| Relationships |
|---|
| The mRNA, DCAR_029255, is a part of gene, DCAR_029255. |
| The genetic_marker, MK019065 9_3905397, is located in gene, DCAR_029255. |
| The genetic_marker, MK019067 9_3905836, is located in gene, DCAR_029255. |
| The genetic_marker, MK002789 K0233, is located in gene, DCAR_029255. |
| 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_029255 | DCAR_029255.mRNA | mRNA | DCARv2_Chr9:3902527..3911440 |
ACTATATAACAAACTAATAAAATAATGGCAATGAGATAAATGAGAATGGC
GGGTTTTGCCTCAATTCCAAACGACCCCACATCATCATCGCCGTTGAGAT
TCAATAGAGTGGGTCCCACTCCTCTCCACCTCATCACCACCTCCGCCGGT
CTCCGCCTCGGCGATGTTCTCCGGCGGCGATTCACCGCCGACGCTACTCA
TCTAGGCCTGGTTCTCAACTCATCTATTGAGGTAATTATGCTTCAAACTA
CTCGCTCCGATGAAATACGATTATCAAAACTTCGATGAATTAGTAAAATC
CGTTCAATTTAGAAGCGTCTGATATAATTAATTTATTCCTGTTTAATTTT
AACTTCGATAAACTAATAATTTTGATAAATTTCTAAAATTATCTCAACTT
AAGGTTACTATTGAATTTTGTTTAGTGTTAAGCTTTATAAAAGACTCGGA
TCAGTGTTGTTTTGTTAAAAGGCGCAATATGTTAAGAAGTGAAGGATCTA
ATTTTGAAGCACGAGCTGCTGTTAATCGCTTACTATTTTAGCGAAAATTA
AGATCGTAGATTTTGACAAAAATATATTACTTATTAGATTTATAACTTTA
ACTTTCAAACGTAGCAGAGCATGTCTAATGTAAAATAAATGTAAAGTAAT
GATCAATAACAAAGCATCAATCCACGATGTTCAACAATTCAAAAGTTCGG
AGTTGTTTTGTTCAATTTCTGGTAACATTTTTGTGTTCGAGCTGTTATTT
TAATCTGTTAATAGACGAGATGAGATATGTTACAGATTTGTGATGTCTTG
AATGTTGTGTCAATGTGGAATGGTTTACAACGATTTGTAGGAGCAGGTGT
TGGTAATAATCTGAATGTTGTTATTTGCTTAGAGATGCTTGACTGTTGGT
GTGTGAACTTATTATCTTCTATTGATTTGAACTATAAAATTGTTGACCGT
TAACCTATATTACATATTATTGTTACTCTAAATTTATGTTTCTGCATGAC
TTGTTGACTCTTTACAACTAGTCGGGCGACTTGTTGACTCGTAGATTCCA
AGGAACCAGGAACTAAGGCTCGAATCGGCTCCATGATAACCATGTTGTAC
CTGGAAGTAGGTTTAAAAGATTGCATTACACTAATATTGTGGAAAAATGG
GTCATTATATCATGAACTCAACTAAGTGTTTGCGAACTAGTTAGCATTGG
CCACATGAATCCTGGGACATGTTACATGTGATGACTTGTGTATATCCAAT
ACCGTTCAACAAGTAATATTCAGTTAACCTTCGGTAGAGAAAATTAAATT
GATAAGAGAAGGATAGATATAGAGGTTGCATGATTAGCAGAAATCTGTAG
ACTATATGAAATTAAAAATATTTATGAAGCCTTTTACAGTTGGTGGAAAT
TGCTCAGTCCTTTATATTTTTATTTACTTGAATCATGCGCTGAAAATAAA
TAGTAGTAGAAAACATTCCCATAGGCATACCCCTATTAGGTCCTAGGCTT
