| Relationships |
|---|
| The mRNA, DCAR_027666, is a part of gene, DCAR_027666. |
| The genetic_marker, MK009819 8_20788164, is located in gene, DCAR_027666. |
| The genetic_marker, MK009822 8_20788674, is located in gene, DCAR_027666. |
| The genetic_marker, MK007912 TP111258, is located in gene, DCAR_027666. |
| The genetic_marker, MK009816 8_20788896, is located in gene, DCAR_027666. |
| The genetic_marker, MK010979 8_20790755, is located in gene, DCAR_027666. |
| The genetic_marker, MK006265 K3709, is located in gene, DCAR_027666. |
| 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_027666 | DCAR_027666.mRNA | mRNA | DCARv2_Chr8:20786251..20792734 |
TTTCGCTTTATGTATTTCATTCCGTTTCTTCCCCTGACTCTCTAAATTAG
GTTAAACCGTTGAAAGCCTCTTTGTTCCGTTTAAACCCCCACCAGCAAAC
CAAACAGAATTACAAATCTGTTTCTAGGGTTTTTGTTCTGCTGGTTTATT
CACTCAGCTGTCGATGAGGAATCTAAAGCTATCAACTGAGCTCACCTCGA
TTCTCGAGCTCCAATCAGAAAACGAAACCATTCAATTCGCCGCGTTCGAC
ATCGAGAAGAATCGCTTGTTTTTCGCTTCTTCAACTAATTTTATCTACAC
CGCTCAGCTTCCTTCTATTCATGTATATATTCTTATCTCCGTACTCAAAT
TTATCGATTTTATCGATGTTAAAAATACACCGTCTCTGTTATGTTGTGAC
TGAGAAATTTCAATTTATTACCTCACTTGCAATGTATAAGTAGGTTGTAG
ATATACATGAATTGTTATATTGTAATTCATTAATTTATCGATATTAAACG
CATTATCTCAAGGTTGTGTATGTGCAACTTTATATGCAATTTATAATTAG
GATGTTGATAGACAGGATATATTGTATATGTAGTGATATTGTTTGATATA
TAGGATGATAAGTATGAATTGGAAATGTTTGATCTTGTATTAGTTCAGTT
GTAGAATATATATGAGCTAACGAATTTTGGACTGTGTGTTACTGTTTAGT
TGGATAATAATGAGGTGACGGTTGATGTTTTAAATTTTTACCTTTAAGTT
ATTTTTTTACGAGTCTGTGTTTGTTGGGGCTGTAAAATTGTGATTAAGGC
ATTGAGTATCGAGTTGGAAATCTGATTTATAAAGTAGAGGTAAGAAATTG
AGAACTGTTGTTTCTAGATATAGGGTGTAGTATAGATAGTCCTTTCGTTG
TATGCTAATGACCGAAGCAAGGTGTTAATTTTTGGAATTTGAGTTTTTTT
TTCCCTTTGTATTATACATGGTATGTGGTAATCATTCTATATGTGATTGT
AGCATAAAAAGAAATGCCTTGTGTTTTTGTGTTAGTACTTAGTATTGAGG
GCGTAGTTCATTTGAGAAAGTTTTGTTTATAAACTTTGAAATGCTTATGA
TTTGGCAGGATGGAGGTCGGAGCAAGACATCTTTACCTGTAGTGGTTCAG
CCAATTGATTTAGACCATGAAGACTTTATTACTTCCATGGATTTTCTCAT
GGAAAAAGAAGCACTTGTGGCAGGCACTTCTAATGGACATCTATTGCTAT
ATAATGTTGATGACAATGCAACAGAAATTGTTGGTCATGTAGAGGGTGGT
GTCAAGTGCATCTCACCTAGTCCAGATGGAGATTTGCTTGCGGTGGTTAC
