| Relationships |
|---|
| The mRNA, DCAR_026415, is a part of gene, DCAR_026415. |
| The genetic_marker, MK003289 K0733, is located in gene, DCAR_026415. |
| 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_026415 | DCAR_026415.mRNA | mRNA | DCARv2_Chr7:36076728..36084543 |
ATGGATGATTTGGAGAAGGCGATTTTGATTAGTTTTGATGAATACGGGAC
TGTTAATCCGCAACTTAAGTCACAGGCGGTTGCTTTTTGTCAACAAATTA
AGGACAATCCGTTGATTTGTAGTATTTGTGTCGAGAGGCTGTGTTATTCG
AAACTAGTTCAAGTTCACTTCTGGTGCTTGCAATGCTTACATGAGGTGCT
TGGTGCCAAGTACTCTTCGATGAGTCCTGACCAGAAGGCGTTTGTTAGGA
AGTCATTGTTTTCTATGGCGTGTTTTGAGGGGATTGATGATAACAACTCC
ATTAGGTTGTTGGATGGCCCTGCTTATATTAAGAATAAGCTTGCGCAGGT
TTTGACTACTTTGATTTATTATGAGTACCCGGGGGTGTGGTCTTCCGTGT
TCCTTGATTTTTTGCCGAATTTGAGTAGGGGTGCGGTTGTTATTGATATG
TTTTGTCGGTTACTGAATTCGCTTGATGATGAATTGATTAGTTTGGATTA
TCCCCGGACGCCGGAGGAGACTTCTGTTGCTGCACGGGTTAAGGATGCAA
TGAGGCAGCAGTGCATATCTCAAATTGTAAGAGCGTGGTATGACATTGTC
TCTATGTCCAGGAACTCCCATCCTGAAATATGTGCTAGTGTTTTGGACAC
TATGAGGAGATATATTTCTTGGATAGACATTGGGTTAATTGTAAATGATA
CCTTTCTCAGGTTGTTGTTTGAGTTGATTTTGGTTGATGGTGGGTTGGAT
CAGCTCAGAGGGGCTGCTGCGAGTTGTGTTCTTGCAGTAGTATCCAAACG
TATGGAGCCACACCTGAAGCTAAATCTTATAAAAAGTCTTCAAATTAGTA
GAGTTTTTGTTTTGTTAGGTGAGGATAAGGATTCCGAGTTGGTTGCTAAT
GTAGCAGCTTTGCTTACTGGGTACGCTACCGAAGTTCTGGAATGTTACAA
GCGCTTGAATGCCGAGGATAAAGGCACTTCATTGGATCTTTTAAACGAGG
TTCTGCCGTCAGTTTTTTATGTCATGCAGAATTGCGAGATTGACACAACA
TTCAGCATTGTGCAATTTCTTTCCGGCTATGTTGCCACAATGAAGAGCCT
TTCTCCATTAAGGGAGACCCAACTTCATCATGTGGGTCAGATACTGGATG
TGATACGTATTCAGATTCAGTTTGATCCCGTATATCGTGACAATCTCGAT
GTATTGGACAAAATTGGGAAAGAGGAAGAAGATAGGATGATGGAGTTCCG
AAAGGATTTGATCACATTGTTCCGTAGTGTAGGTCGTGTAGCACCTGACG
TAACCCAAATGTACATTCGGAACTCATTGATCAGCTCGGTTGCAGCACCT
CCTGAAAGAAACGCAGAAGAGGTAGAAGCTGCTCTGTTCCTCTTCCATGC
ATTTGGAGAATCTTTAAGTGATGAGGCACTGAGAACAGGAAATGGTCTGT
TGAAAGAGCTGGTACCAATGCTCTTATCGTCAAGGTTTCCTTGCCATTCT
AATAGGCTTGTTGCACTTATATATTTGGATACAATAACCAGATATGCCAA
GTTTGTTCAAGAGAATAACCAGTATATACCTCTGGTTCTGGCTGCTTTCT
TGGATGAACGTGGTATACACCATCCAAATGTTAATGTGAGTCGCAGAGCG
AGTTATCTTTTCATGAGAGTTGTTAAATTACTCAAAGCCAAGCTCGTGCC
TTTCATAGAGACTATATTGCAGGTATTTGTTCTTTGTATATATCTGAATT
