| Relationships |
|---|
| The mRNA, DCAR_010253, is a part of gene, DCAR_010253. |
| The genetic_marker, MK006482 K3926, is located in gene, DCAR_010253. |
| 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_010253 | DCAR_010253.mRNA | mRNA | DCARv2_Chr3:17061257..17068408 |
TAAAAAAGTTTCCGGGAACGTTCACTTATAAAAACACAGGTATCAATTGA
TAAGTGGAGATCATTGTATTCCACAAGAGAGCATTGTATTCCAACTTGTC
CTTTCCTATTTCAATTTTTTCTCCCTCCAATCTTCAGAGATTCATTTCAC
TGGCGGTTTAATTCACGGCGGCGCGACCGTTGAACCCTTGCTTCTCAGCG
CCTCTGGCCGATTAGATTCTAATTAGCAATGACTATTTTCTGCTGATCAA
GATTTAGGTACTCTCTCCCTCCCTCCCTCCCTCGCTCTCTCTCTCTCTCT
CTCTCTCATTTATGTATTTATGCAGTGTCTTCTGATCTGCTGTACCTGGA
GATTGTTATGACTTATGCACATCTAATTTGACCTGTTCAACTTGCTATTT
AGTCCTTCAACTACACTTCCAAAAACAGATTATTATATATGCTGTATAAT
TCCTTATATATATGAAATTATGGCTCAAGCTGCTTTACCTGCAAATTTCT
ATCTTGCTTCTGCCTGTCCAGTTTGAATATTTTAGTTTCATAATATTTGC
TGCTATAACTGGATCAGATAGGTACTTTACACTAAATTTTACTATCTTCG
TTTTATTAAAAATCTTGAGCCTCTCAACATATACTTTACATGTTAGATCA
TCGCAAAACAGTTCTACTTTTCAAATACCTACTGTCACATACCTAGTTTA
AGTGTACAATTTTTTTTATATTGTTTATTAACTCCACAACGAGATATAGT
TAACAAGAGTTGGCGAGTTGCTACTATAATACGATTTGATTTATATTTCA
GGATTCCTCCTTTTTATGTCGTCACACATATTTAAGTTACTTTAGTACAG
ATTTAGGCATATTGAAGAAAGTAATTTGAAGTTTTGTAATGTTTTGTTAT
GTATGTACAGCCTATCATTTGCGATGAAGACTCTTGGTAGTGAAGAGTTT
GATGTAGAAACTGGAGAATTTGATAACGAAAGAGAAAAGTTGATACGGAG
TAGCAGAGTAGTTCAGATAAACAATCAGGCGTTGTTATCTGGTTTAGCGT
ATTGTCTATCGTCATGTAGTATGATACTGGTTAACAAGTATGTTCTCTCC
AGCTACGATTTCAGTGCTGGAATATCTTTGATGCTTTACCAGGTTACGTC
TAATTGTTTAGTTTTTAATTAAGCTCAAAGAAATTCCATACGCTAAAAGC
ACTCCATATGCTTAAAAAGTTTCCTTGTTTCCTGCAGAACTTTGTTTCAG
TATTAATTGTGTCTATGCTGAGTACCCTTGGCGTAATATCAACAGAACCA
TTGACGTGGAGATTGATCAAGGTGTGGTTGCCTGTAAATGTAATATTTGT
TGGGATGCTAGTCACAAGTATGTTTAGGTATGAATTTTCTCTTTCTTTCC
ACTTACCAATAATAATTTTCAGAGTTTGCCATTAAAAAATCTTTATATTT
TGGGCGAGTTTTAAGATGAATATTTCCCGTCAGATCAGAATGAATAAAAC
CTTGAATTTTGGTCATCAATCAGACACTTAAAAATATATAAGGTTAATGT
ATGAGTAAAGGGATGGTTCACTTCATGTTGAATCTGTTTTGAGTTGGATG
CCTTGATTGGATATCCTTGCTCCTATGGAATGCCTACTGGCTAACATCCT
ACACATCACCCAAGCATATATGTCCACACTGTCATGTGAAAAACGTGCTG
CAAGTGAGGAAGAGGGGGGCTGTGTTATTCAGATTATTAATTCTATGCAG
TTATGAAGCATTGTGGAATATAAGCCTAGTAGAATCTCCGCTCGTCACCA
TTTCTGTTGAGTTTGCTGCTTCATTTTTACAATAACACTTCATATATTCC
CTAATTGTAAGACCTACTTATAACTTATACTAGAAGCCTTGCATTGTATT
