| Relationships |
|---|
| The mRNA, DCAR_027784, is a part of gene, DCAR_027784. |
| The genetic_marker, MK006082 K3526, is located in gene, DCAR_027784. |
| 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_027784 | DCAR_027784.mRNA | mRNA | DCARv2_Chr8:19318955..19325998 |
TTTACATATTATTTTAAAATTCTTATAATCACTATATTTATATTTAAAAA
TAAATTTTATTTATGAATAATATTGTTTGTTGTAATTGGTATGATTTATT
AAATTCTAATTAAGATTTTTGGAGGATCCAATCATGTATTTAGCATTTGC
CCGGATAAATAAAAAAAAAAAATTGGGATTTGTTGCCGTTGAAGAATGAT
GATGAACTAAAGAAAAAACTCAATTACCTCAACAACCATGGAGGCGACGG
CAGCACTATCGGAGCTAGAGCGTGTCCAAATCCAGATTCTCCGGCGAATA
TCCGACCTCGAACTCCGCGTCGGCCTCACTCACTCCCCTTCTCCGGTCAC
AACCGCCGACAACGACGCCCCCGCCGAAGCTAATCTCTCCGGCCACACCA
CCGAAGCTCGTCTCTCCAACATCCTATTAGAAAACGGCGTAAACGACTTC
AAGTTCAAGAGAGTTTCATTTGATTACTACAACTGGACCTTAGATTCTAG
ACGTGATGCTCTTGGCGCCGCGTCTATTGATCATCTTTGCAAGAGCATTG
TTATGGTACACATTTTCTACATTTACACACTTGTCATTTATTTTGTACAT
TACAATTATCTGATTCTCGAGCGATATGTTTGGTGTTGTTTGGCATTATT
TTCTGTTTTTAAAAATGACATTAATGTTGTCTAGAGTTAAAATGAAGCAG
TGGTTGTTGAATTTTTTAACATTGCTCTCGACTTGTGACCGGAACTATTT
GAACAGGGAAGATCAATTTGGAGAGGTACTACCATATATATGATCTAAGT
GTGGTGCGAAAAACCACCAAGGTTTGTTAAATTTAGAAGGCTTAATACCC
TTTGTACCCTCAATATTTGGGGGTGTGTACTGATACAGCCTCAATGTTTT
AACTCGGGCGATTCAACCCTCCAAGTATCTGATATGTTTTGATTAGCCCT
CATATCGGGATGAAGCCAAAAAAGGGTATATAAGGGAAGGTAAACTTGAC
AATTACTATTGAAGATAAAATTTGCTCGTTCATTTTAAAACCAAAAAAAA
TACATAAGATGTGTATTTTAACTCTTTTAACCCTCAATGTTTAATGCAAC
ATCAAGGATTAAAAAGGCATTAAGAGCAAGTCGAAGAGCTGCCTTATCTT
AGACGCCTTATATGATATCTTAAGGTAAAATTTAGGACATTTGATGAAAA
AAGTTGATCGAACAATGTCCTAGTGATGCCTTATATCACTAGGTTAACAT
CTTCAAACCTTATTTTTAAGGCACCTCTCCTTGCCCTATCCTATATTTTA
TAATAAATTATTACACACCATTCTCTTTGTCTCTCGACTTTATATTGTCC
TTTAGTGATAAAAGAACACCTTTAATGATAAAATATTAAACATATAGTTG
GAATAAGGCACATTGTTGGAGTTGAAGTTAGTTAACTATGTCCTAAATCA
CCGGGACATCTTTTATTTATTATATTTAAGGCTAGAACTAGGACATTGTT
GGACTTGCTCTAAGCCAATTTATAAATGAGGCTCAAATCTATAATAATGT
TGTGTATTGACTCTTGACACATGTTATTTTGAACTTGAAGTGATCTATAT
ATCTTTAACTAATTGTGAAACTCGACCGAGATAAAACGGTTTAATTATCT
GAAATTAAAATATTGGGTATCTTAGCAATTTATGTTTGCATTGTAATTTG
