| Relationships |
|---|
| The mRNA, DCAR_022657, is a part of gene, DCAR_022657. |
| The genetic_marker, MK005240 K2684, is located in gene, DCAR_022657. |
| 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_022657 | DCAR_022657.mRNA | mRNA | DCARv2_Chr6:9104453..9109251 |
AAAATTTAAAATATTAAAACTATTAAAGTTTTTTTTCCCGATAAGTAGTG
GAAAATTAAGTGTACACCTAGAAACTGACCCATAAAATTTGTAGGACAAT
GGTTTCCAATTTTGTTTCATTATTTTTTCTTTCTTGTAAGAAAATATTAC
GTGCTTAAAAAATTGATATCTGTCTTAATAATAAAAGTTCCTTGCTATAA
AGCTAATTAGTCGCTAATATTTTCTCTAACTTTATCATTTTAATTATACG
TACACCGTTGATCCATTATCAGAAGCTGGTTTACTTTCCTAGTATTTACA
GTTTCCACGGGCAGTTGATGCATAATCTTTCCAGTTCAACAACAAACATC
ACACAAAATATTAACCAAAACATTACACAACTAACATAATCATTCATAGG
AATATAAGATGATAAAATTAAAACCTGCAATCCCCACCTAGAGACCGGAG
GTAGAATTAACAGCACTTAAAAAGATTAACTTCATCTTCATCATAGACTA
CATTACATTACTCAGCTACATACTACAACCAGGTCCCGGATCCCATTTCA
CCTTCATCTGATTCTTAGCTGCAATCTAAGAGATAGCAATAGACACAGTC
TTGGACTTGGGTGGAGGCACCTTCTCAATCGACACAGTCAAGACTCCGTT
CTCACATTTTGCAGTTATAGTAGATGCATTGCAATTCTCTGGTAGCCTAA
ACTTCCTTGCTAATTTTCGAGGCAACTTCCTCTCCAGCTTTATGTACTTG
CACTCTTCTTCCCCATCTTCGCGCTTCCTCTTCCCATTGCTTTGAATTAC
AAGTGTATTCCCATCTTCAACAGTAATCTAAAACAATAATAAATCATAGC
AGTGAACAATGTAGTATTAAACTTTAATACTGGTACAAAAATTTGTGGTA
CAGAAAACTATAGTTTCTTCACCAGTAATCTACAAACAAATTACAAATCA
AAAACAGCTCAGCAACAATGTAGTTTTACAGCTAAATCTCGCTAAACAAA
TGCTCTCAAACCATATTTGTTTTATTGTTTGCTAATTGAAGATTATATTA
AGAGGAAAGAATATAAAGGACTAAAAGAGCTAGGGGGATTACCCCTTTGA
AGTAAGGAACTTGCTCCAAACCTTTAGAAAAGAACTAGAAGGTTCACACA
AAATCTAGATAACCAATCAACCTTGTACAGCAGACTACTAATTCTAATAT
CCACGGAAACAAGTATTTTAAACTTCACAGAAGAGAATAATTTCTCTCGA
ACTTGAAGCTTTACTTTATGCATAACTGAGTACGAAGTATTAGATGCTCC
CAAATTGTTAGGACTGCGATAACTACTAATTTATTAAAGTAAGTTATCGA
GTGGGATATACACTAATGTCATGACTGCAATAACTACCAAGTAATCTATT
TATTCATTCATCCTGCTTTAATTAGCAACCTTCAAATCAGAATTCCACAA
ATGCAACAATGTACAATGCCAACGTATACCGCCATTTAAAAACAACCACT
TCAAATGAAAATTCCTTCGATCTATTTTAGAATGGGGAAGAAATGGTTAC
CTGAATGTCGGATTTGGATAGGCCAGGGACATCCATGTAGAAAATGTAGT
TATCCGAGCTCTCAAGAATGTCAACCGGTATTGAATCGAACCCGCTTTTC
GATTCATGAGACCTTGATTGGGAAATAAGCTTGTCAACAGCTTCAGGCAA
