| Relationships |
|---|
| The mRNA, DCAR_006533, is a part of gene, DCAR_006533. |
| The genetic_marker, MK016680 SSR0024, is located in gene, DCAR_006533. |
| The genetic_marker, MK011070 2_26420019, is located in gene, DCAR_006533. |
| 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_006533 | DCAR_006533.mRNA | mRNA | DCARv2_Chr2:26412802..26420187 |
ATGGAGGACAGAGAAACAGAGATGAAAGAGAAGCTAGAATCAAAAATAGG
CAAATTACACAGTGCCCAGATGGATCTTATTGCTTCTCTTCAAGTTCAAG
TCCCTGATATCGTTTCTGAAATTGATCTTTCACTCAAAGTCATATCTTCT
TATGGTGGTAAGCCTTATACACCTTTAGCTAAAACCCCACTTCCAATTCC
TACTAAACCCCCCAAGATAGCAAAAACCCAGTTCAAATCTGTGCTGAATT
TGAAGAATGAGGTTGTTTCGCAGTCTTCTGGGGCGAAACAAGAGAGTTTT
AAGGGTTTGAGTAAGTCGAATGAGGTTCCGGGTGGTGGGGATGGGGAAAG
ATTGAGTCTCGATAGGATTGGGGGTGGGGGTAAGAGTTCGCTGTCAATTG
TTAGGTATATGGTGGCTGTTTGTTTGTTGGAGAGGGTTCCGTTTACGCCT
ATCGATTCATCGACTGTGTTGATGAAATTGGAGAATAATGTTAGTGGGAG
TAATGAGGAGAAGGCTGCGTTGAGGGAGTTGGGTGGGGATTCAGGGGGGA
TTGTTGGTGTGGAAAAGGCGTTGAGGTCAATAGCAGAGGAGAATGGTGGG
GTGGAGTTGGAGGAGTTTGTTGTGAGTGGAAAGTCCAGGGTTATGGTTGT
GGAGATTGATAGGGTGAGGTTGGTTAAGGAGTTGCCGGAGAGTAAACAAC
AGGCTGTTAAGAATGAGGGGAATTTGAGTCAGGGTCAGCAGGCAGCGACA
ATAGGAGGGGGAGGGGGTGAGTTTAATAATAATAATAATGGGATGTTTGG
AATGGGGGGGCCGATGGGTAGGGCTCCGGATGTGTGGATGGGACCTGGGG
ATCCGCATTTTCCAGGAATGCCGCCGATGTTTCCTGGGAGTGGAGGTCCA
GGTGCAATGATGGGTCCAAGGGGTGGACCAAGAGGAATGGCGGGAATGAT
GATGCATAGGCCTCCAATGGGTCCTAATGGACAATTTGGTGGACCTAGTC
CGACTTCCATAAAACCCAGGAGTGAAGAAGATGATTTGAAGGATCTTGAA
GCATTACTTAATAAGAAGTCCTTTAAGGAAATGCAGAAATCGAAAACTGG
AGAGGAGTTGTTGGACCTCATTCATCGACCTACTGCCAAGGAAACTGCTG
TCGCGGCTAAGGTTTGTTATTTACTGAACTCATAGGGAACACACACACAC
ACACACACACACATCATTTCCATCTTGATGAATTAAATAAACTTGGGCTG
TTTGTTAATGACATATGGCATCTGGATTATCTAATTACAATTTGATATGC
GGAAGCATTCTTTGTCATCATCAATCACACATGGTAGACACCTTGCATCC
TAGAACAATGTTAAAGTTATCTGTAAACATGGTGTTGAGGACATGTTTGG
TGCTTATGTTGATTTCTGCTTTTCATGATAAAATATGAAAGTTATGTGAA
CTGCCCTAAATAATGGAACCTGTGGATATCTGATTGATTCAAGTTACAGA
CTTTCCTATTGCCTCCTTTTTAGATACTTGTATATAACTGATAACACAAT
GAGGAATTGAGGATACAAAAGAGTACATGAAGTGTGTGTGTGTGTGTGTG