GTCAATGTAATGAACGTATTAAATATTTTCAAATTTAATGACTAAAGATT
ATAAAGTGACAACTAAATGACTGTTTTTAATCAGTATTACCAATACTTTT
TATACATTCAATAGAAAAAACACAGTATTTATTTAAAAAAATAAAAGCGG
AACACATGGGTTATATGCTTGTATGAATAATGTAAGATGAAGAACAAGTA
AAGCGTTTACTATGCACAATTAATATAGGCAAAAGTGCACATCTTTTATA
GATGTGTCTATCTCAAAGAAGGAAAGCTAGTTTTACTAATTTTAAACAAC
TGCAATTTAGCTGTCACATTTTGTTCATTTACTAATCAAGTGATATAAAA
TACCAGGCTTGGAATGCAAAATGTAACTTTCATTTGTCTTTATATTTTGG
GGATTTCTATTCCTTTTCTTAAACATGATATATTGTCTTGCTTTGTGTGC
CTGTGTTGAAGGAAGTTTTGCATAGAAGAATCCACCACTTCGATGGGTAT
ATATTTCTTCAACGGTCATACGATGCTTGGGCAGCCAAATGGTCATCTAC
CTTACTATTTTTTGGTGGAGAGGGGAGTAAAAACAACTATTTACGTGGTA
GAAATTCACAAATGAATTCATCCAGAAAAGACGCATTTAGTAGAAGAGGA
CTAACCACTGTGCTCATTGCAGTTAATGTCGTGTGAGTATTAAGTTTTTT
CTTGCATCGTTAATATAGTTCGAATTTCCCTTTTCCTCGGCCATTCCCAA
GTTATCCTCTTATTTTGGTGCCATTATCTCAATTATGTTGGCATTCATGT
TACCCCATTATTACACATTCTAAATTTTCAAATAGTTTTTGTTACATATT
GCAGTTGCTACTCCACCTAGGTAACTAGTTTATGCATGCAGGGTTTACCT
TGCACAGATGGCAACACAAGGGAAGCTAATGCTCTGGGGTGCAAAGGTCT
TGCTTGCATAGACATCATCATATCAAACTGTAAACATATATTTATACCCT
TTTATTGCTTGATTCACAAATTCCTAACTGTATCTATATTACATACACTT
GCAGATTAATAGTCTAATAGACAGAGGACAACTATGGAGACTTGTGTCAT
CTTCATTTTTGCATGCAAATATTGGACATCTCCTGGTCTGGTGTTTACGC
GCATAAATTAATTACGGAAACTATTTTGAAGTGTGAATGTTAACATGGGT
TTTGATTTTTGTAGATCAACTGTTATTCATTGAACTCTATTGGTCCTACT
GTGGAGAAATATAGTGGTCCTGGAAGATATATGGCAATTTATTTCATCTC
TGCAGTTGCAGGTAACTATCAATACTTAAATTATGTTTTGTTTCGCCTAC
GTACATTGTATGTTTTGTATTACCTGATGAAGTTGTTACTATGGACTAGC
TTCAACAATGAGTTATTGGTTCTGTAAAGCACCAGCAGTTGGTGCATCTG
GAGCAATATTTGGATTAGTGAGTTGTCTTTACCCCTACAGTTTAACTTTC
TGTGATTTATCATGCTTTTAAATAGAGTTAAATGCATTTTTCACCCTTTG
GTTTTAACTAAATGCACTTTACACCCAATAGTTTTACAATAAGCACTTTG
TATCACTTAACTTCAAAACCTGCCACACTTTGGACACTCTAAACACTTTT
TTCGTCATACTTTGACCGTTACCATTAGTCAATCTAGGGTATATTTGATA
TTTCTCATTAAAAAAAGATTTATTTACATTTTGCATCCCTTAGATTTCAG
TTAAATGCATTATGAACCAATAGTTTTGCTTATATAATCATTAGCCATTT
CCCGTATTAATATTGATGAGGAGCTTTTACAATTTGACTAATATATTAAT
CGCATCCAAAATTATATTACAATTTAACGTGAGTAACAAATACAAGAATT
