| Relationships |
|---|
| The mRNA, DCAR_023642, is a part of gene, DCAR_023642. |
| The genetic_marker, MK003514 K0958, is located in gene, DCAR_023642. |
| 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_023642 | DCAR_023642.mRNA | mRNA | DCARv2_Chr7:3572711..3581404 |
ATGGGAAGCACAAAGACTGTGGGGCCCTCAGGGCCGGTGCCGCGGCGTGA
CCCGTACGAGGTTTTGAACTTGTCCAAACAAGCTTCTGATCAAGACATCA
AAACTGCTTATAGAAAGCTTGCTTTGAAGTAATCTTTTTTCTTTTCTTTA
TTTTTTTTTAATTTTTAAACTCAACTATCATCTGTTATATTTGTAAAGTT
TTGGGCTTTATTTTTTGTTGTATCTTTGTGTGGAATTTTAAGATTTTGTG
TTGGTGATTAGTTGAGTATGTGGACTTCATTTTATAAAGAATTTTCATTT
ATTGATTATACTGGCATGTGCAATGGGTTGATTTGATTAAAGATTATTTT
TCGAGAAGTTATTGTTGTGTTTGCTAGAATTGAATGAATCAAAGGATTTC
AATTCGATAATAACTATTAATTTATTGGTTGTGCAGGTGAATCTTGGTCA
TATCAGATTATATTATGAGAATAACTGTAGGATTTTGTGCTGCTAGAATA
GAAAGAAGTGAAGAACTTTAATTCGATGACAATTGTTGCTTTATTGGTTT
TGTGTATAAAATGGGTAGATTAAAATCGCGGGCATTGATTGCTGGTCTGA
AAATTAACCGCGGATATTAAAATTTGGAAGCGATTTTGGCGGACTTAATA
TCCACATAGTTTAAATGTTGTTTCATTGCTAGTAATAATAATCCTTTAGT
GAATTTGGCCATTGCTCCGAAATTTTCCTATGAAATTTGTAGCAACTGTT
GAAGATATTGAAATTTTTTTAAGAAAATCTGATAACGCCTAGGACATGCT
AGTAATGAGGTTTCTTTTTTGTTGTTGTTGTATAGGTATCATCCTGACAA
GAATGTCAATAATCCTGAAGCTTCTGAACTTTTTAAGGAGGTTGCCTATT
CTTATAGTATTTTATCTGATCCTGAAAAAAGAAGGCAATATGACAATGCT
GGATTTGAGGTAGTTCTCTTTAAAGAGTAACCCCGTTTGCAAATTAATTC
GAGCTTAGAAGAACTTGGTCCTACTAATTCTATTTTTTTTCCTATGCATT
ATCAATGTTTTTCATTATATGCTCATCCATGATTTAACTTTAACCTACCA
CAACAAGTTTGTGGCAGAAGAATATGATGGATTGTTGTAATAAGACAACA
TATAGACTGTCATGGGAGGTGAAAAAGTTTTTTTTAGGTTGTAGATTAGT
AAAATGATTTCTAGAGTTAAGTTGTTATAGGCAGTTTTCTTACTAGTGGG
AGGTGAAAAAGGTTTTTTTAGGTTGTAGATTAGTAAAATGATTTCTAGAG
TTAAGTTGTTATAGGCAGTTTTCTTACTAGTGGGAGGTGAAAAAGGTTTT
TTTAGGTTGTAGATTAGTAAAATGATTTCTAGAGTTAAGTTGTTATAGGC
AGTTTTCTTACTAGAAACGTGATATTTTCGCAAGAGGATGACAATCACAT
GGCGTACAAGATAAATGAAGATCACAAGAGCATATATAAGACTATAACAT