TGGTTTTGGCCAGATACTAGTGATGACTCATGATTGGGATCTGTTGTATG
AGACGTCAATCGAGGATCCTGCTGAAGAAATTGATGTAAGTAAGAAACTC
TTCCCTTTAACCTCGATTTTGGTATCTCCTTTTAATTATAATTTTCTTTG
TTTGATGCATGTGATGCTAACCTACACCACATGTTCATTTTAGAAACAAA
AGCACTAACGATTGTGGTGAATGAACTACACATTTCCTTATAATTATTAG
CGACTGTAATAGCATGTACTTAATCTACCTTTTCTCTGCATTAATATAAA
ATCTATATCATATCATGTAACTAATGTACAAATAAAAATAACTGAAGTTT
ACTAGGACATGCATGGAGCCCTTTATTAACGTAACTTATATAATTTTCTA
TGTTTTATTTTATATTGATCATAATCTGGTTGATTACTTTGTTGAAGGTG
GGCCAGTTGGGAACCTCCATTTCGTGGAGAGGGGATGGAAAATACTTTTC
TACAATAAGCAAGGCACATCATTCAGTTCCCATGAATAAGAAAATAAAAA
TTTGGGAACGAGATACGGGGGCACTTCATGCTTATTCAGAAGCAAAGTCT
TTTATGGGATATATTTTAGAATGGATGCCCAGTGGAGCTAAAATTGCAGC
TGTTTATGATAACAAGGACAAACATAATTGCCCTTCAATAGTTTTCTTTG
AGAGGAATGGTTTAGAAAGGAGTTCATTTAGCATAAATGAACGGGTTGAT
GCAACCATAGAAAATATCAAGTGGAATTGTAATTCTGAACTTCTTGCAGC
TGTTGTCAGGTCTGAAAATCATGACGCCCTGAAGATTTGGTTTTTTAATA
ACAACCACTGGTACCTGAAACAAGAAATTAGGTATTTGAGAAGGGATGGA
CTGAAGTTCTCGTGGGACCCAACAAATCCATTCCAGTTGATTTGCTGGAC
TCTTGGTGGCATTGTCACAACATATAACTTTGTGTGGGTTACGGCTGTCA
TGGACAATTCAACTGCCTTGGTCATTGATGACTCCAAGATACTAGTTACT
CCCCTTTCCATATCGTTGATTCCACCTCCTATGTTTTTGTTTGAATTAAG
ATTTCCGCGTGCTATAAGAGAAATGGCTTTTTGGTCCAACAGTTCTAAGA
CTCTTTTGGCTGTATCTTTGTCGGATAATGCTTTGTGTGTTGTTGAGCTT
CCTGTAGTGGAATCTTGGGAAGACCTAGAGGGTAAAGAATTCATTGTTGA
GCCTGTCTCTGGGAAACCACTAGGATCCTCTGTGCATCTCTTATGGTTGG
ATTCACATGTTCTGCTCAATGTTCCACATTTTGGCTATAACCAGAGCAGT
GACCTGGTAAAATCTTCTTCACGCAAGGATTGTTTGCCTTGCATACAGGA
AATCGAGATCACGTGTTTGGAAAATCATATCCCTGGCACAGTGACATGCT
CAGGTTGGAATGCTAGGATTTTTGGTCAGATCTCACTCGAAGGGATGGTT
ATTGGCCTTGCACGAAATCCTGTTCTTGATGGTTCAGCGTTTGTTCAGTT
TATTGATGGAAAAATCTTTCAGTATAGAAAGCAGGCAGGAGCTGTAGTAC
CGTCTATTGGAAACCATACTGATATCAGTATGAGTTTCTCATCATCTTGT
CCATGGATGAGCGTGGTTCCTGTTGGAGATTCTGATCCATCAAATCCTTT
TTTGCTATTCGGGCTTGATAATTTTGGTAGATTGCATGTCGGTGGCAGGA
TACTGTGCAACAACTGCAGCAGTTTCTCATTTTACTCCAATTCCCCTGAT
CAGATGATTACACATTTGATTCTTACAACTAAACAGGATCTGCTCTTCGT
AATTGAAATTAGTGATATTTTGTTTGGCCAGCTAGATGCCAAATATGACA
ACTTTTTACCTGTCATAAAGAAAAGACGCGGAGAAGAAGAAAGTAAGAAT
ATAACTTTATGGGAGAAAGGTGCCAAAGTTATAGGTGTCCTGCATGGAGA