GATTGTTTATACGCATCGAGTAGTGTCAATTAATTAATGTCACATACAAT
TAATTAATACAGTTTTGTCATAAAAATTTATATAAAGATAAGATATGTTA
CTACCATCATCAACTTTATTAACATATAATAATAAAGATGATATAATTTT
ATAATTTTTTTTGACATATGCGCACTAATTAATTTTATGTGATATTAATT
AATTTTATGTGACACTAATTAATTTTATGTGACATTAATTAATTGACACT
AAGTTCATATAAACAATCGGTTTTTGTACTTGTTACTCACATTAAATTAT
ATAATTTTTTTGAATGCAATTAAGATGCTAGTCAAATTGTAAAAACAATA
CATCATTAATATTATTAGAGAAAATGATTAATGATTATATAAGCAAAACT
ACCGTGTCCATAATTCATTTAGTCAAAACCTAAGGGATGCAAAATGTAAA
TATTTTTTTTTCAAAATGAAATACCTTAAATACCGTCGGTTGCCTAACGG
TAACGGTCAAAATATGACGGAAAAATGTCTAAAGGGTTCAAAGTGTGACG
GGTTTTGAAATTAAGGGATGTAAAGTGTTTATCTTAAAAATATTGAGTGC
AAAGTGCATTTTTCTAAAACCAAAGGGGTGCAAAATACATTTAACTCTTT
TAAATATTATGCATGGACGGGAATCGTATTTATCATAATATGTCATAGTG
GGATTCATTTAAGAGCATCTCAGTTGCATCACTCCAAGTCTGATGAAGAA
TATGGAATGGAATGCTTCGGATTTGTATCTGACATACTGGTAGACCTATA
AAATATGCTCAGGAAGAAAGGGAGACATATAAATATATAGAGTTTAAATC
CCCCCGCCCCTCTACTCTGGATGCTAATTGAAGGCATTTCCTCTTTCTAA
TTGTATGTGTTCTACTTGTGATCCCTTTAATCAGGTGGGATCTTATGCTA
TGTTTATATTCCGGCATAGGTACCTAAGTAATGAAAGTGGTGAAGGTTTG
CAGCACGTTGCAAGGATCATTATGTTAAATGCGGTATATCCATCAGTCCT
CTCAACTTCCATGGAAATGAATATTTCATCTTTTATCGTATATTAATATC
AATTTGGACTGATATACTGTCAATATCATCAATAATATGACATAATTATG
TCATGAGTATACGACATTATCATTGTACTAGCTACTGTAGGAAGAACTGC
CACCAAGTTTCATATTACCTATAGATTGAGGCTCTTGCCTCTCCTTAATA
TGCACTAGACATAATAATATATACACTTTTCAGTTCTCTGCCTATATCTG
ACTCTCCTCTCTACTATGATCCCTTCTATTACTTACTGTATTTCTCATAT
AATCTGAGATGGTATCATACTAGGAGTAGAGAAGAGGAGAATATTTCTGT
TAAAGCTTTGAGTTTTCCCAAAAAACTCAAGCTGCCCAAGTGCCCCGTTA
GGTTCTTTGTATTTCAGCCCCAAAACAAATCAAAGTTGTAAACCAATACA
TATCAGCGTTACACCTTTTTTTCAGTTCTCAAAAAATCCACCTGAGACAA
AGTTGGTTGTCTCTCTTATGTGAAAATCTCAGCGTGTTTCGAATTCTTGT
CCCAGTAACAGCTGAAGTAGTATGCTATATGTCTGCATAGTGCATATATA
CACGTATACAGTTTACTATGTCTTATGTCGGGAGATTAAGATTTCAATTA
CTAATTATTTGTAGTGAAGGTGAAACCAAGACCGCTAGAAAGCCGTTTTT
TTTGCTATACAACTCTATCATAGATGGGTGAAAACCGTAAAGAAGAAAAA
CCAGTGAGCTTTATTGCTTGGCTGGATTCAGAAATTTAGCCCCGATCTGG
TCTGTGGTCACAGAAGGGGGAGTTGGACAGCCTGTGTTAAATGGGCTAGG