GTTGAGCAATTGGCTCAGAGCAGCACTTGCAACATCACCATTCAAATACC
CTGCCATCTTCACTCGCTTTCAAAAATCACTCTGCTACATCACACAACAA
ACAACAGCACAAACAAATTAAACTAAAACTAAAACTAATACAACTTTCAC
ATATATAGAATAGTGTAATTTCTTGATTTTTGAACTATTAGTCAATTAAG
CCCAAAAAAGCAAGACTACAAATTCTAGGTAATTAAAACATGAATTTACC
TAAATACACTTGATTAACGATAATGAAGTTTGGGAGATTTTGTACTATGG
TGAAAAGTGGGAGAATCCATGGATTATAAAGACAGTGAGCAGAACGTTCC
AGAAGCTAGTTCTACTACTTATCTCGCGGAAAGTCTAGAACACTCACCAA
GCAGCAGCTTCTTCTCTGCGTCTACACGTCGTCGTACAGTTTCGATCAAT
TTTATGAAATGCCATATTTACCCCAAACAAGACAAGAGTGAATGGGCTTT
TTAGCTCGTTTACCGGATGGGCTTGAATCTGGCTACCCAGCCCAAAAACA
TGTTATGATTTTCTGACAGCAACGGCAAAACGACGTCGTGGCCACTTCTC
CGTCGACATATGTCCACCGTGAACAGCTAACTCCGTCATCTTCAGCTCAC
CATAACGACGGCAACTACAACTACAGGTTACCTTTTCTATCACTATCTCT
ATATGTATTTGCATATTAATTTTTGTTTAATTTGTGTTCATTTCTAGGGT
TTATACATTAAGCACCATTCGAGCTTAATCAAATTGAAATCAGTTTACTC
TAACTAATTAAAACACTCACATACCTAATATGTGTGTGTGTGTGTATGCT
TAATTCTTGTTTCGACATCGCAGGAACTGGTAAGAAGCGGTATAAGCTAT
GTCTCGGTTTCGTGCAGCCTTGCAGGCTTCTCTCACTGCTACTAAAAGAG
GTAAAACTCATTGATTTGGCTCTTTCATGGAAATATAGTTTCTAAAAAAA
ATTGTAATTGCTTTTGTTACTAGGTATGTAGTATTTGTATGATTATTAGT
GTGAGTACATGGTTTATAGCATTGTCGAACGAAATGAAAAGAGAAGGTTT
TGGTACACGTATGTATTTGTATACGAGAATTTATTCAGTTGAATATATCT
TTGTTTTTACTTGTAGCTTTGACATGGAATGTTGAAGACTTGATTCCTCC
AAGCGAGCGATTTATTTTCAACTTTAATTCGAAGGAAGAGCTTAAAAAGT
GGCATTTGTATTCTGATTCTGAATATGGAGGTGCGTGCTTGCTGAAGTTT
GATGGTTTTGTTGCTTGCTTTTGAGTTGTTTTGAACATCTTGCTTCTGAC
CTGTGCAAGGTGACACTAGTACAATGTGTCTTGGATTATCTGTGTTGTAG
TTTTTTAGATGTTTATGACTTGTACACTTGACAACAATTCTTCATTACTC
ATGCACTTTAATAGCACAGCTAATCAAACTTCATACCCATTTTTTCAAGT
ACTGGGCTTTGCATTAATATCTTGATTTCTAAAGTTATATAACTATACAA
TCTTACTTTATGTGGCTATTTTGCAGGTTTGTCGTCAGCATCCTTGGAGA
TCACAGACACTGGAACGGAATCAAGTAATACTGGTTAGTAGAAACTATAC
ATCTGTCTGTCATTACATATCTAGCCGAAGTACAACAGTATACTCTATTT
GGGACTACATAGAAAGTATATCAATTTTATTAATTTTGAATATTAATATG
TTTAGGATATACTAATACATGTTTGAATAGCAGAATTTTCGTAATTTGTG
TAGAATGGTGGTCATGGCAGTCTTAATGCTCAGTGTGACATTGTGTACTA
AAACTAACATTTTGGCTCAAAATTCTGTTACAGTTGTTGTAGAATAAATT
TATTAGTATGTGCATCTTTTGTACATTTTAGTAGCTTGCTCGTAAGTTTG
CTTAATTTGTAGCTGGTCACTATCCGGTGATAAAAAAAAGTTTGGTTGAA