AAACTCGGGTACTTCTATTGCTTTGCAACCCAGCTCCCCTCATAATATAC
TTGTTTTGTTTTCTCAAATATTTCTCAGAGCCTGCAAGACACAATCGCTC
AATTCACGAGAACACATTGTGTGGAAAACGACCTCTTGGTGGCAGAAAAT
GGTAGTCACATATTTGAGGTAATTACCTCATTTATTGTCCTGACAAGGTG
ATGATATTTAATGACCTCCACGTGTCTTTATCTTATTTATGGTATGCCTA
CCTCTTAACAATATGTAGGCTATTGGCTTATTAATTGGAATGGAAGATGT
GCCGGTGGAGAAGCAAACTGATTTCCTTTCATCGCTGCTTAGTCCTCTTT
GTCAGCAGGTCAGCTTTAAATTGCAGTGATGCACTTAAAATTGGGTTGCC
TGATGTTTAGGAATCTTCACAGACTTCAAAACAAACTTGTATCCACTTAT
TAACCAAAAATGTCCTTGCTTGCATAATATAAACTTTTGTTATACTTGGT
TCAGATTGAGGCATTGCTTGCAAACGCCAAAGTTCAGAACCCAGAAGAGT
CTCCAGCGAAATTATGGAATATTCAGCAAATAATTATGGCCATTAATGCC
CTCAGCAAGGTTTTAATAGCTATTAATCTGTTATATATCATGTTTTCCTG
CAGTATTTATTAGTGTTATCAGTGATGCTTAATTTTAGATTTGCTCCCCA
AGTTAGCAGTGTACTCATGTTATTTGCAAGCACATTTTTTAATTCAGATA
TTTAAGAATCTGTCAATAGTAGACAATTATCTAAATTTAATACAGTACTA
CATATACTCTTTTTCTTTTGGTCATAAGACTTACAGTACTACATATACTT
GGTCTGATATCGAACTTTTTCCTGTTCTTAGGGATTTAGTGAGCGACTTG
TTACTGCTAGCCGACCTGCAATTGGTCTCATGTTCAAAAAGGTTTGCATT
AGGATCTATGCATCTCAACAGCACACACACACACACACACACACACACTT
TATCATTGACTTACAACTCTTATGATTGTCTTGATGTAGACATTGGATGT
ACTTCTACAAATACTTATCATCTTCCCAAAGATAGAATCCCTGCGGTATA
AGGTAGGAAATTGTTGATTCTGCTGTTTTTGGTTTTGCAATGTGATAGCA
ACCTAATTCCAAATCTGCTGTTCAGGTGACGTCGTTTGTACATCGAATGG
TGGACACGTTAGGTGCATCTGTGTTCCCTTACCTTCCAAAAGCTTTGGAG
CAATTGCTTGTGGAAAGTGAGGTATAATACTTTCCTTTTTGTATTTTTGA
ACTTGTCTGTATTTTTTTGTATTTTTGACCTTGTCTGTATTCTTAATGAG
GCAAGACTTTACATTTTATGCTGTATTTTTTGTATTTTTGAACTTGTCTG
TATTCTTAATGAGGCAAGACTTTACATTTTATGCTGTATTTTTTGTATTT
TTGAACTTGTCTGTATTCTTAATGAGGCAAGACTTTACATTTTATGCTGT
ATGAAAATAACAGCAGAGACTAGCCCATAGTCTTTCCAGAGATGCAAGCT
TTGCTTGCTACCTGATAAACAAATATTTTTTGAAAGATATTGAAAAAGAT
TCGTAGTTATAGTTAATGCTACTATTGTTTAGATATAGGTGCATGTTGAC
CGTATTTCCTCCTTCCCGCTCTCACTTTTACATTTCCTCTAATTGTCCAA
GCCCTCTACGACTCTTAATTTCCTTCGTTTAAGCAAAGCAGTTTTTGACA
ATTTTTATTTATAATTTCAGCTCAGTGTTACTTTCTCCATCTATATTGGT
TGAAGGCTCTATTTAAAAAAATAAAATAAAATCAAAAGCATTATATTTTT
TTCCCTCTTTGGGATAGCTTGAACTCTATAAAAGCTTTGCAATTCTGGGG
TAGAGTTTGGGACTTAATACTGGGAGTTGTGCAGTGTTGTTGTTTTGTCA
AGAATCAAAATATGGCGCTAGCATAGTTTTCTTTTTTGTCATTAACTCTT