CTGTTCTAACGATGAAAAAGATTCAAAAGGAAGTCAGCTTCCTCGTTAAA
AATTTGGCGGGAGTTATTATGAAATATGAAGTGAATATATATATGTGGAT
CCCCTCGAAAAATGTTGAATAGTTACTTTCTCAAGGGAGAATTCTGTTGG
GATCTTTGGTATAAGCATATCAAGTCTTCCTGGTTATAGATTTAATTGGG
TAGAATGAAAATAGAGGGTTTGTTGATATTATGAAATTCCACCAATCTAT
CGTGTTGCTGCAAATTAAATAGCTCAGAGGGCTAAGATCCACTGAAGTTA
TCATGGGACGGTACTTGTCTAGGCGAGTTACAACCTCCTTCATCAAAACG
CATCTAAAGCAGCAGAACTAGTACTCCCTCTGTTTTAAAATATAGGTCGT
TTGACTTTTTGGCACACACTTCTAAGTGCCTTGACCGCATAGATAAAATC
ATTATTTTTTTAAAATTTTCTTTTTTGAAAAAAAGAAAATTTTAAAAATA
ATAATCATAACTAAGCGGTCAAAAGACTTAGAAGTGTGTGCAAAAAAGTC
AAGCGACCTATATTTCAAAACAGAGGGAGTAGTATATAACAGATATACAC
ACAGTTCCCGCCACGACTGCAAAGCAGCAGAATTAGTAGTATATATACAG
ATATATGCACACTGTTCACTGCCATAAATGACAAAGCAGCAGAAGTAGTG
GTATCATGTATGTATATCCACACAGTTCAGTGCTATATCTTGCATCAATT
TATCCAGTGCTGACAGCAGCACCTCCTTGTTAATTCATTGAAATCTAGTG
ATCACAAAGTCGAATCTCAGTATCTTCAACGGATTTTCAGTTGAACTGAT
TGGCCGTAATGCTGACAGCAGCACCTTCATTTGACTTTGACACGAGCTAA
AATGTAAAGTACGGTCACAAAGTTGAGTCCCAGTATCCCCAAAATTCTCA
CATCTTGTTCCCAAGATATGTTTTGTTGGACGCTTAGGTTACGCCCAATT
TCCTAGTGTTCCACTCTTCAATATCGATACAGGTCTTCCATCCCAAGATG
GCATTTCAAGTGAGGGGTGTGTATCAATAATATGACATAATCAAGCTCAT
GTCATCAAGACGACAGATCATTTTACTAGCTACTGTAGCAAGAGTAGCCA
CCAAGTTTCATATTTCCTATATACTGAGGCTCTTGCCTCCCTTGTAACGT
TCAGTAGACATAATAATGTATACACTTTTCAGTTCTCTGCCTATATTTTT
CACTCCTCTACTATGATTCCTCCTAATACTTTCTGCAATTCTCATATATA
CTCTGAGATATAAATGTCTGAACAACTGTTGTGCAGGTTATTGGGCTCAT
GTCAAAGGGAATCGACAATTGGGGACATGTAAGTATGGGAACAGAATCCC
TTTTCCTTTCCTGATTGGTTTTATTTCAATCATATATATCAGTAGACTTA
ACCTAATTTGTCTCTTTTTTAGATATAGGTCATGCCATGTATTTTGTTGC
ATTTGCTACTGAAAGTTAAGGGTCCTGGTCCCCAGCATATGATTGCTGGG
GTGCCAGTAACTAACACACAGCACCTGCACCGTTGGATCACTTCACGGAT
GGCCCAGATTTAAAAAATTTCTCGCACGTACAGCGCTTAAAAACCGTTGT
ACGTCCAGCGTACAACGCTTTTTAACCGCTACGTCCAGTGTACAGCGCTT
ACAACCGCTGTATGTATAAATTTTTTTACACGTACAACGCTTAAAAAGCG
CTGTAAGCATAGAACGATATAAAAAAAATATTATGAGATTATTAAAGAGG
CAGGATGGTTTTGGTCTTATAATATCACCTCCTGGAACATTTTCCAGCCA
GCTCCAGATCCCCACTGGAAATATGAATGTTACAAGAAGATAAATCAATG
