACCGACCCTTCTT
CTATATCCACATATCTGTATGTATATATTCATGGAAGGCTCTATAAGTAG
TTGAAGGTTCTTAAAGATTTCATTTTGTTTTGATTTTTACGGTTGGAATT
GAATTATTACAAGAAAGAAATGCAGTCAATAATGTTACATACATTTTCTC
CACCCCCCTTGTCTTTGAATTGTTTGTTTTCCGGTTATTCGGCTTCAAGT
ACTATTAGTAGACCTCGCTTCATTAATTTAAGGTTTGATTTTTGCGGTAG
GAAACTTGACTTAGGATTTCGAAAGAATTCTAGTGCTGTTAATGTAGGAA
CAAAAGATATTAGTTATGTTAGGAATGTTCGAGAGGATGATGAAAATGAA
GAAGATGATGATGATTCTGATATGGATTGGGAAGCCGAATTTATTGGTGA
TCTTGACCCGTTGGGGTTTTTGCCCCCTAAGAAAAGAAAAGAGCAGAAAG
AATCGAAATTGCTTCAGGATACGGAAAATATGGATTGGTGTGTGAGGGCG
AGGAAGGTTGCGGTTAAGTCTATTGAAGCTAGAGGATTGACACGTAAATT
GGAAAACATTGTTAATCGGAGGATGAACAAGAAAAAGAAGAAAAAACCAG
TTCTCAACAAGAAGAAGGGAGATAAGGTGCTTAAGGTAGACATTGATGAT
TCTGATGTTGAGTCCGAGTTGGAGGAGGATGATATTGGACTGGTTAATTT
GAATACACTTCAAGATGCTAATGAACTTAAAAATGCTGTGAGTATGCTGG
CTGGTGGGATGTTTGCAGAGAAGAGAGAGAAGACAATGGAGACTTTCGTT
CAAAGGCTTTCTCAGTTTTCAGGGCCTTCTGATCGCAGGAAAGAAATTAA
TTTAAATAGAGATATAGTGGAAGCACAGACTGCGCAAGAAGTATTAGAGG
TTACTTCTGAGATGATCATAGCTGTAGGGNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAGGGAAAGGATTGA
GTCCTTCACCTCTCTCTCCATTGAACATTGCAACTGCACTTCACCGAATT
GCAAAGAACATGGAGAAAGTATCAATGATGAGGACACATAGATTGGCGTT
TGCCCGTCAAAGAGAGATGTCTATGCTTGTGGGCACTGCAATGATGGCCC
TGCCTGACTGCTCGCCTCAAGGTGTTTCAAATATTGCATGGGCATTGTCT
AAGATTGGAGGTGAGCTTCTTTATTTGTCAGAGATGGACAGAGTAGCTGA
GGTCGCGTTGACCAAAGTTGGTGAGTTTAATTCACAGAATGTTGCAAATA
TAGCAGGTGCTTTTGCTTCGATGCAGCATTCTGCTCCGGAGCTCTTTGTG
GTGTTGTCAAAAAGAGCTTCAAGCATAATTCACACTTTCCAAGCACAAGA
AATTGCACAACTTTTGTGGGCTTTTGCTTCTCTGGATGAACCTGTGGATG
CTGTGCTAGAATCATTGGATAATGTTTTTAAAGATCTGGACCAATTTAAA
TGCTGCCCAGCTGAAGAAAAAGTTAACTACATTGAAGCAAGAAGTATAGA
AACCAATCTTGATGACGTTGTAGATTATCCTGTTCTCACCTTCAACAGAG
ATCAGCTCGGGAACATTTCTTGGTCTTACGCTGTTTTTGGGCAAATGGAA
CGCAGTTTCTTTTCTCATGTGTGGAAAACGTTAAGTCACTTTGAGGAGCA
ACAGATTTCAGAGCAGTATAGGGAGGATATCATGTTTGCTTCCCAGGCAT
ATCTTGTTAACCAATGCCTGAAGGTTGAATACCCACAACTTCGGCTGGCT
CTCAGGAGTGATCTTGAAGAGAAAATCGTCCGTGCCGGAAGAACTAAGAG
ATTTAATCAGAAAATGACCTCCTCATTCCAGAAGGAGGTAGGTCGCCTTC
TGGTAAGCACCGGAATTGATTGGACCAAAGAGTACGTTGTCGATGGGTAC
AGCTTGGATGCAGTCTCAGTTGATCAAAATGTTGTTCTTGAAATTGATGG
GCCAACACATTTCTCCAGAAATACTGGTGGGTGCCAGAATAGCCTGTTGT