TGTTTCCCTCAATTTCTGGTTGCAGCCTAAAGAGTTGGTGAACTTCCTTG
TTCTAATGAATCAGTTAATGTGCAAATTCCGAACTGCAGTCCAAGATATA
ATGGAAGAAGTATACCCTGTTATTGCGGGTAGAATTTTTAATATTCTTCC
CAGGGACGGATTTCCTTCTGGGCCTGGTAGCAACACTGAGGTAATTGACA
TTATTGAATGGAGTTTATAGGAGTGAATGTTTGTGCGGGTAAGGTATCTT
AAAGATCTGGATTTTAGAGAGAATATAATCGGATAGAAAGATCTATTCGC
TGTTATAATGGCTGATATTTTCAGATATACTAAAAACTAACTTTATATGT
AATGTTATGTCCTATCTGATCTAGTTCTTGACTGTTTTTCTCTCGAGATA
CTTATCATTTATTGCTTTGATTAGTAATAGGTTTTACCCGGGACCGACCC
AAAATGTAAAAAATAGGGTTCAAAATAGATTTTTTTTTTGTGTGTGTGTA
TTTCAATTTATGTCGGATTTTCAATAGAGGGGTCCGCGGCGGTGTAATTA
ATTGTTCCTATGGTGTATTTATGGAGTTCATTATTTTGTTTATCCCCATG
TTATATCCCTAAATCACGCGTTCTTCATTTCTCATCCTCTTCTGGGCCTG
CTTGACACATTTTTCGGGCCGCGGTTTAGACTATGATTATATTTATATAC
AATTAATTTTCATAAAGCTCAATAGAGAAAGTTTTTTATTATATATACAC
AATCAGATTTTTACACAAGGTCTCAAACAATTCTATACAATTCAAAATGA
TTTCTTTTTTGTTTTTTGTATAAATAAGATTTACTTAAAATACTATTTTT
TGTGTAACAATGTGAACATATTTAATTTGATAAAATCAAACATATTATCA
TCTTTTGATAGTTTCGTTACTATAAATTTATATTTTTATATAAACAAAAA
TCTTGAAAGTGAAATGAAACACAATTAACTGGTTAAATTTTCTTAATGTC
AATTGCTATATATACAAAAAATTGATCAACTTGGTTTATCAACTGGTTTA
TGGATATTTGTTGAGGTTGAATATATATTTTTAATTAATTATAATTGTAA
TACGAGATTGATGTGTGCTTAGTTGTATCATATATTTATATATCGGATCT
AGTAAATTTGTGTATATGAAGAATGGTCAACTCTTTATGACTAGTCGTTC
AACTAGTCACGGGGGGACTCGTACCCCGGGCGTCAAGGCTTGACTTGGCA
CTGTAATAACCACGGTAGCTGGGAATGGCTATTGCAGGTTGTGTACCTGC
CTATCTGGCCTCAAAATCTGAATGATACTTTAGTAGTAAAGTCGACTTCC
AGTCAAAACAGAAGCAAGCTATCTGGTTTGAATACCCAATCACTTCAACG
CATCAATTTTGAGCTATCATGCTCCAACTGCTGCTTAATACTAATTTTAG
GATGCATGATGATGCTTCTGAAGGCCTAAAGAATCTTGGCTGGAGCCCTA
TATTTGATATTTAGAGTCCTCCAGAATTAGTGTTGTAACTTGCTAGTTAT
TATAACTATTTGTCAGAGTTGTTCACTGGTTTTACCTATCTAAAAAACCT
ACTAAACAAGAACAGCCACCAACAGAATCTGACTGCTTGCTTACAATTTG
AAACTTCACTTAATCTCCAGGTCAAAACTAATTTGATTTTTATTTTGCTC
CAAATGTGTTTATGTATCGAAAACACATCAATTCCCCTAACAGAGCGAGT
TATTGATGGTGCTTGCTTTAAATATGTTTATTTCATCATTTTTGGTTAAC
ATTTTCTACTTGTTATATATTAATGTAAAGAAGAAATTTATTTTTAGGAA
ATTCGTGAACTGCAAGAGCTCCAGCGCACGGTGTATACATTTCTTCATGT
CATAGCAACACATGATCTGTCCGCAGTGTTCCTTGCCCCAAAAAGTAGAG
GATACTTGGATCCGATGATGCAATTGCTATTGCACACTTCATGTCATCAC
AAAGACACTCTCATTAGGAAGGTCAGTTGTACTCTAAATTTGAAATTTGT