ATAGATAACACATGAACTGTGATGGCCCAAACACAATCAACATAAGCAAC
AATGTAGTCCCATCAAGAGAGCGAAATTGTTTAGTCAAAGAAGTATGTTA
AGATCTTTAATTACTAAAATTTATAGGACGTTGTCCGTTCTCTGGGATAC
CTTTATATAGGTAAAATATCTAAGCATGCATAAACCTAGGACAGAATTTG
AATAACATTTGATATATCTGATAATTATTTGGTCAAATGCATCTACTCAA
AGTATTTGGTTTGACAGAAATCATGCCATTTGCAGGTTGCATATTACTGA
TAAACTTTTGATATTTTGATAATTTGAAATGAGGACGAAGTTGTATGGTT
TAACGAATAGACCTAAGGAGAGAACACACTTGCCTGCTTTTGGCATTAAT
AGAGGACTACAGAATGATAGTTTGTTACCAGTCTATTGACCCACAGTTAG
CTATCCCTCCTTGCGTGTGCATTTTCCCAGAAGACATTATAATTGGCTTG
TTTTTCTCCTTGACGTTGCCTGACAAAGTTGTGAAAATTGGTCTAGTTTT
GGCTCGTGGTGGACCCTGTTCATGATTTTACTTTTTGTGCCTTCTACCTA
ATTTCATTGAGATTATATTGTTTCTAGGGATCAAGCTTGGGACAGAACAA
TTAATTATAATTTATAAGGACTCATTTAGTTATATACTCTGTAATTAATC
CCTTAGAGAATAGTTTTCACTTTTCACTGCACTAAGGGGGATTATTTAAT
CTCATAACTCTCTAACAGATATATTATTTTCTGTGATCTGGACTCTAATG
ATTAATTTTGTGTATAAAAAGGATTAAGTTTTGGATTAGTAGTCAGTTTT
AGTTAAAGTTAAAGAAAAAAGTCCCATCCCAAGCATCATTTTTGCAAACA
AACATCATCTGATGAATTTGAGAGTTTTTGACCAATATTATTGCATTGCC
TCAATTATAGTTTTTTTTCATATTTGTGAATGCTTCTGAAGCTTATCTTT
GTTCTATTTTTCTTTGAACTTATTAGGAATTTTTTCTGGGAATCTCTCCC
TGGATGTTACTGCGGGATCAAAGTGGAATATCTCCCGGAGTGGCTTCTGT
GGTATGCGGTCGAAGAAGGTAAATATCACCATTAGTGTTTATTTGGCTGA
TATCTTATAAGTAAATCAAAGCCTCAATGCTAAACATCCATGTAGCTTCC
TTTCTTACATTCCTTTTATCAGGACTTGGAAGAAAAAAAGTAAAATGTAT
TTTTTTTTTTGCCAGCCAATAGCTTATGTTATAGTCTGTAATTGCCATGT
GGGGTAATGTTTGTTCTTACTACTGAAAGTGGAATGTGGGGTAGCTTATA
CCTCTTTTCTCAGTTTTTTTCCCTTGTGGCGTCACTTTTGATGGCCTGCT
CTGGGATTGAGAATAGTATCTAAATACACACCCTTGTTTAGTTTGACAAA
TAGTGGCTTGTTGTTGATAGGTCACGAGGTGTTACAATTTTGTAAGTTAA
CATTTCTCCACTATGACTTCAGTATTTCACAATGAAGTATTTGGAAAATA
TATTCTTCAGTTTTGTTTGGAGATCTTTGTAGCTTGTTCCCTGCCAAAAA
TATGTTTATAATTATTCTAAGTAGATATTGTATGTATTCGCTACTGTTTC
TTAATATATTCTGATTACCAGTAAGAAATATTGAAATAAAAAATTATAGA
GTGAAGTACACTGGTGTACTTGAACTTTGGGTGCCAAGCCAGTTGCAGTA
CTATACTTTGGAAAGTGTCACTTGTAATACTGAACTTTACTTTTGATTAC
ACTTTATCCTGTTCAGGCTGTTTCAGCTGACTCCTCGGGTATATTTTTTT
TGATCCCTCAAGTCAAATTCAACGTCTTTATTACCTGTATATAGCTATCA
CTCGACCGGACCAATATCAATCTAACAATTAGGTCTTCCCCAAATACAGA
CTACCCTGTTTAGCCTCCTCCTTCAGAGTAGAAAAACAGTGGCTGCATGA
