| Relationships |
|---|
| The mRNA, DCAR_017343, is a part of gene, DCAR_017343. |
| The genetic_marker, MK011216 5_15490812, is located in gene, DCAR_017343. |
| The genetic_marker, MK004150 K1594, is located in gene, DCAR_017343. |
| The genetic_marker, MK005184 K2628, is located in gene, DCAR_017343. |
| 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_017343 | DCAR_017343.mRNA | mRNA | DCARv2_Chr5:15488431..15495248 |
CCCGTGTCCAAAGGTGCACCAAAAGCAACTACACCGTCTATCTAAAACAT
ACAGCTTCAGCTTCGTCTCCTTTCACCCCGTCCCCATCTGTCATCACTAA
TCTCTCTCTCTCTCTCTCTCTGAATCTCTCTCTCTCTCTCAGAAGACAAC
AAAATCTCTGCGAGAATTTCACAAGACAGTATGAGATTAAGTGCATTGCA
GTGACAACGACTTCAACTTCCGAAAACCTCAGGTATTTTTCACTGCTTTC
ACTTCCTCAGCGCTTAACATTTATCACTTGGCATACAGTGCATCTAAGTT
TTCACTATCATCTAGTGATTAATTAAGTAGCAAATCAGTCAGCGAATGCA
GACAGAGACTGACAGTCTGTATTATAGGGGACCATTCCGCTATAATATTC
AACTACTTATTATATGGTTACAAAGCACTCAATTAAATAATGCGATGAAA
TTAGCAATTAATCCATGATTAGATTTGTTTGTTTCGTAGATAATGATTGT
CCAATTTGCTGGTCCCTATTGTCTCTACAAACTAAGCCAAGCATTACAAT
GTGAAGCATATGACTCTGATTAGTGTGTGCGTGTTTCTATATATTATATG
TGTGTGTGTTATTATTGAGGCGTATGTGTTGACGGTGGCATTGTAATTAT
TGTTAGTTGAGAATGGGAGCGAGTGATGTTGGAGAGGAGGTAGGGATGGC
AGGGGGACATGATGAGAAGATTTTCGTGACCGTCCGGTTGAGGCCTTTGA
ACCGGAAGGAGATTGCGAGGAATGATGTGGCGGATTGGGATTGTATTAAC
GGCGACACTGTCATTTACAAGAATGCTAATCTTTCTATGCCCGATCGGTC
TATGTATCCGTCTGCTTATACATTTGGTAAGCTTATATTTACTATTAGTT
TTTCTTGATTTGTGTGTGATGTATGGTGTATGTTTCGGTTTGTTATGTAC
AATGGTACTTAATTGTCTTGTATGGACACGTTTTTAATGTTAAGCGCTGT
TTTGTTTCCTAGAGGTTTAATTTAAAGTGGAAATGAATCATTTTCGGGGA
ATGGGGATTATCTGATGCATTTTCCATTTGTGCTCGGCCGGTGGAGTACG
AACGGGTTTTAGATTTGGTTTATAGTCGGATATAGTTTTGTTTATGGTAA
TTCTTTTCAATTGATGGTTCAAGTGTATATGTGTTGAAATGAGATGGAAT
GGAGTGCATGAGCATGACTATGTTTTTTCCATTAGACGTTTGTGGTTAAG
CTTCAATGATTTTGATGTATACTAGTTATCATAAGAATAAGAAACTAACA
ACAATCACTGCAGTTGTGAATTGTCGAGTTTAACAGTATTTTTCTAAGAT
TGTTCTTATAATTTTGTTCATTCGTGGTGGGATTTTGGGGATCCAGATAA
GGTATTTGGTTGTGATTGCTCTACGAGGCAGGTGTATATGGAAGGAGCCA
AGGAAGTTGCTCTATCAGTTCTAACTGGTATCAATTGTGAGTATACGTCT
CTATTCTATTTTATTCCCTTCTTTTTGTCATGAATTTTCTCTTGACTTTG
TCGCAAATGTATACGACTCCAGCTAGTGTTTTTGCATATGGACAAACAAG
TAGCGGAAAAACGTTTACCATGACCGGCATTACTGAGTATACTATATCTG
ATATATATGACTATATACAGAAGGTAATTAAAGTCAAGTGCATCATTTTA
ATGATACAGTTTTAGTTCTGCATGTTGCATTCAGTGCCTTGGTTGATTTG
CTAGACATATATGGTTGTGTTTTTTGTAGCACACAGAAAGAGAATTTCAT
