| Relationships |
|---|
| The mRNA, DCAR_016218, is a part of gene, DCAR_016218. |
| The genetic_marker, MK004069 K1513, is located in gene, DCAR_016218. |
| The genetic_marker, MK018251 5_1290374, is located in gene, DCAR_016218. |
| 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_016218 | DCAR_016218.mRNA | mRNA | DCARv2_Chr5:1290091..1297184 |
ATGTTTCTGCGTGAGTTTTATAATGGTCTGTTTCATGGTTCGTTGCTCTT
TTCATATTCTGTAAAGCCCAATTTAAATACTTTTCGGCTTCTTTGAGCCC
AAAATCATAAGCTTTGATGTTGTCAGCCCGTATCATATCCAATTTAACTT
TGTGGACTCTTTCTTACTGTAATGTGCCCGTTTAAAGGCAAAGCCTAAAT
GGGAGGAACTAGGCTTATGAAAAGTGGAAATGAGTGAGGGCTCGGCCCTG
ATTTATTTATAATGAGTTATTTGATAAATCTGAACGATTAATATGTGAAT
AATATATGTGATTAATTTGAATGAATAAAATATCTGTATTTTAAATGAAT
ACTCCCTCTGTCCCTCTCATTTCTTTACCGTTACTATTTTGGGATGTCCC
TCTCATTTCTTTACATTACTATAAATAGTAAATTTTTCTCATCATTACAC
CCACTATCTTCCTCTACTATCTCATATTTAACAATAAAAACTACTATCAC
ACCCACTATTTTCCTCCACTATCTCAAATCTATTATTAAATATTGGTAGT
TCCTACCACTTTACCCACTTTTCATCTAACTTTACTCATTTTTCATACAT
TGTCTTGGTCTCCGTGTCCCCCTCCAATGTAAACAATTGAGGGGGACGGA
GGGAGTATATTTTGGGGCTGTTTACCTCTTTTAAGTTGTTTCAGTTGAAG
TTCATGGCCTGTTCTAGTTATGTGTTGTGTTTTATGTGACAGCTACAACT
ACAGTTGCAACCATCACAGAAAGAAAACCCAATAAATGAAATTGTATGGG
TGTTATACATTTATGATTGAAAGGGGTGTACCATAAATGTTTAGATCCTA
GATCCTTAAGCTGCTTTCTTTGAAGACAGGCGTNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNGGGAAAGAGTTTGTGGCCGGAGGGTTTGGTGGGGTCGCCGGAATAGT
GTCCGGATATCCGCTAGACACGGTGAGGATACGGCAGCAGCAAGGTGGTG
GTGGGTCCAGGACGGCGCTGAGTATCTTCAGGAATGTTGTTGAGAAAGAT
GGTCTTAATGGTCTGTACAGAGGCATGGGTGCACCCTTGGCTTCTGTTAC
TATTCAGGTTGTTTTTTAGAATAAAACTGATTTATATTGCATGATCCTTT
ATGTTAGATGGTGATTTGCTGATTTTTGCCTCTCTAATTTCATTGAATTT
AGGAAGATAGTATAAGTTGTTCGTGACTAGGATGATCTGTGTGAAAAATA
AAAGATGTTGTTGGCCGGTTACTTAACATGGTATCAGAATTCCGTACGAT
TGAGAGGGATGTTTAATAATATAAGATTATGTTGGGGTGATTGGTGATGA
CTTAGGGAGAGGGGAGAGGTGTGGAACATTTCTGTTTAAAAGTGATCAAA
CAAGAGGTTAAGGGCAGGAGCTTGAATCTTAGTGAGAATTAACATGAGTG