CATAATCGACTGATACACAGTACAGTATGAAACATTTCCAATTTTACTAC
TTCACCTCAGATGGCAATAGTGTAGAACTGGGTCAAGGACAAGCTGTGCA
AGGTTCCCCATTTTTTGACTACTGATTACAAGCCTGTAAAACACCATTAA
AAGTAGTGTCCGTTCGTCAAGAGCCTTCGTGTATTTCCTGGAGAGCGTCA
AAGCCATGTGGGCATTTTATGGTGGCGGTCGATGTGGTGAGTTGCATTGG
TGATAGAACAAAACCCTTAGAACTGTGATGATAATAAGTTTAGAAATGGC
ATTGTAATTGCAGTGTTGATTTTAGCTTTATTCAATCAATAAGTGAGATG
TCAGTTGGGTGTTCTTGATTAGAGATTTTTTGGTTGGACGTATTTTGATT
TTGTATTAATTTATAATATGCAAAAACCTATTATACTGTTGTCCGTTGAT
ATTTTGTGGTGGAACAAGCAAAAGTTTAAAGAAATTTAATTACTCAAAAA
GAATTTAACGGAAATTGGAATCTAGCATTGCCACAAGACTTTTTAAAGCA
TAGTATTGCAAGTGGTCTAACCTGAAGTGCTGATGCACGAAGTGCATTGT
ACATAAATTAGTTCTCTCAGTATTGAATGCATATTTTTTTATGTTAAAGA
ACTTTTTCCTTTTCTTTTCCTTTCTTACAATACTATGGGAAATCAGGCAA
TATTCTGTTCTCTTGTGATTTATGCAGTTTGACGGCTTCATTGATTTGGA
TCCATACGACACAATAGCACTAAAGCTTAAAGGAGATGGGAGATGTTACA
TATCAACGGTAATTTTTTCATTTTGTATTATCCTGACAAACAAGAATTAA
ATTTGTGTAGCTTTTCTCTTGCTGGTTTTACCAAAATACCTGTTCAGGAA
TATTCTTCTGATCTAGCGCTCAAATGAATATAAATCTGTTATAGATCTAT
ACAGAAAATTGGGTAAATTCGCCTGGACAAGAAGAAGATAACTCATGGCA
AGCGTTTGTTTTTGTGCCTAAAGATGACTGGTATATTGCAAAGGCAAGTT
CTTTTCTATGAAACTTGGTTAGTTTTAACATCGTCAGTGTAAATTGAACT
ATTCTGGAGTGTGGTCTGTCCATCTAATTATGGAATTGGTCAATATTTGG
GTGATTTAATAATCTTGGTATGTTCATCATTTTAGCCCATGATACAATGA
TATTATCCGATGGTTTGTTCTACGATTTAGCCCATTATGATAATGATATT
TATCCGATAATAGCAATGTCATGAGACTCACCCGGATGAAGAATAAAACT
GCCTCGAGTCATGATCTGATTACGTAATTGTTTCTTGCTAGATCTGTGAT
TGTTATTTTTGTGATTGAAATGTGAAGTGAGTGTGTATATTTTATGTTTC
ATGCTTATTTGAATTGTTGGAATAAGACTTTTATCTTCTTGAATTACCTG
GAAAGCCAAATTAACAGCCAATAACTTTAATAAAATTATTAACGAGTTTT
TCAACAGATACCTCTTGCTCGCTATCTACCAACATGGAGAGGGAACGTCA
TTGATGCGCAAATGGAAATGAATCCGTCCCGAGTTCTTGGCATGTCATTG
TCTGTCAATGCGGAGGGTGGACCGCCAGGTGCTAAGTCTGGTCCAGGTGA
CTTCCATGTTGAGATTGATTGGGTCAAAGCCTTGAGAACAGTATGAATTT
GCATAAAATGTCCATGGAATGTTGAAATTCAAGGGTTTTATAAGGGATGG
AGAGTAGCTGGTTAGTGTTTACAGTTGTGTGTTCTGTTGTCAGAACAAAG
TGTAATAAGTGTTATGTTTTGTACAAGCTATTTCCTCAAGGCAATGAAGG
GTCTGTGCTCTGTCGTAATAACTTGAATTATCATAACATCCAGAAGTGTA
CACTAAATCGTGAACATGAGGAAGATTGTCATGTCCGGTAAGCGGTAGCC
TGGTTCTAATGCACGTGTGTGTATGTCTTTCTCTGCGACTCCGCCTGCAG