GCTCTATATATGAGACCAAATGTAAATGCTTAATATGTACCTACAAGTAA
ACTATACAGAGCAGCTTATAACGGTATACACAAGTAATTTAAGTTTCTAT
TTTCTTTCATTTGTGCATGATATCCTTAATTCCCCTTAATACCAAATTAG
TGGTTGTTTTATATATGACTCATAACCAGAACTGTTGATTGATGCTTGGT
GATTCAGAATAGATTAAATATGTTTTGCTTGTTTTGAGTTTGACCAATTA
AAAATCATATAAAGCACATTTAACATTTGGTATATAATCAAAGATTTCAA
ATCTGTAATTGAAAAAGAAATCTGATTCATTTTAAGAAAGTACACCAAAA
GGAGACGTCTGAGTTTGCCAAATGTTTAGGAGTTCCTTTACCACATCTTT
ACTGGAACCATATCCTCTAGTTGAATTCTTAACGATCACATTTAAGAGTC
CATCCCTTTTTATAAGAGCAGTATTACTATTTATAAGGTTGCAATAATTG
TAATTTTCTCAACACAACAGTCTCGAGGTGAGTCGGTGTATATTGGAGTC
CTTGACTAGTTCTCCTCTAGTCGCATAACAAATATGCTTTTACATGTATG
ATTACAGTATATATAAAATATAATGAGTAATACTTAAACATGGGACGACG
CAACAAATTTGTACTTCAAGTTAACATGTTGAATCCAACACTACATAATC
AATCATTAATTCTAAACTCAGTGCTATGCAAAACAAATGACACGAATAAA
ATGGAATGAAATGTTGTCATCGAGACTCAGTTGCCTCACAATCACTACTC
GTAAGCTCCAAATCTTCATTTTCTTTTGACTAAATAAAGAAAAAAGATGT
TGGAGGTCTATAGAGGTATAAACTCGGGATAGCTTTAGGATGCCAAATTA
GAACCAAAAGCAGATCATTTTTATCTATTTTCTTGGTGGGTCATCATATG
AATGGCAGTTGCATACTTCTAAGCACTTTGTTTTCTTACTCTTACTCTCA
CTCTCACTCTCATTCTATATTCATATTTATCTTCAGTGTCATATAAATAA
GATATTTTTACTTCTTTAACCACATCTGTCTAGGTTTTGGTTGCTTTAGA
CGCTTAAGTAGGAACACAAATGCCTTTGCGTGTCTTCATATTTCTATATC
ATTATAGGAATTTCCTCACGTTATCACGTGGTTATGTGAAGTGCTTATTC
AATATACTTTTATACCTGTTGTCTGCTTTACGAAAGTTTAATGTTTCTAA
TGGGATAAAGAGTTACACTGGAAGTGGTGTTCTTGTTCTATTTAGACTAA
TATTATTCACGGTTCTTGCTTGTACCTTTGGTCTGTTATATGTATTTCGG
AAATAGGTGTGAACTGGAAATTATACTGCATCTTTTTTAGCAACAATATT
TAGAAAGATCTTCCTATCATACATTACTAATAGACGAGCATTGTGTTCTA
ATATTAATTGATCTTCCTGTATTGCATTGTATATATGTTAATTGTTGAAG
TATATATGATCCTGTTAGGCCTCCCTTTAAAATTAATTGATATCCCTGTA
TTGCATTGTTTAAGGTTTTAGATGAGTTGATTACTTAACATGGTATTTTG
ATTTTTGATTGAGGGGAAGTATTGAATAATATATTATCCTGGTATGGCCT
CCCTCTTAAGACCTTAAACTTTGAATGATTTGGTTACTTAACAATATATA
ACTTTCTCATGGCACAAAATAATTTTTTTTCATATATAAAAATTCTGTGT
CTTAGGACTTGCCAACATATAACTTTCTCATGGCACAAAATGATTTGTTC