TTTTTTTTTTTAAATTTAAATCCTATAACTATGTTGTGTCCTGATAAATT
ATATGTTCTCATTGGAGTTGTAAATAGCATTTGTTGCGCCTCAACTAAAC
ATAAAAGTGAGGAAATATATGTGGTCTATACCTTTAAGTTGGTGGCTCTT
CTAAATCTCAAAGTGTTTGGGAGGGATTGGTTGTATCATATATTAATTTT
GATACTTTCCCTTACTCGAAATCCTTTTTTTCCTTAAAGAGTGGATCACT
TACTTAGTTACCGCTCTGCTCTTTTAAAGTNCTCGACTTGTGACCGGAAC
TATTTGAACAGGGAAGATCAATTTGGAGAGGTACTACCATATATATGATC
TAAGTGTGGTGCGAAAAACCACCAAGGTTTGTTAAATTTAGAAGGCTTAA
TACCCTTTGTACCCTCAATATTTGGGGGTGTGTACTGATACAGCCTCAAT
GTTTTAACTCGGGCGATTCAACCCTCCAAGTATCTGATATGTTTTGATTA
GCCCTCATATCGGGATGAAGCCAAAAAAGGGTATATAAGGGAAGGTAAAC
TTGACAATTACTATTGAAGATAAAATTTGCTCGTTCATTTTAAAACCAAA
AAAAATACATAAGATGTGTATTTTAACTCTTTTAACCCTCAATGTTTAAT
GCAACATCAAGGATTAAAAAGGCATTAAGAGCAAGTCGAAGAGCTGCCTT
ATCTTAGACGCCTTATATGATATCTTAAGGTAAAATTTAGGACATTTGAT
GAAAAAAGTTGATCGAACAATGTCCTAGTGATGCCTTATATCACTAGGTT
AACATCTTCAAACCTTATTTTTAAGGCACCTCTCCTTGCCCTATCCTATA
TTTTATAATAAATTATTACACACCATTCTCTTTGTCTCTCGACTTTATAT
TGTCCTTTAGTGATAAAAGAACACCTTTAATGATAAAATATTAAACATAT
AGTTGGAATAAGGCACATTGTTGGAGTTGAAGTTAGTTAACTATGTCCTA
AATCACCGGGACATCTTTTATTTATTATATTTAAGGCTAGAACTAGGACA
TTGTTGGACTTGCTCTAAGCCAATTTATAAATGAGGCTCAAATCTATAAT
AATGTTGTGTATTGACTCTTGACACATGTTATTTTGAACTTGAAGTGATC
TATATATCTTTAACTAATTGTGAAACTCGACCGAGATAAAACGGTTTAAT
TATCTGAAATTAAAATATTGGGTATCTTAGCAATTTATGTTTGCATTGTA
ATTTGTTTTTTTTTTTAAATTTAAATCCTATAACTATGTTGTGTCCTGAT
AAATTATATGTTCTCATTGGAGTTGTAAATAGCATTTGTTGCGCCTCAAC
TAAACATAAAAGTGAGGAAATATATGTGGTCTATACCTTTAAGTTGGTGG
CTCTTCTAAATCTCAAAGTGTTTGGGAGGGATTGGTTGTATCATATATTA
ATTTTGATACTTTCCCTTACTCGAAATCCTTTTTTTCCTTAAAGAGTGGA
TCACTTACTTAGTTACCGCTCTGCTCTTTTAAAGTTTAACATGTTAATAT
GAGAGCTGAAATGTATCAAACATTTTATTTATCACACTCTTTGTTACCAA
GATTCGGAACGAAGTGTAGAGCATGAGTATGTGTCCAAGTGTCAGACTTG
ACACATTTTGAAAAATTACATATATGATTTAAAATACATGTCTAAGTGTC
CGTCACAGCCCACGGGTACTCGAGATAAAATGAAGAGTCTGGATAACAAA
GCACACCCTATGGATTTGAATTTCTGTTATTGATATTACTCAACTAAAAA
GAGTTTGAATTTAAACTGGACTTTTCAAGTAAATACAAGCAAGAATGTAT
TATGTATCTTTGTCAGTCCCACAACTGGATTATATTTTATCTAGAATATG
GAATTTTGTTACCTTTATAAGCTGTATTAGCGTTGCACAGCCAAAGTGCA