TGTGTATTTGCATTCTTTATCAGTCATGGGAATGAGAGTAGTCTACATTT
TAAGGTGATCGCTAACATGCTGAAGGTGGTTGTATGCTTTAGCTTTATTA
TGTATTTAGTTGTATTCCACCGTTTTGTTCCTTCTCTGTTATCACTCACG
GTCTCTAGTTATGAAATAATACATATACGCGCGATGCGCCTGCTCGCGCG
CACACATTTGCACTTATAATTATTTTGTTAAGTTGGTAAATAACAGTTGG
CTAAGTATGCCATCATGTTCAGTTGTCTCATCTCGGCTATCAGTATGACA
GTCTCAGCCTCTAATTAGGAGATAAATCAATAATACGTTTTCTCGTCTGC
ACGCGGACTTATATCTATTTTGTTAAGTTGATAAAAGAAACAGTTGGCTA
ATAAATCTACTTTTGTGGAAATATCCATATTTGTATATTGTATGTATATT
GTAATGATAGTTATCTTTGCTTCCCTCAATTTGTTAGTGCTTTTACCATT
ATGACTGAATTAATACTGCAATGATTTCAGTTTAAAAGCAAAGGCGGTTC
CCAAGTAAAGGAGTATTGCTCAGCTCTTACCAAAGAAGATTGTAGGCGTC
AATCTGGTTCCTTTTTTGCGTGTGAGAAGGTCAGTATAGCTACAGTCGTG
TCATTGTAGTAAACAATTTTTGAACTCTGGTTGTAAATGTTGTAAACTAA
GTCATCTTTTATTTTTATCCTGCCGAAATGTCAATGAATTTATTCATGTT
TAGTCTTCCAAGTGTCAGCTATACATTACATTGAGCTAGGTTTGTTTTAG
TAGGTAATTTTTAAAGCTTTCATTAAATAAAGGCTTATTAGTTCATTCAG
CTTTCTATTCTCGGTGAGTTGAGGCCCGTTCTAGGGTTTAACAACTTGCA
GCAAGATTTATATATTTCTAATTAGACAGTTAATACTGTAGGCAAATTGA
ACAGTGGCTATTTTGTGTACTCGGGTGAAGTACAAATGTTGATCTTAAAA
GCTGTCATCACACACATTTACTTATATTTCATGTGATGGGCTGTAATGAG
TAGAAAGTTGTATTTATGGAATCACTTTGCTTGAAACAACTGCAGTTATC
TAATATCATATTAAAGAATTATTTTGTTCTCAGGTTCATTTTCGGCGCAT
AATTGCCCCTCATACTGATGTTAATCTCGGGGACTGCTCCTTTCTGGATA
CATGCCGACACATGAAGGTGAACTCTGTTTTCTTTTAAGCTTGTATTTCT
GCAAGTGAAAGATTCTTGTTATTTACTTAACTAACAACTCTTATTTTATA
ATAGACTTGTAAGTATGTTCATTACGAGCTGGACTCAACTCCAGATATAT
CACAAGTGATGATGGGTATACCTCAAAAGACACTCAAGCCTCAACGTGCC
GAATATTGTTCAGAAGTTGAGCTTGGTGAATCGCAGTGGATAAACTGTGA
CATTCGTAACTTCAGAATGGATATCTTAGGCCAATATGGAGTTATAATGG
CAGATCCACCGTGGGACATTCATATGGAATTGCCTTATGGAACTATGGCG
GATGATGAAATGCGTACCCTTAATGTTCCTGCTTTGCAGACTGATGGTTT
GATATTTCTTTGGGTAACTGGACGGGCAATGGAGCTTGGACGAGAATGGT
ATGTTGCCGCATGTGTTTTGAGTTAAAATGACTAGTGTAGGAAGTATAGA
AGCTTATGATCGTAAAGTCATGCATATGCAGTCCTTTCTGCCCTATATTT
TTCATTGATTGAATATGATTTCATTATCTCTCTCCTTATCTGTTGTCTAC
TTTTTTTTAATGCCTTTTGCATAGAAATGTATGTCATACTGTCATAGTAC
CCTCTGAGTGAAATTTAACTTGTGCGTCCATATTACTGTAAAGTCTTAAA