ATGTATAGATAATTCTGTGTTTAGGTATTTAAGGTTCCTCCTTCTGTATA
ATGGTGGTGTGTTAATATTCTATTGTGGTTTCTAAATTACATTGTACCAA
CAATGTTATTATTTTACTCATCTATGACTTCTCAATTTTTTAAAAAAGGC
TATCGATGCTGAAGGCGTGGATATGGAAATTGATTTATCTAATCTGGGAA
CTGTCAATACTATGTTTGCTGCATTATTCAGGTATCTTACTTTGCAGTGT
TTATTATTATCTCAAAAGGGAATACCTTACCCAGTCACTGCATATATATA
CAGCAAGCTGGGTGTTCCTATTAAAACCACCATTTCTGCTAATGTTCTTG
AAGAAGCATTAAATGGAACTGTTACAATCAGACCCCTTCCGCTGGGATCA
TCAGTTAGTGGAAAGGTATACATTTGCTTTAGCCTGTATAGATTGCTCTT
CAGATTTCTTTTCTACTGAAAATTGTAAGTTGTGGGCCAGGTAGAAAAGC
AATGTGCCCACTTTTTTGGTGTTACTATAAATGAGGAACAAGCTGAGGCA
GGAATTGTAGTCAGGGTCACTTCTGCTGCACAAAGCAAATTTAAGGTATA
ATGACATTCATAATGATTTTATCATTCTTCGAAAAGATTACTTAAGCCCC
TCCCCCACTCGATGCATCTGAAGAAAATACAGTGATCATGGCGTGTTATA
AATGTATGTGTGTGGTGCTAACTGACTGATTGGCATGTGAACATTTATAT
GAGTGTGCTTTTGCAGCTTCTTTACTTTGAACAAGATGCCACTGGAGGTT
ACGGGTTGGCTCTGCAGGTATGTAATAAACAGTTGCTATTTTGCCAAATA
ATGTTATTATGTGATAATTTCTAGTCCGCCTTTAACATACCTCGAGGTTC
GAGTGTTCTTGAAATTTTTTTTTTAAAGAAATGCTTGCGACATTTTTGCT
GATATTCTGAGTTTGTTGATCATCATATCGAGGCTTATTGTTTGGCTACT
TGTATGTACAGCAGTGTTTGTGCGTATTTTGTATTGTTGTGCTGATTTGC
AAACTTTAGCATAATTATTTATAGATTGAGTGCTTCTAGTATCTCTTCTG
GATAATGTCTGTTCAATTTGGCTTATCGACTTAAAAAAAAAGTTTACCAA
AAAACACAAGACATATATATTATTATGAATTGATATATTTAATAAATTTG
AGGACTGATTTGTGACTTTAACTATTCTCTGAAGAGATAGGTTTTCTACC
CCCTGTTCAAACCCTAAAATTTAATTTTTTCTACGTTATACGTACCTTAC
TAAGTCCCATCAAAATTATGTTTGATTATGGGTGGGAGCCAGGAGCTACC
ATGGGTGTTGGCCCTGGGTGCCACTAATTTGAAGAAAATGGCCCAAAATA
CCATTGCCGGAGAAGATGATCCCGACCTACCACTTTGCAATCCAAAACGC
TAGATCGTGTGACGTTTATCCTCTTTTCCTTCTTAACGCTACACGATTAG
CATTTTGAGACCCTAAACACTATTTCATGCAGCGTTTTACTTCTAAAACG
CCAGATAGTGTTACGTTTTGTAGTGATTTTAAGCCATAAACGCAACACGA
TCTAGCGTTTTCTTCCAAAAATCGAAATGCTGGATTGTCTGGCGTTAATA
AATGGTATTTTGGGTCATTTCCCCCAACTCTGCTATTTTGGGCATTACTT
GTGTGTTTTGTGGCATATGGGGCCTCTTCTCAGCTACCATGGGGGCCAAA
AGTATATTTGAGTGCCTATATACTTTTTGGTTGCAGAACATAGTAGAGAC