TCTAAGTACTTTTCGTGATTAACATGAGTGTCTAAGTACTAATTACATAT
TGTATGACATGTTAAGAGCAGCTGTCATTAGGAATTAGGATCACCCCCTT
TTTAGAAGTAATTGTGTTCCAATAATCTTAACGTAATGGGAGAATAAATT
GATACTGTATGTTACTAAGGTCTGATGTTGATACGCCAACTTACTCAAAA
AAACCTGTTTTAGGGATTGAACCAGTGGTCAGTATATCATAGCGGATCAC
CTGTAGGACATTGTTCAACTTCAGTGTCCAATTTAAGGTCTTGGAGTAGT
AACTTAACACCATTTGTTTATGAACCTTTTATATAGTATTATTTCAGAAA
TGTTTCTCTTTAGCAGTTGCATATATTATTCTCGAGATGATCCCAAAGTT
CAAATTATGGACCTTTCGCTTTTGAGATTGATTGGTAATTTTCGGCTGTA
TTGTGTGAGACTCCTGCATTGCCCCCTTGTGGCCTACACATACAGATATG
TTCGGCCCATACCTAAACAAGGAAGAACGTTCAAAAAGAGCATCCTAGAG
AGAGTTTATCATCTAAATTATCAAAGCATAGAACAAAATCTACAGGCTGA
AGGCCTCAGTCATATAGTCGTAGACAAAAGACTCCAATTATAGCCTCCTT
GCCGCCTTACGATAATTAAATAGAGATTATACATTGTGTTGTTAACCAAA
TAAGTAGTCTCTGTTTCTTAAATTGTATTATATTGCCAAAAACGTATTCA
CTTGATGCAGTTAAACTTGATTGATAATAATATTTGCCAGTGCAGAATGC
GTTGGTTTTCCAGACATATGCACTGCTATCACGAGCGTGTGACTCATCAG
TTCACCCCACAGACCCTCCGTCTTACAAAGGAGTTTTGCTGGGAGGATTC
GGAACTGGTGCCATACAAAGCTTAATACTGGCACCTGTTGAACTTGTTAA
AATTCGAATACAGTTGCAGGGGAATGACCCTAACAAGGCTGTACAAGTAC
AGAAGCTTGAGGGTCCTACTAGTGTTGCCAAAGGCATATACAGGGCGGAA
GGGCTACGGGGAATCTATCGAGGTTTTACCATCACAGTACTAAGAGATGC
TCCTTCGTATGGTGCCTACTTTTTGACATATGTGTTGGGCCTTGGCCCAG
AAGTATAAGAACGGCCCAAGGAGGAACAAGTCCAGATAACAAGCATGCGT
AATTCACGTGCTAAAGGCCCTATAAATACAGAGGTGCTAACACAGAGGAA
GGGGATTGGAAATCTGAGAATAGACTAGTGATATACATTCTGTAATATAC
GTATATATATATACTGTTCCAGCATTTGGCGCTAGAAGGAGGGGAGAATC
TGCCATGGCGGAGGAGGTAAACGAGACAAATCAAGTTCCAAAAACACGTG
AGGTATTCGTGAACCAGGAAAGAAAAACCAGAGCATACAAGTTTGGACCA
AAAAAGTTGTTTGAAAATGAAGGAGGAGGTGAATCTCGCGGTGGTCCGGC
TCACTCAGATCCAACTGGCGGACGGGGTAAGCGATATCGCCGTGCACGCA
CACTAGTAGAAACACCGCAGGGCAAGAGGGTTTTAACCAGTGACGCGAGG
TTGCACTTAGAAAAACTCAAAGCGAAGAGGCAAGCGATTGAAAACAGAGA
GCAGTTGAACCGTGAAGCGATCAAGAGCGAACTTGACGCCCTTGACCGCG
ACCGGAGATGGATAGAGTTTCAGATGAAGTAGAGGCATGCGGCTGAGAAA
TGGGAAGAGAAATTTGCGAAAAGAAGGATGAGCATGTTGCTTCATCCGAG