TGAATCTGCTGTTATCTTGCAAACAATCAGAGGAAACTTGGAGTGCATCT
ATCCCAGAAAATTGGTTGTTGCATCGATTATCAATGCGTTGGGCCAAAAG
CGTTTTAAAGATGCACTACACATGGTAAGGCGGCATAGGATAGATTTTAA
TATCATTCTTGACCATTGTGGTTGGCAAAACTTTCTTCACTCAGCTGCAG
AGTTTATCAGACAGGTTGATAATCTGGCCTATGTAACGGAGTTCGTCTGT
TCCATAAAGAATGAAAATGTGATGGAGACATTGTACAAAGAGTTCACATC
TTTACACAAAGAGGAGTTTAGTTTAGTTGATAATAATAAGGTATCTTCCG
TACTGCTGGCTGTGAGAAAGGCACTTGAGGACCAGATAGTGGAATGCCCC
GCAAGAGAACTTTGCATTTTGACCACCTTAGCTCGAAATGAACCCCCAGC
TCTTGAAGAAGCTTTGAAGAGAATAAAAGTGATTCGGGATATGGAACTTT
CAGGTTCCAATGACCCTCGGAAAATTTCTTACCCTTCTGCTGAGGAATCT
TTGAAGCATCTCTTGTGGTTATCTGATCCTGATGCTGTATATGAAGCTGC
ATTGGGTCTTTATGATCTGAACCTTGCTGCAATAGTTGCATTAAACTCAC
AGAGAGACCCAAAAGAATTTCTTCCTTTCCTTCAGGAATTAGAACAGCTG
CCAACTTTATTAATGAAATATAATATTGACCTTAAACTAAAAAGGTATGA
AAATGCACTTAGACACATCATTTCTGCAGGAGATGCTTATTCCGAAGATT
GTATGAACCTCTTGAAGAATAATCCACAGCTTTTTCCGCTAGGACTGCAG
CTGACAACTGATACTGTTAGGAGAAGGCTCGTCACTGAGGCCTGGGCAGA
TCATCTTAGTGACATAAAATGCTATGAAGATGCTGCTACGACCTACTTAA
GCTGTTCAAATTTAGAGAAAGCTTTAAAGGCTTTCCGTGCCTCTGGTAAT
TGGGCCGGGGTGCTGACAGTTGCTGGTCTCATTAAGCTGGGAAAAGAGGA
GGTCATTCAACTAGCTCATGAGCTGTGTGAAGAACTTCAGGCACTTGGTA
AACCCGGGGAAGCTGCTAAGATTGCCGTAGAGTATTGTGGAGATGTAAAT
AGTGGGATCAGTCTCTTAATCAGTGCAAGGGACTGGGAGGAGGCTCTGAG
GATTGCTTATTTGTACAGAAGAGATGATTTAGTTTCAGAAATCAAGGATG
CATCTCTTGAGTGCGCAAGCGTGTTGATTGGAGAGTTTGAAGAAAATTTG
GAAAAAGTGGGAAAATACTTGGCTCGCTACTTGGCAGTGAGGCAGCGGAG
ATTATTACTCGCTGCAAAACTCAAGGCAGATGAGCAGTCAGTAAATGATC
TTGATGATGATACTGCTTCAGAAGCTAGCAGCAATCTCAGTGGAATGAGC
GCGTACACCTTGGGGTAAGCTAGTTATCTTTACATCATCTTTACATCCTT
TGTGTCATGATCTCAGTTTACATCTTACCCAGATGTGTAGTCGGCCATTT
CTCTCTTTCTAAAGAACCTTGCCGTATATAACATTCTCTTAGCCATTCAG
CTGTTGACTAATGATAACCCTACAAGTATGTCCAAAATAGACATGATTGA
ATCTGCCAGTTAAGTCCAGTACTTTGCGAACCATAGGTTGTTTCATCTTA
ATGTACAGAAAGTCTCATGTAATGTCAGTCGATAGACTAGCTTGTTCTGA
TATAATTGCTTTTTTAATCGTTTCAACTTAAAAACCGCTGGAGTTTTGTG
GTGTGTGTATGGTAATATCACATATATAAATTATAATACATGTGTGTGCA
ACTTACTCAAATAAATAGCTCGAATACCGAAGAATATGAACTTTCTACAT
GTGATCGTCACAAATTGAATTATAATGAAATTGCTTTAGGGCGTTTACCA
ATGTTAATAGTTAATGATTGCACGACTCGAACAATTTTGAATTTGCCTCT
GAAATAAAAAAGAGAGCAACTCCCAACTAATAAGACTCCATTTTGATGTA