TGCATATCTAACCCCTAATCTTTCCTCAAGTCTTACTATCAAATGCTGAT
AGTTTGAGTTTACCTTGGAAGGGTGTTTGTTTTTAGATAAACCTTAATGC
CATAAATTAGGACAATTTAATTGCAAATGGCACGCCAAGTTGGATTACAT
TTCAATTGAAAAACGTTCTTAATTGAAATGACCGTTTTACGTCTAATTTA
TATGCAGAACATGTCCTCATTTTTCGGTTAAGTGTGTTCTAATTTCTGGA
AATAAGTGTGCCATCCAGCACGTTGATAATCAATCATATTCAAGAGAACA
GGTTCAAGTGTCAACATTGTGCCAAACTGTAGGGTGTACACTAGCAAGCT
ATATTAAAGAAATAATGTATTAAGGCAATGGTGTGGAAAGCACTCTCACG
CTGTACATGCAATTCAAAACGATGTGATTTGATGCAAGTTTCAAATCGGA
CAAAGTGGTGGCAATCTCAGTTTACAGTTCGGGTTCGTGTCTATAAATTG
GTGGATTTCAGGTCAAGCTAAAATTCCCTAGAATTGCATGAAATTGAAAA
TCTGAGTTTAAGGGAATGAAATTCTAATTTCGGCTCATTTTGGGTCACTC
ACGGGTTGACCAGGTCATTTTTGGGCCACTTTTGGGTTTTGTCTCGGTAA
ATCAGGTGCGAATCGGGTCAGGTTTCGGGTCTTGTCTGATATTGCCACCC
AACAAAATAGTTGTTTGTTTATGCACGCTTAAGAAGTTACACTTGAATAT
TGACTCTTACATTTTTTTGCGAGTTTGTGCCTTTCACCGCTTCACAACAA
TCTTGTAATATCCGGTGTTTAACTTAAGAGTTCAACCATAAGATGAATAC
ATGTATGTGAGTTGCCCTCTCTATCGAATGCTTATCACCATTGGATAAAC
AAGTCTGAAATTTGAAATTTATTCCATCTGAATGGTGTTTAATGTCAAAT
TTACATGTTGATTATTGTATACTTGTAGATTATTGTATATTTAATAAGCT
TACTTGTGTATGTACTAAAAAATTTATTGCACTTGTTTATGTGCCCATTT
CATTCTGTCACTTTAGTATAGCCACTCTACTAAATCATCATTCAGATTTC
ACATATCCCTTTAACATATATGTGAATTTAGCAGTCCAATTCTGGTCATT
GCACAAAAGTTATACAAACCAGTGTGTACGGTAACATCTTTGGATAGACA
TTGAAATGACTGCGAGACATTGACTGGGATTACAATAGAGCAACTATGGG
TTTTTATTATCAAATTTAGTGTGTGTATGTTGGCCTGCTTAATACAATAG
TTAAAGCAACTATGTAGTTGTTCTATCTTGATATTTTTAATTTATGTTAT
GTATGTTAGCCTACGTAATACAATGTTTTAAGCTCCGTGCTGTGTCCTTA
AGAATGATCTTTAGGCTATAGCAAACATTTTGTGTATACTTTTGCGTATA
ATACCTACAGGCTACAGCACCCTTTAGCTATGCTGGGCGCTTCAGTTCTC
TGTCCAAGTTTGTTCATATGGCATCTTTTCCTCTTTTTTCAGTCTAGAAC
TTTGGGGGTATAAGCGCGTGGAAGAGATCATCTGGGTGAAAACTAATCAA
CTTCAGCGAATAATCAGAACAGGACGCACAGGCCATTGGCTCAATCATAG
CAAGGAGCATTGCCTTGTTGGAATAAAAGGAGATCCAATTGTGAATAGGA
ACATCGATACTGATGTAATTGTTGCTGAGGTTCGAGAAACAAGCCGCAAG
CCAGACGAGGTAAAAATAGTGCATGTCCTCCATTCTAGATATACATGTAA
GATGCTTATCAAAGCTTATTGCATATTGTATTAATATGTAATACTAAAAC
AGAAATTGGAGACAGGACCGTAACATATAGAAAAATTCAGATTTGCTGGT
CGTTAAGCATCTATGAGGTAAAACAGTAGATAACTAATATATAACTGATG