TATCCAACAGAGGATTACGAACCCTCCTTTCGAGGTTTAGCGTATAGTGA
ACGCTCTAGAAGGGAGGATTCGGTTGGCTCGTATAGCTCGTTTTGACGCA
AGAAGAAAGCATCTGCAGATGATTGTTCGGAGCATGAGGAATTGAAGAAG
GATTGCTCAAGTAAAGGTCATTCGTCAGAAGTGGTGAAGTTGTGAGCCAA
AATAACGGCTCTCAAGGAATTAGTGAAGACGCGGTCTGGAGGCTTAGAGG
TCCCCGGTGATAGTCCATTATCGGAGGATATTGAGAATGCGAAAATAGAT
AGGCATTTGAAAATACCCTCGATTGAGCAGTTCGATGGAACCACTGATCC
GTTGGACTTTATCAATATGTTCGATGCAAGAATGAGCTTTTTTGGACACA
CTGAAATAGCAAGGTGTCGTTTCTATTGTACATGCCTCAAGAGTACAGCG
CTTGAATGGTTCAACAACTTGCCGCCTCGCTCCAAAGAGTTGTGGCAAGC
GCTGAAAACGAAATTCAGGACGAGGTTTTCTGGCAATGGAAAGCGAGGAA
GACGAGAGTGCTAGATCGAGAAAATTTTCAGATCTGTAAAACACACACAT
AGACTTTTCATCTCTACAATAGACAAAAAAATCGGAGCTGTGACCGCCGA
ACGGCGCTGTTCAGATAGTTGCAAATACTCTGATCAGCTTTAACTCGTCG
GAAGTGATGTTGAGGCGTCACTCAACGTGCAGTTTGTTGAGATAGGCGTG
AACAATTTGTTCTCCGTTCCCGACGACTTCAACTTTTGTCAATATTGTGG
AGCTATGTGCCATCGCAGCGGCTGAACTACGCGCCCCAAGATCAGAGATC
CGACATGTGTCTCATTCTCGCAAACTGTTGAACCAAAAAACTTAACAGAC
CTCGTGAAGTTCATCAGTTCACCAGCTCATCAGTGTTTTAAAATTAACTC
ACGGAGCATCCTTAAAAGTCAGAGCCTAAAGCGTTGTTAAATCCAGCTTG
TGAAGCGTCCCATCTGTGAAGCGTGCTTCCTGTGAAGCATTTCTCTGTGA
AGCGTTCCCGAAGCATCCTTAACAGCTCTTGGAGCATTATTAATTGCTTT
TTGAGCGTCCAATTTTTGAAACATTATCAATAGCTCTTCGGCGTACGATT
TATGAAGCATTATCAATTGCTCTTTGAGCGTCCAACCTTTGAAGCATTAT
TAATTGCTCTTTGAGCGTCCAATTTTTGAAACATTATCAATTGCTCTTCG
AGCGTACAATTTATGAAACTTTATCAATTGCTCTTTGAGCGTCCAATTTT
TGAAGCATTACTAATTGCTCTTTGAGCGTCCGATTATTGAAGCATTATTA
ATTGCTCCTTGAGCGTCCAAATTTTTAAAGCGCTCCTCTGTGAGGTGCCA
TGCCTGTGAGGCGTCTCGATTGTGAGGCGTCCCGCTTGTAAGGCGTCCTA
CTTGCGCAGCGTCTTTAAATACAACTCTTGGAACATGCTTAATTGCTCTT
TGAGCGTCCAATTACAATTCTTCAATACAAATTACAAATTACAAATTACA
AATTACAATTCTTCAATACAAATTACAAATTACAATTCTTCAATACAAAT
TACAAATTACAATTCTTCAATACAAATTACAAATTACAATTCTTCAATAC
AAATTACAATTCTTCAATACAAGCTACAAATTCTTAAACGACATGTTTTT
GACGTATCCTTCAATACAAATTACAATTCTTGGAGCGTCCAACTCTTGGA
CTCTAAGAGCTCTCTTAGACGATGATATTACAGTGGATAAACACTTCACC