ACTATCATCTCCGTAGAGAGTACTGAGAAATATATATTTCTTTACAGGCA
GGTAGATACAGAACATCTATCTAAGTGAGTTTCAAGCTCCAAGTAGTAAG
GTAAATTACTTAGAATATCTTATATTGGCAAATAGGTTAGATGCTCTGAG
TTCAATAAAATTGGTTCAGATTTTAAGAAGTTCTTAAGGTAAATAAATTA
TATTTTTTCTAAATAAAAAACAAAGTCTACAAGACTGGTTAAAAGCTACT
TGCCAAAGTGCTTGTAGGTCTGTCACTGATATAATGCATGGTTAACTTGT
CAATAGATATAAGGCTTTGGATATTAAATCAAATCATGCTTTATCATTCA
GGAAGACTATTGATCTTAGGTGTGGTCTTTGGCCCAATAGTCATTGTATT
ATCTGGTACCTTTGACAAAACTGTTTCTTGCTTCAGTCATGAATTTTTTT
GCCTTTTGAGTATTCCTGCTCAAACTGATTGTGATAAAAGAGATCGTCGA
ATCGTGGTCAGCTGAGAATACATTTGTTCAATAAACTTTGCACAAACACA
TAACTTCGTGATCATGATGTCCATATTATGATTATGAGTATCTTGATATT
CTATTGTGCACAAACACATAACTTCGCGATCATGACGGCCATATCATGAT
TTTGAGTATCTTGATATTCTACTGCTCGCTAACTAGGAGAATTACAAATT
TTCCTTTCTATTCTCTTAAGTTAGATTTTCCCGAACTGATAGAAATATAT
CACGTATACCCCAACAATACTATCATATTGATGTGGCACATTCTTATGCA
GGTAAATACTCAAGCCCCATCAAGCATCACGGATTGTAGTAACCGTGACA
TGTCAAAATATTATGTTGTTGTTGTGCAGGTTTGACAACTCTCATCTTAC
GTGTATGATCAGTCATTTTGTGGAATCTGTTATCTTATTAGCATTAAATC
TATAGCTTTTCGTTGCAGTATACTGCTCGATTCAATGCCGAGACTGTGAA
GAACTTTTTATACACTCTTAACAATGGAAAGATACCCAAGAAGAAATTCA
ATTGTAAGTCTAAACGTTTAATCTCTTGAAACAGTATAAATGACTGAAAG
TTTCATATGGAGGCAACTAAGCATTTTGTATTGTAGTATGTTATACCTGA
TAGGATAAACGTATGCTAGGTTTCTCTTTCCTAGTTTCAAAACCCTCAAA
AAGGTTAGTTTATGTTTGCTAACATCTTTACTCTTTACAGACCCTACTTT
CAAGTGGGACAAACTGGGTGTGTTAGCTATGGTTCACTTGGGGATGGTTG
GGACCTTTGGGTTATCTAAAAGTGTGACTAATAAGTTATTAGTTAAAGTA
ATTGGTGTTTGCTACTCCTATTTCTTAAAATTAATATAACTGCATATTTC
AGAAACCCACAGAAGGTCTTAATCACGCTAGTCATTACTGCACATAAAGT
ATATTTAAAATTACTACAGAACTTATGTCAATTTTAATGAGTTGGCAATT
TTAACTGATAGGAGTATGTTATAAATTAAACTAGGCCTGCATATAAATTT
TCTTATCTCTGGCTTATATGTATTACCACATGAGTGAAGAAATTTTGACT
GTCCAAGTATCTAGATTTAGGAGCCTACTATTGTTGATTAACAACACTAG
TTAGCTGATCTTAAATGGTTTTTGTGTTTTCTTTCAGCACTGAAAGAATA
TGATTCAGAAATTTGCTGCATTTTATCTTTTTACTGTTTGTTCCTATTCT
CTCAATTATTAACAGCCATGTTACATGGAAATGGTAAAACATGTACTTCA
TATTTAAGCTTTGGCTACTGTAACTTTCATTTGATATACATTTTCTGTAG
TGAGGCTTGCTCCAGAGGAGACATCACGGATGTTGACTGGTTATGAACAC
AATGGAGTGACATGTATCGGCATGAAAACTGACATTCCGGTAAATTAATT