ATATCCAAGTCCCTACACCTGTTTTTTCTGTACCATATTTGAGGCATATC
TAAACGTTGCTGCCTTGCTGGAACCCTGAAATTACTGTCATCCTTTATAA
CTTCCAGAATATATGTTTTTGACAAGAATTTGTATACAGAGCATTCTGGA
TCTCTACCATGTCTTACTAGAAAAATGATCATCTTCAATATTGAAGCAGC
AAAATGATTAAAGTTTAAATTATAATAATAAATTTCACTAGGTTGTGCAC
ACTCTAGGTTTCTCTTCTTTAATAAAGTTTGGTGTTCTGCCACTAAGTCA
ATTTTCTTTTCTTTGCTAATTAAGAGTCACGTTTATATGAATTAACAAAA
TATATGTTTCACCCTCTCCTTTCCCTAATTTCATGTGAATTCAATACAGG
ATATGTGATGCATAACTGATGGATATTAGATAGAAAAACAGGTATAATAA
TGAACTTAGTGGATAAACCGCAGAAACTCACTATCCCAAGGCTTTTGCCC
CCACGGAAGGGATAAAATTCACAGATTGCAACCCATGATAGAGATGCAAT
TCGATATTCAACAATATTTCGATAATCAAGTCTAATTATATTGTGGGGCT
TACAGTCCTTATATAGCAATACAAAACCCTAATAATAACCTAATGGACCG
TACAATTAGCTTTATTATAAATAGACTACTTATTTAATAAGCCCCTAACC
CTGCATATAACACATATAGATAATTACATTATTTGACTCTGCACTAAAAG
TTGAACTAATTAAAAACACAACATTAATTCCCTATTTTCGTTCTCCATCA
ATCTCCCATTGTTAGAGAAAACTCGACCATGATTTTTGCGGAAGGCAAGA
ATCATGCAAAACTGAACTACAATGAAGAACAATTTTATGCTCTCCTTGAA
CATCTGCTCAGGTGCAAAATACTCAGAAAACTAACAGCCAAAAAACGTTT
GAGGTGCGAAATATTCTGAAAACCGACTACCAAGTGAAGGAGGTGCAGCC
AACTATTCTGGAATGATGAAATAGTGATGTGAACAGAACCGTCATGAACA
GTAACTCCAGCAATGAATAGTGAATTCGATGAACATATTTTTTTTTTTTC
CAAAATCAAAGATCGCCCAACAACTAAAAAAATTGATGGAGAAATCTAAG
ATGTGATACCATTTGCTGCAGGACAAGATGTAGAATGATGGACATTAGAT
AGAGAAACAAGAATATTAATAATTTGGGTGGATTAAAGGCAGAAAACCCT
CTAGTCCTAGTGTTTCGCACTGGGGAAACGGATTGCAACCCATGAAAGAT
ACTCAATTCAATATTCAATAGTATCTCGAATCTCGATAATCAAGTCTAAT
TACAATGTGAATGCCAATATAGGTATAGAAAATCCTAACAACATAATCAA
GTCTAATGATCATATGGGGTTACTATGCTTATATAGGAATAGAAAATCCT
AGTATAACCTAATGGACTAAGGCCCACTTTATTATAGATAAACTACTTAA
TAAACTCCTGACCCACTTATAAAACATATAAAGAAACACATATTCTATCT
TTACACTATATATACTTGAACTAACTAAAAAAATATACATCAATCCCTTA
TTTTCGTTCCCCATGAATATGCCATAATAATGGATTTTTAATATTAAACT
TGATATTAGACGCTTTTGTACTACTATCATTGAAGTGGATAACATATATC
GAATTTTTGATGCAATGTTTTCAGCGGATACATACGCTCCGTATGCTTAT
GAATTTGTTTGTTTGGTCTTATTAAACTAGTTGTGTTGAATTTTTCTCAT
AGTTGATCTTAATGTTTTGCAGTCTAAGGTACATTAATGTCGCCATGGTT
ACAGTTCTGAAGAATGTTACAAATGTAATAACAGCAGTTGGTGAAATGTA
TCTGTTTAGTAAGCACCATGACAACAGAGTTTGGGTTGCGCTGTTTTTAA
TGGTATGTTACCTTTCGAGATTATTGTCTTATGACTGTGATTCTCTCTCC
TTTTTTTGGGGTGGGGTGGGGGGTGGTTTGCGTTTCTGGGATTGCTTTGT
TCAGGCTTACTTTCTGAGTCCACATTAAAAAAGCTGTGCTCGGTATAATG
CTGCACTCGCAAATGATTAGTCACGTGATCAGGTCATTGAGATAACTACT