AAGTCACGTTGTGGAGACCTCAATGAAATTCAAGAAAAAATAAATTCCAG
AAAGAGATATCTTCACCGCCTCTTCAAATCGAGGCTTCATCACATATTTA
GACTCCTTGTGATGATGACATGAGTACTCCTCTCCATCATGACGATGAAA
TTTCCAATCTCTGTCAACAACAGCTGAAACGTTACTCTTTTTATATTGGA
ATGCATATCTAAAGATATGCATACATCTAAAATGGTTCAATGATCAGCCT
CATCGCTTCAGCGGCTCTAGTTCATTATTTCAACAGCTTCAGTTACGTCA
AATGGCCTCTTCGCTTCAGCGCCTCTGCCTCCTTTCACGGCTCCTCAAAC
GTCCGAAGCCCTAGTCGTCAATGACTTCCAAGGTTATGAAACAGTACTCT
TTTTTGAAAAGCACATCTAAAGATCTGCATACTTCCGGGAGGCCTCAAGG
AAGCCGACGCTAAAATGATTCAATGATCAGCCTCATCGCTTCAGCGGCTT
CAGTTGAAATAGTAAACCGATGAAGCACTGAAATTTTCAGAAAAAATACG
CGATGTATATGTCAACAGGAAACAAATGAAAACTCATCAAACTGCCTAAA
ATTTGAGATGACAAAGACATTTTTCAGAAAGAAGGGTGAAGATAGAAGTG
CTGAAATATTGGACCGATGAACCAAGTGGAAAAATTGTCTGCCTCTTCAC
TAAATCGCTTCACTAGCTCGTCGAGGATCCTTTAAAGGGCATGCAAAGCC
TTACAATGGTTCATTTACCCAAAGACTAAAGATTGGACTGCACATCTAAA
GATCTGCACTCTTCCAGGAGGGACTCAATGTGAGGTCACAATCCAGCCCA
AAGACAGAAGAAGCCTATGAGTTCAGTTATAAATATTAGAGAGAAAGACA
TGATAAAGGGTTGGCAAATGACAGAGCTTCTCCCTTGTGATAAATAAATA
AAGATAGAGGGAGGCAAAAAGGAAAAGATTTGAAAATTTTATTTTTTAAA
TCAAATTATAAAACAGGCCGAAATCCAAGACAGTTCAAAGGCTCATCTAA
AGATCAGCCTATACTTGAGGGGGGGACAAATGTTGGGCCTTGGCCCAGAA
GTATAAGAACGGCCCAAGGAGGAACAAGTCCAGATAACAAGCATGCGCAA
GTCACGTGCTAAAGGCCCTATAAATACAGAGGTGCTAACACAGAGGAAGG
GGACTGGAAATCTGAGAATAGACTAGTGATATACATTCTGTAATATACGT
ATATATATATACTGTTCCAGCATTTGGTTGGGCCTTGGCCCAGAAGTATA
AGAACGGCCCAAGGAGGAACAAGTCCAGATAACAAGCATGCGCAAGTCAC
GTGCTAAAGGCCCTATAAATACAGAGGTGCTAACACAGAGGAAGGGGACT
GGAAATCTGAGAATAGACTAGTGATATACATTCTGTAATATACGTATATA
TATATACTGTTCCAGCAATATGAATTTGTTCGAGAGCAGCTTCATCCTGG
ATGCCGAAAAAGTGGCCAAGAAACCTGCAAAACAATGCTTATGGCAGGAG
GTCTTGCTGGTGTTGCAAGCTGGATATGCTGCTACCCTCTAGATGTTGTT
AAAACCAGGCTTCAAGCTCAGTCTCCATCATCTCCACTAATGTACAATGG
TATTGTTGACTGCTTACAGAAGAGTGTTAAACAAGAAGGATATAATGTCC
TATTTCGAGGATTGGGAACTGCAGTTGCTAGAGCATTTGTAGTTAATGGG
GCTGTCTTTACTGCTTATGAATCAGCTTTAAGGTTATTCTTTAACGGCAA
CGACAACAAGCATGAAACTGTTCTGTCAGACCACACAATCTAG