CATTCGTGAATTACTGTCTTTTTTTTCAGTTTGTTTGATTCAGTTATACA
AAATGAATATTCTTAGTTTGCTTCAATGATTATATGCATCTCTGCAGGGG
TCCCTTTGGGGCATACTGTGCTAAAGCGCCGTTATATTACTGCTGCTGGT
TGGAAGCTAGTATCAGTGTCTCACAACGAGGTAACTTTCTAAGTCTCTTT
CATGGTTTTATATTCATCTTTTAAAGGAGAAAATGACATTGTTACATCAA
GTTTTTTAGTTCAAGTTACCAAAGTTTCTACCTTAAAAGTAGTTCTCTCT
TTGGAAGTCCAAATGAGTTGAAGAAACAGAGAAGAATACGGTGTGATGCC
TTTTTGAGCTTGATGACTCTTAAATGCTCTACTATATAAAAGCATATGAA
ATGTTCCTTTAGTATATATGGAGTTCAACTTGAACGCTAAGAAATATGCG
ATGGTTTTGCTTAGAACAGATTTATTGTCAAGGAGTAAAATGGTTCTTGC
CAGTTGTAAAACTTATAGAAAAGTAATTGCTTAGTCAAAGAGGAAATAAT
TGATTGGCATGAAATGTGAAAGATGAATCTCTGCTGCCCGAAAGCATCTT
TATGTTAGTATGCCCAAAGTTAGGATCATGCTTCTACCCATGCCTGTCTC
CCAGGACTTCTTATATTGCAAGGACTAATATTAAAACTGCCTTGTCATGA
AAAGAATGAGAACTAGTTACAGGACTATTTTAATGATTGAAAATGAAGCC
TCTTTTCTTTTGACAGGGACTAGATAGAAGATAACTTGTGTTTGGAATTT
TTTTTTGTCCCCACAAATAATTGTTTTTCATTTTCCAAAACTATAAACTC
TCTACCAGTTGCTATATATTATACAATTCATCCTTCCTGAAACATTATAT
TTTTTTGGAAGTAAATTGAAAAATGACATTTGGTTTTATGACAGTAGAGT
TAGTATTTGGTTTCAAACAAGGGATATAATATTTAAACTATTCTCAAACT
TGATAACGAGTGATAGCCCTAGCATTGGTGGTCTTTAGTGACATCATAGT
CATTTTCTCATAGTAAACTGCAATTTAAACTTATCATATGCTTGCTGAAA
CACTTAGTAGAAGCTCTTTTTTAATAGGCAAGTTATCACTTTTTCGACCC
GAAACTCCAAAAACCTTGAAATTAAAGTAAACTATACTGTAGATTCTTGA
CGATTTAGAAGAAGACTTGTGATAAGGGTTCCTACAAGCTTTTGTAGGGA
TGGTTTAAAATCATCAAGTTGCCAACTAAGGAGACCTTCAACCTTTACTG
CTCAGAAATTACTACATATAAAAAGCAAAGTCAGCTTCAACAACATATAT
TTAATTAAGGGTAAATGAGCTAAATCATCAATGTACTATATTAAAACTTT
CGGTTGGATCACCAACCCGAAAAGTTTTCAGTCAAATGCTTAATCTATGT
CAAACTTGCGTATAGGTTAACACTGTTAGTCCCATTAAAAATCCCATTGG
AAATGTGACGTGGAAGCTTACATGGCATCAAGTTTAACAATGAATTCGTC
ACTCAACTTTGTATCATTTTCAATTAGGTCATCGGCTAAATATTCAGAAA
GTTTATGGTATAATTAAATTTAAAATAAAATATAATTATTTAATACATAT
ATTTTTCAATCGATACAAGCAAACAAGTATTTATAGATAAACCATTTTCA
ATTCAATTTTTTTCGATATCAATGAATTGTACTAAAGTATTAATTTTTTC
AGTGTTTGATTTTATCCGAATGATTAAACTTTAAACAAATTCAAACTGAT
ACAATTATCATAAACTGTTTGTGTCCACTCCCTAATTTCCTGTTTCCTCT
TTATATGTTTCTGTCACATCTGTCTGGATTTTTGTGTTCTTATATATCCT
ATTATGTTTGGTTGACTCTTTGCAGTGGGAGGAACTCCATGGGGAATTTG
AGCAGCTAGACTACCTCAGAAAAATTCTTGAAGATCATATTGGTGGAGGC
AGCGACAGTGATACACAATGA