GCTTGCAATTTCATACATTTTTGTGCCAGATACTAGAATAATAGCTCATA
GTTCTACACAATTTCAGCAATTCTTTATATGTAGAGTGTTGACTTATTTT
GATTCAGACCACTGAACATACCTTAATCTGTTTATTTTTTGAATTGGGTT
TCATGAAGCTATGTGATCCTCACGGAAGAAGTAATAAGAGAACAGATTTG
CGAGGTATCAAAGTGGAAAATTTAATCAAGCACGTCATGTAGTGCTCTAA
ATAAATTATATACGTCCGGGAACACAAGGAAGAAATAAAAAAAGTATTTT
TAAATAAGTTATGTGCATTTACTTTTATAATATGAGTTTATTTTTTCATT
ATATTTATTTTGTGTTCATGATACATTTACCCTCATTACTAATCGAACAT
ACGGTTTGAATCACGGCCATATTAGCCGGAGCCATTCCTGAAGTCAAAGC
CAAAAAACTTATGATTATTCCTTAATTATCTGTCAACCCTAGCTTCACCC
TGTGCTATAAGAACTCCATGTTGTTCCCAAAATCTCTCCTCGTTGAATAA
AAATATTTTGGTTTCGAAATCGAAGAAAAGTAGTGATTTTACAACCTCCC
TCTCCCTCTCTAATTAGTAACATTCGTATCACCTCCTTAATAATTTCATC
ACCTCCTTGACTTGGTACATTGTTACAAAAGGAGAAGAAGAAGAGAGAAG
TATCATTTAACTAATTCTTTTTGTTTTATTAATTCAAATAATTCCAACAA
TGGGCTTCCTTCATAAGCTATGGGATGAAACGCTGGCTGGACCTGCGCCT
GACTCTGGCCTCAGCAGACTCCGCAAGAATGCAGTCTCCGATCGATCATC
TGGCCGTCATGCTCTTGACAAAATCCCGATTTCTCGCACCATCACCATGC
TCCGCTCTGACTCCGTCCCATCTTCTCCGACCACCCCCACCACTCCCGGC
TCTCCATTTTCGCGTAATTTTTCCTTCATTTTTCCTGGATTCTAATATAT
GTGATCAAGATGATAAATAGAGAAAGAGAAATCTGATATTATTCTAAATG
TAACATCCTGACATGCATGTCTGTTTAGGGAATACTATAGTAAAAACTCG
AGAAATGAATAGTAGATCTTTTTAGTGTGTCCATGTACACATACTAGAAA
ATCTGATAAATAATTTTTTCTGTTCCAAAGATATTCATTTACGGATCTCT
ACTCTAGTAATCGAATCACTGTATAACGAATTTATTAGCCTAAACAACTT
AATTGGTACATGTAATGCACCGTTTTTTCAGCTACTTCACCAACTGGGGA
ATTCAAGAAACTGACTAGGAGAAAATCGACATCAGAATCATTACCTCGAC
CTCCGCCTAAGAGTCCAACTGGATACGATTGGTAAATTCCTGGAACCACA
TTATATACAATCCCAAATATTTTCGCAATTCTCAATAATGTGCAAAATTA
TGCTGTTGCAGGATTGTTCTCAGCGCTCTGGATCGTTAAGAGAGGAAGAA
TCATTTTTCGCGTGTCGACAGAATAACAAGCAGATAAACATAAATATTTT
ACACTAATTACTACATATCTGTAGATACATATCAATCAACTCGTACACAT
GATCTTAGTTCACAGCTGCATTTCGGCCGGGCCCTTGCTTCCTCCATGAT
GAAATTGGAGTGATGCCTATGTTTTTTTTTCGATATTTTGATTTTATTTT
TTCTTTTGTATGTATTAATTTGTCCCCATGGTCTGTGTTCTCGTCCTGCA
AATTGGGTACATGTAATATAATTCTTCTATCAATGGACTTACTATACAAC
TATGCAACTCCAGCACCTTTCTACTCTAGTAAAGGTCATAAGTATGGTCT
GTTTTCTGTTTATGATTCAGGATTTCTCTTCTAGCTGAAAAGGATTGTGT
TCCCAAAACTCAATTCATGTAATGATAAAATCTCGGTAAAACAATGTCAC
CAATAGTCGGTTCCTCACAAGCAAGTTTCTATGGTTAAAGT