GGATAACTAGAGTTGAATGATTTAGTTTTTCAAGATGGTGTAATGTTTCC
GAATTATTTTCAAGCCCAATTTTGTTTTAGATAGGAAATCTGCAATGTGA
TTAATTAACTGTTTGCTGTGTTTTTTTCCCTAGGGTAAAACAGATGTTAA
GTTAAAATTGTTTTTTTTTGCATTTTGCAGATTATTTCAGCAATCTCTGG
TGGTTTTACTGATCTATCTTTTCATGCTATTGGCTATACGTGGCAGATTA
TTAATTGTTTCCTGACAGCATCATATTCTGTATGTGTTTTATTTATATCA
TACTATGTTGGTTTGTCCCAATTCACCCTGAATCTTACTAACAGTCACTT
CTATTTCTTTCTTCTTTTTTCACTGAATTTCCTCATTCAGGCTTTTGGCT
TTGGTTATTGCCCGTGGTACTAGTGTTTACATTGAGTCACTGGATAGTGG
ATACATGTTCTTTTAGTTTTTTGCCAGTGTCAAGTGTTCTTTACTGTACT
TACTTTCTCGTGCTCCTCCTGATCTCACTCTAGGATATATTCTTGGAGAG
ATTAAGCAAGTCATTCTATACACTGAGAAGTACAGAAGACAACCATGTGT
ACACTAAAAATTACTTAAAAGTTATAGAAGCAGGCCATTTAACGTACACC
CTGATGTTTTACTGTACACCAACGTATCAGACTCCAGTATGGCAGTATGT
ACCTAGTAAGAGATGGCATAATACACAATGATACAAGTAGACTCTGGCCA
TTCTGGTATTTTCAGTTACCGTGTCCAAAGATATTTTCACATATCATATA
TAACATGTCAATTCAGCAGAACAATTTTCTTTTTTGCCAAAATAATTACC
TATTTTTAAAGTGCTGGCTTTTCTAGTTTTTCTTTGATTTCAACCGGAAA
ATTAACAAATGTCATAATCTAATAATAGTCTCATGATAACATTAACACCA
AATGTTAAAGTACTGTATTATTTATATATTTAACTTTTATATATATGAGG
GTAGAGATATAGAAAGATTTCAGGTCCTTGAGTACAGATTGTTCGTCGAA
ATTGAAAGATGCACTCCTATTGTTTTCTAATTAGTTTTTCCCGCCAATCA
TATGCAGCCAAGTAGCATCTTCTGGATCTTCATAATGGAACCTTTGCTTT
GAACCACTTATAACTAATTAAATACCCGCTTGTCAAACTTTTTTAGTAAT
TCCTTTTGGGATTCTTTTGTCCCTGATAGTTATCAGTATATAAACTAGAT
TTTGATGATTCTTTATTTTTCTAATATAACACCTGCCTGAATTTTACCTT
TTCTATATCGATTTGTGATGCAGTTGACACTGCGTAGGGTTATGGATACA
GCAAAAGTAGTGACAAAGTCCGGAAACTTGAATGAGTTTTCGATGGTTTT
GCTAAATAACACCCTCTCTTTGCCCCTCGGTTTACTTCTTATATTTGTGT
TCAATGAGGTGGACTATCTTGCTACGACGTGAGTTTTTCTGTGCAGCATC
CTATAAAATTAATAAGAAAGCTATGCATGTAATGTAGAAGTCCCATAAAT
ATATTGATGCTTTTTTTTTTGACTACCAATAAATATATTGCTTCAAGAAA
AAACATATTTGATTATAATAATAATGAGTATATCTTTGTATAATTGTGCA
TAAATCTTCATTGTACTATGGCTTAATATGTTGAAGGTTTATAGAGATCA
AAGCCATCCAGCTAATTTATATCCATAGTGCTAGTCGAAGTTCTGTATAA
TCTTTCGTTACACTGATATGTCAATTCAAGCTTTATCTGCATGTTTTTCA
TAAAATTGTTACGAAATGCACATTACTGCATAAAAGCAAAATATTTACAA
ACCTTCAGGCACTATTAACCATTCCTTCTCCGATGTGCACTGTTATAAAA
GGGTAACAAGGCAGCATTTGTGATTACAGATTTTGAAATTTGTTTTATAG
CTTTCTTAAAATTAAGATGCTTGCACTTGGTCTTTTGTTGTATAGTATAT
ACTTCAAAATTTCTTCTGGTTGGAAATACACTTATCTAAAGGTTCCACTT
CACCTTAATAACATACTCTGCCCTTGCCCTACTTTTTGTTTTTAACAATC
GTGGTGGTCTTTTCCTGACATTTGTTTATTGTCACCAGCATTTGTAATAA