GACTTTAGTAGCCTTCTAGCCCTCCGTTATTCTTCATTTCCATAATACTT
TGCCGAGCATTTAAACAATTAAATGTATAATATTTATATGCCTGTGGTGT
GGTATTATATAAGTATGCTTTTCTATATCACACACACACACACACACATA
TATGTATGTATACATATTTTAAATTAGCTTTAGATATTTTTGGTTACTGC
TTTCCGTAGTTTTCATAGTAATTTATATGTTTGCACTCTTTTTTGATGAA
ATTTTTGCCTGCCAACTCCCTGGGCTTCTATCATGTTTTTCTTCGTTCGT
ATTCATAAACACACACACACATTCAGTTAACATCTAATAACTTCAAATGG
AGAAATTAAATGTTACTTTTCCTCAACAGAGGAAAAGAATTTTTTTTCTA
AGCTATAAAATTTAAAAAAAAAATTTCTTTTCAAAATCATTGCTTACAGA
AACCCTTCTATAGCAAATCACATATATTTGTTGCATTATTACCCAACCAG
ACAACCCACCTCAATATACTATCCTCTTTTTTTTTGCTAAGTCAATATAC
TATCCTCTTGTTTTGCAACAGTTAGAAGCTTTAATATTTAATTTCAGTCA
TCATACATGCTTTCTCTTTCTAAATCATGTTATGTTAATCTGAGGAGATA
AGTAGGGACAGTTGTCTTCGCATTATTGTTTAGTGTTTAATGAAATGGGA
TTGTTATAGCATGGATGTGATTATTATCCGTCATCTATCATAGAGTCCCT
CCAAAGATTTTTTTGAAGCTGTTGAATATGAATTCATCTCACTGATACAG
AAGTTTTTAGCCTTTATTGGAAATTAAATGTGGTTCATATATTTCATATC
ATGGTAGTTGTATTATGAATTTAATTAAAATGAGTGGAAATCATTTACAT
ATTTTAACTTTTCTGAAAATTAAGTTAATTATGGTTGAGTCAGTTTTATT
TGGATTAATCTATTATTCAGCTATTAGGATGCTTTAATTGGATATATTGT
GCTCTGAGAAGTACTCCATTTTTTCCTTTCATCTATATCTTATGAAATTC
AATATATTGAAAAAGATTCAAATAATGTTCTTATTATATGCCTGAATTAT
GTGTACCGGCTAACATGTTTGGCTTTGCTTATATATAAAGCAACGCATGA
GTTTGAATTTGTTCAGCCAATGTATGTTTTTGTTCACAACAATGTAATCA
TTTATCTCGCATGTGAAATCTGATACTAGCAAAATGAACCACGGCTGCAT
CAAGCACGATCAAGTTGAAGGTGACTTTGACTAATTTGTTCTTACAAATG
ACCTAAATATTTGTAGAAGCAACTTACAGTCCTCATGCATCTTAATTGCA
TAACATTGAGGTCAACTCCTGCATACAAAGCCTTTTTGCTAATCTTTTGT
TTGTTAACACAACATTGAGATGAGGAAAGGATCATTGTTCGTTAACATAA
AATGAGTAAAATAGGTAGGTATAAACTATTAATGTTTATTAAAATATGGT
GTGAACGTTTAATAGGTAACTCGTCTATTATTACAGGTGATTTTGGACGA
AGCAATTGTGAAACTTAATCCTGATTTCTTCTGGTTAGGAGGTGGAGAGA
TAGATTTGAAACTGGGTATCAGAACATCTGAATTCATCAACTATCTAAAC
CCTTTTGTTGTGAGCTGCAGCAGTTCTTAACCTGCCATGTGCATAAATCA
TTGATTGCTGGCAGGGCATGGTGTAAGGGTCGCAGAGACTACGATTGTAT
GGTAATCTGTCTGCCTGAAACTGAAAATAAAAAAGTGCCATTATTATTGA
TTTCTTCTGTTGTGTCGTTTCAGAAATCCAGCTTTGGAATATTGGCAAAT
ATTATTCGGAGAATTAGTTTGCTGAACTTGATTTTTTATTCTCTTAATTT
ATTGCCTGAAGGAAACAAGTAGCGAATTTGTTATCTGTATGCAGTTCTAT
TCTTTGTTTGTTGGAAAGACCTAGCAAAAAATTTAATGGCTG