CAACAATATGCGAATTTCACCTTAAATTTCCAGTGCTTTGGAAGTCCAGT
CATTATTTATATATGCACATAAACAGACGCAAACAATCGTGGCTTCAGTT
TATTAATGTTTTGTTCCCTTTCATTTAGGCATGCGTACAAATAATTACTA
GACTGATCAAGGATTGGTGTTCCAAGCGCTTTGGAGAAGAGAAGGTAATT
TACCCTTTCAAACTCTGTAGTGGATAAAATTTTCAGCATTTGGTTTACTA
AGGTAGCAAGGTCAACGCAATTTCAGGTGCCTGGTTTCCAAATTTTTGTA
ATCGAGGCTTTCGCAACGAATTGTTGTTTGTACAGTGTGCTTGACAAGTC
CTTCGATTTTCGTGATGCAAACACTGTAAGTCTATGATTAACAGTTCTTG
GTTTTATATACATATATAATTTGTAAGTGGCATGCAGGCTAATCATCTGA
TATGTTGATGATAGTTTTCCTTACATTTGAATCTTCGGCAATTTATCGTT
AAAATACTATGCAGTATGAATGTCTAAGGACTCCATATATTGAAGGATTA
ATTAGTCTGCTATCCTTCGTAGCCTTTTCATTGTTCTGAGTTCCAAACCC
AGTATTGTATTAGAACTGCATCCTTCTCCAAGGCTAAATATAAAAACTAG
GAGTTGCAGATAGCAGGGCTATGGTAAGAGGTGAATTAATTTTGGGTTAG
CTGCTTTTCTGGTTGCTTTGCATACTTCTCACTGACTCACTGTTAGCTCC
CTTAGGATCTATGTGAGGCGACTATCTAAATAGATAGTTGCTTATTATAT
ATCCGTAAAAATTAAAGTTACTTATTAAGGATTTTTATTCGTCATGCTGT
TTTCTACCAAATTGCTCCTGGTCTGACTTTTTTCCATGATTTTATGACAG
CTTGTCTTACTAGGAGAAATTGTAGTGGCTCAGAAGGTCATGTATGAAAA
ATTTGGCAATGACTTCCTTACTCATCTTGTATCAAAAGGTTTCCCGGCTG
CACATTGCCCCCAAGCTCTGGCAGAACAGTATTGCCAAAAGATTCAGGTA
AGATTTAGACCTTTGCCTTATGATATATAATATGTGGTAAATTAGATCTT
GTCATGGGAATAATGGGATCCAGGCAAAATTTTCTTCCCCTTTTAGAAAT
TAAAACGTGTAGTGATATTTGAAGCAAGTCAAGATACCAAGTTCTGTATA
TTTTGAGGGCAGCTTATTACCAACATACCAACATTGGCATATGACTTTGC
AAGCTAGAAATTTAGAGCCCATCTTCGTCGCCATTTACCTGGGCCTCTAA
TGTTTTAGGCTACTTTCTTTATTGTTGTATATGTTATACATTTCCTTGAG
AGCTTGGCTTGTCTATAGCAACTTTCATATATTCATCTCCATTGGATGCT
AAAATTTGTTGTTCTAATTTATATTGACAGGGGGATATAAAATCATTGAA
GTCATTCTATCAACTATTCATAGAAAACTTGAGACAAGAGCAAAATGGAA
GTCTTGTTTTCAGATAGCGTTGGCATATCTGAGCCATTTGGTCAAATTTT
AGAATTGTGGGATGATGATGTTCTGTAATATTGAAACAGTTTTGCGCACG
GAAGGTTTGTACTTTTGCATGCAGCAGAAAGAATTTAGAACTTAATAACT
CTCTTACGGATAATTATATTTCCTTGCACATTGCAGGTATCGTATCTGTA
TATAACTTTTCCCAAAGATCTTATGGCATTGAGAGGTAAACACCTCTTTG
ATCTAAATGTCCACAAAAAAACAAACATATGGTGACTTATCAATATTGAT
TTCGATCTGTTTGTACAGGTTTCAAAGTTAATTATTGTTTGTGGTCGTAG
ATAATTTTTTGTCTGGTCATATAATCTACTGAACTAAAATTTAGGATTAT
TATATCAACTTAGAGAGTAATATAAAATACGGTTATTAAGAATTCCTTCA
TCTATTTGTACTAATTTATATATAATTGCTGTAGCAGGTGTATATTTGCG
GAAGCAGTAACTTGA