TGTGATTAGCTGAAACTCATATGTGTTTGTGATAACTGTCAGACCACTTC
TGAGGCTACCCACGTTCTGGTTGGTGATAACTTTAAGTGGATTTTTGGGT
TTAGCGATCAGCTTCACCTCTATGTGGTTTCTTCATCAGACAAGTGCTAC
TACCTACAGGTTAGAAATTTTCATTAGGTTTATATAAGAGTGGTTGTCTC
TATTTTTGACTCAGATTTCGGTTAAATCATATACTATGGTTTATACTTCC
TACTTTTCAATTTGATATTAAGTTCTGATCTTTTGCTTGCTGAACCTTTT
CTTCACCTGAATTACTATGGATTTTTAATCTACTTATTTTCATTTATCTC
ATCCAACCTTAGTAACTTCCAAAAAAAAAAAATTCAGACCTATCTATGCT
AGAGGAACCATATATTCTGCTTGCACTCTTATTAGAAATGATGCTTCACA
ATACTCTAAAGAAATAGTAAACGATAAGAACCGGTTTCTCACAGAGAGAG
CCCCTATATATATATATATATATATATATATATATATATATATATATATA
TATAAATATGCCTGTTTTGTTTCATTTAATTTTTAGTAGAGTGAGTGAAG
TTTATGTTATTAAATTATAATCACTATTCAGTAGGTTGTACTTTGTAGTA
TTATATACTTAAATTTTTATACAAAAAGCCATCTGTACAAAAGTCATCTA
TGTTGATTTACTTTACAAATGTAATCTACATGATGCATATGATATGGAAG
GTTTAATTACAATCGAATTCATACACTTATGGACAACAACTTTAAGAGAA
AGTTGTACCTCTATACATTTGGAAAAAGCTGGTTTTCGGCTTTTGCGGGA
AGCAACTACTGTTTTCTTTCAGTATCAAACCTCACCAAAAACATCGTGAT
TTATATTATACCGAAATTGATGCGCGCACTATAGTACCAAACAATTATCT
GATTTTTGCAATAATTTTTCTTACATCACATCACTTTTTGAACAAAAATT
CCAAACAAAGCCTTAGTTGAGGGATAAGATTAATCAAATAAATGTTTGTT
TGGTTTAACATGAAAAATATGCATTTTATAAATTATTGTTTTTTAGTCAA
ATGTATATACTCTTCTTTTTTGTGAGTAATCATAATTTAGGTGACCCTTC
TATGCTGTTTTTACTTTATTTGCAAGAAATTATATAGAATTTGTGGGGGA
ATATATAATTATCGAGTGTATTCCTAATTCTGTTATTTCAGTAAAAATCC
ACCTGTTACTTAGGTGGAATTAGCATTTCTGTGGTTCAGGTTTGATCTAG
TTGTAGATTAGCTAGTAGCTGATGAAGCGATGAACTTGTTTCTGATTAGA
GAATTTCATACATTTCTTGTAATTAAAATTTAGTATTACACAGAATACCT
CTGGTTCACATTATACAAGGTGTTGATGGTTTGTATTTGGCTATAACTGG
TGTTTGAGATAAATGAAACCTGAATATTCTTAAAGAAACAGTAGAACAAC
ATAGAGGACTTCATAGTGGTATTATAAGGTGCAAGTATCACGGGGCAAGA
ATTTTTTTTTGTTGAAGCTCTTTCTGTTTTGTAATTGTGAAGACTTGTAG
ATGATTCATCTTAATCTTAAGAAGGTTCTTTTCATTTTGCAGTCTTGTGG
GGTCACTAAATAAGATACCCCTTTCAGTCGCTGGAATCCTTCTGTTTAAA
GTCCCAACCAGTCTTGAGAATTCCGCAAGCATATTATTTGGTAAGCTCCA
TTTCCAAGAATAATCTTTTTTCCATCTGAGCTTACCAAACCATAAGCGTC
GATTGTAATTTGCAGGTCTTGTTGCTGGTGTCTTCTTTGCCAGAGCTAAA
GTGCGGGAGAGATCACAGTCTTAATATGTTGGTTGCTGCTACAATATTTT
TACCGCCCTCAGCTAAGAACAAGCAGCCACATTTATCTGCTTTGTGTTAC
GTATCACAGTACTATCATGGCTCTTAGAAGCAGCAAAAGGTTAAGGAAAT
CGGAAAGAATTATGGAGAAGTGTTTTTTGTAGGATTCTTTTCCCCATTGA
TTTTCCTAGTTCCTAGAAGAGAAGGTGAGCTTATCTGTATATGTTTGTGT
TGTAATGTAATATATAGAAAGAACTGGTGCTATTCTAGCTCCTGATCATT
CACAGATACTGTTAACC