ATTATGAGGACATGACAATGTGCTTTATTGAAGCTAGAGATTGTACCAAA
CTGTTTTAGTACAGTTAGATTAAGTTATATAGTATGTATGGGTCAATGTA
TAATAAAAAAGGAGATTATTATTTATCAAACAGACCACAACCTACAAACG
GTTATTACTCAAAAAACAAACATTTTTTGAAAGAAGAAATATTCCATTTA
GCCCACGCATAGCGGGCAAAAATACTAGTGTGAATAATGCAGACTAGGTA
GATATGTTAAAATTGTTGTATGGGCAATGACAGGAAAAGAAACATACTTT
GTGGAGGAACAAACAATCCTGACGATGTATCATAACATGCTGTTCTGCTG
GCTTAAGTATGGAGTAACCAAATGGTTGCAGGCCTTCAGTGTAAAAAAGG
TACCAATCTAGGAAGCATGAGTGCGGGTGCGTGATACGGAGATACGGGAA
TTCGGCAAAATCAAAAATATGGGAATACGGGTGTGGGGGGATACGGCAAA
TATCAAAAATATTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
TCTACAAGTATACCTGAGTGCAGAGATCTACAACTTATATAAATACACGA
GCAGATATATATACCACTCATACACACACACAGATATATTATATTGTTTA
TGTCGACTAATTAACCTTTTTTAATTGTGTAAATTAAAGTTTTTTTTTAA
AAAAAGTTGCTGGAAATTACGAAAATTGTCATTCTGACTTATCCCCGCAC
CCCCATTTACGTATCCCCGTCTCTGACGTCACCGATACGCCATGTGGCGT
ATTCCGTATGCATTCGGCCGCACCCCGCCACACCCCCGCACTGCGAAGTA
TACCATACGCAGTTCTTCACTCAGGTGAAGTATCTGTGCTTTCTAGGTAC
CAATGTTTTGGATCTCAGATAGAGCTTGTTGAAGTTGCAATATTTTGTCT
TCTTTCTATGAGTAACTCGATGTTGAATGCTGACATTAAACTTTAGCCAG
ACAACTTTGAATTTGGTGCTACAAGATCAGTGTGACTGGTGCTTGAAACT
TAAACTGTGGATCAATGTCAATGTAATTTGTAGAAAAGTTTTATTAATTT
TGGGAACACAGATCCTTAATAACACTTGCCAACATTTTAACTGTGTCACA
CTCACATTATTTATTTACTTGTGCTCTGGTAATGTGATGTTAGGATGCTA
AAGTATATTAGTAAGTATTAAACTATTAATACTTAGTTGTACTGATGATT
GTATATAACTATATATAGTATCTACTTCTCAAAAAGATTAAATATATCAC
ATCAATCTAATATTTGTAAATTTTATCACTAGTAAATTTTGAGATAATAG
TGTTAATATATATAGATTTTTTTTTGGTCACAAATATTTATAGTTGTTTA
AATATTTGTAAATTTGGTAGAATCCAAGAGTCTTCTAACAAATTATTTTT
GGTCACATTGAGTATGTCCCTTTTCCTTGGTTTATAGTTTATACTCCCAT
CCACAGTATTTTCTATTCTACGTCCATACAGGAAGATAGTGAAAAGGCCG
GCAAAGTGACATCTGTGGGGATGTACTTCTTACATTTTCAAGTATACAGG
ATGGATTCAACTGTTAATGCGGTATATTAATTACAGTGCCATTTTCCATT
TTAATCTCTGAAAGACCTGAATCATACAACTTATCATCTTTATGGCTTCA
TATATGGTGGTGCAGTTGGCAATGGCCAAGGACCCTGAAGCTGCCTTTTT
TAAAAGGTTGGAAGGGCTACAACCTTGTGAGGTCTCAGAACTAAAAGCTG