CGATGTGCACACACAATGGTTAAATTTTGGTACATATCAGAACTATATAC
ATTATATCATTGGCATGGATGAATAAGAAACCCATACTCAGGCTAGGCTG
AGAAACATTTTAATGCTTTAAATTTCAGTGCATACACCATAATTACTTTT
GAATAAACAAATATTTATTGGACCTTCCCAATTATTATTTTTTTGAGTCA
AGTTACATATCTTTCTTTTGGATAAAACTTTCTCTTTTGCATTAAATTTG
TGAAAGCATGTATCTTATTTGACACGTTGACCAGAAATTGCAGCCAAGTC
CACAGACAATACCTGGATGTAAAACTTTTTGAGTGCAATTACTTTCACTT
CCATTAAATATCAGTAATACAAATAGTAGGTCTGCAAAAATAAGAAGAAA
ATACTTTGTTTTGCTATCCTTTTCCCTCTGTTTGATGTTTTATTATTCCC
TAAAGACTGAAGGTCACACCATCACATAGCATACAGAGAATTAGGACGTC
ACGTTAATATCAGAGCAGAGTCTGATATGGTTATTACATTTTTTTAAGGG
GTCGAAGAATAAGTTAAATATTTATTCTGATGTATCTGGCTTCTTCCATC
GATTATTTATTGCATCTGCTTTGTTCAATTAATTACTGTTTTCTGAGTAA
CTTTTAAGAAGTGAAGTTAGCACTATATTGACCTATTAATTGGCAGATGT
ACCCGATGCTCGAGAGGATAAGCCCAAGGACAAGAAAGCTAGAGCTGTTT
GCTCGAATGCATAACACACATGCAGGGTATTTTTTTTCTTGCCAAAGCAC
CACTTTTTTAACACTAACAGTGTTTTCTTCTATAGCATCATTTTTTTCAC
TTGCGGTGCTTTTGTACTTTTCCTGATAAATGAATTAAACGGTTGCCATC
TCCTGCTGCCAAGATCATTATTGTTTTGTGTCACTATATGATTTTACTGT
AAATATGGTGTAGAAGTATGATAGAATGAAATCTAACTATCTTGCTTACA
TTGGCCAATCTATCTAAATAGTTTCACCAGTTTAGCTGGCTGAAGCCTTG
CGGTATGTGCTAGACCCAAAGTTGAATCAAAAAATATAATTTGGTCCCTA
TATCTGCAATGCATTAGGTACTTAGTAAATTCATTTTCGGATGGAGGTAC
TAATATTGGGTACCTTGTAAATGCTCTCTCAGCATAACACTTGTGCCTAA
TACACCTATTTTCCTCTTTTTAATATATATAGGTACTAAGTTTTAAAACT
TTCAATTTAAAGGGGCTAAACCTCTCCAGCAATTGCCAGTAAAAAAGATT
TTTTTTATCCAAGAAACATAGGCCGATAGATCTGAGCACGTGACAACAAA
GATTTAGCAATTCCTAACAACAAAGATTAATTTCTCTACCTCCCTAGAGT
AAAGTCAAGTCATAGAACTGGATCAAGAAGCCACCACTGTCTTGATTTCT
GCCTCATCTCCTAATGTTAATAAAGTTTTATTTTCTGCATGTTCTACTAT
TCTGAACTTTAGTTTCAAACTCATCACCGTCACTACAATTTTTTGGTTTG
CTGTTGGTGACAAGTTGTAATAACAGTAGGTCTAAAGTTTTTGTAATTTT
GTGAGATTCAGCCAGAGTATGGGATTTTCATTTAATAAGTTCTGTACATA
AATAGGTGGATGTCACTAGGTAATCAGCTGAATGGAGTCCGGTTGGTTGA
TGAAGGGCTTCGAGCAAGGTTCAAAGCTGCATATCCAGAGGTTGAGGTCC
AACCTCAGTCTCCTCCTAGGGCTTCTGCCATGGAAGTGGACTCTAGTGCG
CCTCAACCACGAAATATGTTTAAAGGGGGTGAATCAACATCAACATCAGC
ACAGTTTGCAGATGATAGAGCTCCAGAGGCAGCCTATGCCCCTGACAAAA
AACCAGTAAATGTTGATGCGGAGATGACAAGCTAA