TAGGAGACCCAATTACCGTGCAATAGAACTTATTAGATGAGGGGATATAA
AGCAATTATCATTAGCTGAAAGATACGATCATAGTTCAATATTTAATGCT
CTTTTATACCCCAAGACCTTGATAATCATTTATTGTTTTCAACTGCACAA
TATGAAATGTTACTTATATTTGCATTCATTCTCTAAAGAACTCCCTCCAG
AAGGAAAATCAATGAAAATTGGTTTTTGGCCATAGCTCAAATTGCAAACA
AAATGCCTAGAAGTTATAAAAAGTAGCCAACTACTAATTTTAGCAAACCT
AAAGATTATGTGAGTTACGATGAAGGGTTATTCTTTTGTTCAAAGTGGAC
TGTAAATAATGCCCAGTGGATGCTTCTAAGGTAAACAAGAATGTCACCTC
ACGAAGGGAAGAGAAACACATAAAAGCAAAAGAAAGGGAGAGAACGAGAG
CTAGTGCATCACTTCCCCTTAAATAGATGACCCAGAGTCCCAGACGGCCA
GACTACTGTTTATTAGAAAGCTTACGAAAGAGTATTCCGTCGAAAAGGTC
AGATGTAAGAACGTAGCTAAGGAGTATGCCATATATACAGCCAGCGATAA
CTTTGAGAAATAGTTTTCTTTTTAGCATGCTTATTATATCTGCTATAGGA
CACGCCATAATAACAACAGAAGCAGCAGCAGCAAGCACATAATAACCTCA
TAATAATAAAAAAAATTACATGTTTAACCGCTGTACGCTAGAGGTACAGC
GGCTACAGTGGTTTATAAGCACTCTACATGCGGGAAAATTTTAAATCGGG
ACCGTCCGTGAAGTGATCCAACGGTGCAGGTGCTGTGGGTTGGTTACTGG
CTCCCCAGCAATCATATGCTGGGGACCAGGAACCTCATAAACAATCAAGT
CCTTGTTTGTATAATTCAAGTCACTAAATGGTAGATGGGAGTTTTGGTCA
GTAACCAAATATTATTGCATCTATAACCTAAAAGTAAAAGTTTTTGTCAA
CTCATTGAACCACAAGTCGACCACGAAGCTTATCACTGAACTACATATAA
AGCATATCAGTGAACTATATTTGATTTTAAAATATGCATTTTCCATCTAT
ATTGACTAACCTCAAACTAAATGTCATTAAGTATTAAACAGAAGCTGTTA
GTACATGTCATTATTTCTGATTTTCTCAAGATCCATATGTAGCTGTCAAG
TCAGGATCTGTGTTCTTTACTTGTATTTTAGGGCTATGTTTTATACTCTT
ATATAAGGTTATGTGTTGGATGCTTAATGACTGCTAAGCTTTTGTAAATA
TGCAACAAGTAAACCAGAATTTTAATGAGCTTAAATTTTAGAATTATATG
AATTTGTGGAAAGTATTCGTGCTTGAGTGAGTTATGCAACTTTTAAGGTG
CAAGTGGTTCATATATAGTTTAGTGGCGAAAAGTAGCCTTTACGTTTTAA
TGAATGTATATTTCAAGGTGTTGCCTGATGGAAAGGAGTTTAAGCATTTT
CTAATAAGCTGACATCTTAGATTAGTTCTATATAGTCGTAATATTCTTTC
ATTGTGCCTTACCTTTCTAACCCAAATTTAATTAATTTAAACATGATACT
TCTAGTTCGGAGGCTTCATAGGTGGAGTTGGAGCATCATGGCTTCTTGGT
CCGGCATGGGAGTACAAAATGCTTACCAATGATAAGAGACGAGCTTTTGT
CGACAAGGCACCGATTTTTTCCCTTATCAAGCCTAAGAGGAGGCCTTCAT
AGATAAATGTCTGTGTAGAGTACTCTCATCTCCCACAGACACGCGCGCGT
CATAAACTGTACAAACCCGGAAGGTGAAATCTGCATGTTTCTTAACTGAT
CACCAGTGATTTTCTTGTCGCAACTCCAGGAAAAATTTCGCCAATCCAAT
AGGAATTA