GGACCCACGTGTTTGCAGTATATGGTTTGGAATTCAGCCTTCTTGTTTTA
TGGTTCTATCTTCTAAGAAGCCTGCCTACAGTGATAGATTAAATTAACTA
TGCAACATATATATGCAGGAGATAACTTCTTTAAAACTGCTTCCTACACA
ATTGAAGCTCTATGCGCAAAATCATATGAGGATACTACTGATAAGCTCAA
AGATATTGAAGCTCAGATCTTAAGGAAGAGGACTGAGCTTCGCCAGTTTG
AGACCGAGTACAGAAAGGTAACAACCTATAGTTTTTCCCTGCTAGTGGTT
TATGTTCTGCGACATAAGCTTGTTGATGATCCATCCCTGATTTACATATT
GTAGGCATTAGCACATTTCCAAGAAGTGACCAACAGATATAGCCAGGAGA
AGCAAACTGTAAGTCTCTGTCCATAGTTGCTGTAATCTTTTTTGGCCCTT
ATACTTGAACAAGAATAAAGATGCAACAGGATAATTGCAAATAAGAGCAT
CTCCAACCACGTAAAACCCTTAGCTAAAGATTATTAGTACATACTATAAA
TAAAAAATATAGAGATTATGTGAAAAAAACTCAACTCCAATGGTACATTC
CCCCTTCATAAATATAGGCCCTGGTTGGAAGTTAGAGGTTTTGGACAAAA
TTAGAGGTTTGAGTCTTGAGGTGTTTTAGAGGGTTTGACCACTAGAACCG
GTAATATTAATGTTTGGTGGTTAGCGGATTGAAATAGAGGTTTGGATCCA
AAAAGCTAATTTTGAAAAAGCTATTTTGAGGAGCTTTTTGGGTTAGAGGT
TTTGGTTTGTGTCAGATTAAGCTGATCAATCAGCTATTTACCAAACAGTT
TTACGAGAAACTATTAATTAATCCGCTAGTCAAAACATCTACTTCAATCA
GCTAGTCAAACATCTAATTCAATCTGCTAACAGCTAACCGCAAATTCTCA
AACAGGGCCAAAGTCACCCTTGATGTTGGCTATATTTGTCAAACCTCTAC
AGGCCTATAAGAAGTCTGTAAGAAGATTCCACTTCATTTAGAACCGTATT
GAAGTGATATATTGTATTTATAACGAATTTAAATTTTAGTAACATACTAT
GTTTAAAATATAGCCAACTATTGTAGCCAATACCATCGAAGCACAATATC
TTACAGGTTCAACAAATTTTACATAATGTTCTAGAGGTTCAATTTAGCCA
ACCTTGTTGGAGATGCTCCAAGTAGTTCATATAAAGATAGCTGTTGCTTC
TTACTATCTTGAAAATATCTTTGTTGTAGCAAAGTTGTGCTGTCTACTAT
ATATAGAATTGACTTCCACTTTTGCTTTGTTCTGTTAACGGATTATAGTT
GTTGGCCTGTCTGTTATGCTTTGCTCATATATAAGGTTATTTAATTGCGA
AGTTGCCTTAATGTCTTGTTCTGTCATAAGCATCTGTATATGTGAGCGTG
TCCTAAAGTTTTCCTTTAATTATGCCAGACTTGGGTAGCCCGAGTTTACA
AGTAATATTTCTCCAAAATGGATATGATTATTGGTTCATTTGCAATACAG
GTTGACGAGCTGTTAAAACAACGAGACAGCGTACATTCTTCATTCACAGT
AAGTAAGCTGACCATCCAAACTAGCGGGGATACGTCCAGTGTTAGCAATG
GAAATAGTAGCAAAATACCTTCTGAAGATGGTAAAGCGGACAGCCCTGGG
GAAGATGGTAGCTCCGATGGGAAAGATAAGTCTGCTAAGAAGAGGTGGCT
AAATTTTAACTTGAAAGGTTCAGCAGATAAAAGAAGTGCTTGA