GAAGAATGAGGCTCTTGCTTGGTGAATAACTACAACTCCAAACTATTGAT
TGATTGGTTTTGTTGGTGAGAATCGTTGCAGACTGAAGCACACACTTAAA
AGCGCTCCCCATTTTAAAATCCTTGATTTCATAGTTTCTTTTGTATTTTG
TGTACACAAGCAAATATTTTAATTTGAATAAAATAGCGCAATTTAACATA
ATAGGTTGTTAAGTAGATCAAGAACTACTCATTAACACGTCAAAAGTACC
ATACAATCTGGCATTAAGGATCACCATATATGAGATGGAATGTCATAGGA
GAGTTTAAGAAAGTCTATCAAGATGTTCAGGAGGTTGATTAATGGTTACT
GAACAGGTGTTATGCAATGGTAAGGTACATGGCTTTATTAAAAATTGGAG
GAAAGAGGGATTTTGCAGATATTAGGTAGTGACAGGGTGAATTGTCTTGA
TATATGGCTTACAAGTCCCCCCTACAAGTTTTGATTTAAAATAATAGAAG
TTTTGACAACTTATGTAATTTTTCTTATTTTCTGAGCGGCTGGTCTTCAC
TCATACTTTGTTGGCTATGTATACACTAGTTCTGCAATAATATCTTTTTC
CTTATTCACTTGTTGCCAATTCTATACAGGAGTTCACTTGTGCTTCTTTT
CTGTTTACGTAAATCATATTTTTTTTAAATTTGGATCTCCTTTGATAAAC
TGCTTTCATGGCAGAACAAGGAAAGGGTCTGCAGCTTCTGTTGCTTCGAG
TACCACTAGCAAGGCTAGAGGGATAAGGCGTCAGCGGAACAGAGGAAAAA
TCCGCGCTGGCAGGTATTTTGTTATTTCTATGTATTGCTCACTACTTATA
TTCATTTCAGGGGTATTCAAAGTTTTAGACCTCTAATCAATCACATACCC
ACTAGTGTTAATTCGAGAATTGTCTTTCAGTCCTGATGAAGAGATGGCTT
TGGTGGAGCATTTGAAGGGAATGTCTCTGGCGGTTGGTTCAAGGAAAGAG
CTTAAATCTTTGTTGGTTTCTCTTGTAATGCTTAACAAGGAAGACATTGC
GAGAAAATTGCAACGAGTAGGAGAAAACTTTCAACTGTGTCAAATGGCAG
CAGTAAGTCTAGCTGCAGATGCGACGTCGAGTGAGATTATAGATGAACAT
GCTTTCTCTCAGGAGCTTTACATGAAGAAAGTAAGGAAAGAATTACTGCA
TTCAGAGGCCTTCTCCTGGCAAGTCAAAATGTTTCTTTCTCTTTGATAGG
TAAACCATTTTATTGCTCTTCTATTTGTTGCACTATAGTCTTCAGGGAGA
TGTTCCCGAGCAATTAATTGTTGGCAACAAACTATCCATTCTTTTTTATC
GAAGAAAGGAAAAAACCCCAGAGTGGGTGTCTAAAGCACGGATGGGCTCA
TGGGCTCACTGCAAGCACACAAGAAATCTAAGGTTAATGTCTTTCTGCTA
TAAAAAACCGTGGATAGTTTGCTGCAACAATCGATTGGCAGGGACCCGGA
CCCTAGTCTTTATTATATTTTTCTTTTTATGAGACAGATACTTATGCCTT
GTTTAAACAGTGTAACTAAAAAGAAACATCATATCCTCAAAAATGGCTAT
CGATGCATATGTTTTATCCTAATATTAGAAGGTTCAGAACGAGTTCCTTT
ATTTGTTTGTAAAATCTTGGTTTGATCATTGATGCAGTTGGTCAAATATA
ATTCTGCCAGCCATACCATAGAATGTAGTTTCAGATGAGATGGAAATATA
TTGAAGCTTCAAATTTAGTCTGAAATCAAAGCCTTTCGATTTTTTGACAT
GCAAATCTGATATTGCAGTTGAATAATGGTCCCATGGAGCAGTTTTTCTG
TCTCAAGCCTATGCATGTACACTCTCTAACCCATGCCTGGGAGGCTGGGA
CCATCAAAATATACAATTGCCGCAAGACCACTTTTTCAAGGCTTATTTTA
TGTGAATGAAGGGTATTAGAATTAGTTCCCTAAATATAATGTTCTTCGGG
CA