TTGAAGTTTTCTGCAATGGAGATCTATAATGAATCAGTTAGAGACCTCCT
CAGCACTGATAACACTCCCCTCAGGCTCTTAGATGATCCAGAGGTGTGAA
CTTTTTCCTTACACAATACACCTATCAATGTGTTGTTGTAGCATGACAGT
TGTTTGTTTTGATAGAGAGGTACCATTGTTGAGAAACTCACGGAGGAAAT
ATTGAGAGACTGGGATCACGTAATGGAGCTTCTTTCTCTATGTGAAGGTA
AGTTTCATCGAACCATTCTTCTGATAGAGGACTACTGAATAAGGTCTAAT
ATTTTGTGCTGCACTTTTGCAGCTCAGAGACAGATTGGGGAGACCTCTCT
GAATGAAACAAGCTCCAGATCACATCAAATCATAAGAATGGTACAACTGC
CGAGCCTAGTATATTATTTTATGATTTGTTTTGGGTGTAGAACCAGATGG
GATTGTTATGTCAATTATATTATTTCATTTGTTAATATTACAGACTGTGG
AAAGTTCTACCCGTGAGCTTTTAAGCAAGGATAACTCGAGCACCCTCGTG
GCATCTGTGGTATGCTTTCGTTCAAGTTTCCATTAATTTTGTTCAAAATT
GGTAAATGATATGTTTGAGAATATTGGACTAAATATTGTGTTTGTTTAGT
GATATTGATGAAAATTAGTGTTCTTTGAATTTAGAATTTTGTCGATCTTG
CTGGAAGTGAGCGTGCATCCCAGTCATTATCAGCTGGTACAAGGTTAAAG
GAAGGCTGCCATATCAACCGCAGTTTGCTTACCCTTGGGACTGTAATCCG
CAAACTAAGGTCAGTCTCTCTATCCTTTTTCCCCCATCCAATTACTTATA
AAATTTTAGTCATTATTTCACTAATTGATAGATCTTTTGATGTTTGAGAA
TAATGTATATTCTGCTATTCTTTATTTGTGATAGAAACTTTAGTCACAAA
TCATCTTCAAGGACTTGCAACTGTTTCCATTTGAGGCATGGTTCTTGTGG
GTACATAAGTACATAACTAAGTTTGCTTAATTATTTTTACGAGATATATA
AAAGGCTTTTGATATTATGACAATATGACATGACAGGCTGGCAAATTATC
TGCTGCTCTCCTATCACACTCACCCACCCCCCACCCACACACACATCTCC
CCTAAACTACCCTTCCCATGTTTGAACTTTACCTTGCCCAGCTGCCCTCT
GTTGGTTATGATAAACTAAAGAAGGCTTATACAGTGCAACGTGCGAAAAT
TTTATTTGTGGTAGTTGTCAAAATATTAACCCACTTTTGTAAATGGTTGC
AGCAAGGGAAGAAATGGTCATATTCCTTTCAGAGATTCAAAGCTAACCCG
TATACTGCAATCCTCATTGGGAGGCAATGCTAGAACTGCCATAATATGTA
CAATGAGCCCTGCACGAGTTCATGTTGAGCAATCAAGAAATACACTGTTG
TTCGCAAGTTGTGCCAAAGAAGTATCAACTAATGCGCAAGTTAACGTGAT
AATATCAGATAAGGCTTTGGTAAAACATTTGCAGAGAGAGTTAACTAGAT
TGGAGAGTGAGTTAAGTACAGGATCTACTTATGTTGCATCGAAGTATTCT
GCACTTCTTCGCGAGAAAGAACTGCAAATTGAAAAGGTACGACTCAAGTT
CCAAAATTAAATTTGTTAGTCTTGATATATTCTTTTAGAGACTATTCAAT
GCTCAGTGTCAGTAACTAGTTCTGCTGTTAAAATTACTCATTATGTATTA
TATCTGAAGTGCTTAATTACGGATTCAACAATATTAATGCAACTGAGGTA
GTATCCCTTAAGTAATACATTGTTGCTGAAATATTTATAGTCCTTCTATA
TCCACAGGATTCTTTCCTTGATAGCACAATAGGGTTTAGCAAACTTTTCA
CCTGTTTCCTATAAGTTCTCTTCCCTTTAGCATTAAGAATTTACTGTCTT
GCAAATGATTGACCCCCACGAAATAGGTAATTTATGGTCTTGATCAATTT
AAAATCTAACCTCTTCTTAACCAGCCCTCTATCTTTCAAGAAAAACTCAG
AATGCTTCAATATCTTTGTGGAGGTTTATGCTAAATCTATTAATTGCGTA
AGGTCACCTTTTTTCCCCTTCTGCATAAATATTAGGTAATTTTTTTTAAA
GGATTAAGAGGTTATTTGCTTCACTTTTAGAAATCAATGTTTGTACTTCA
GTGTATCAGAGGAGATTTAAGTCGATTTCAGATTGGACATAAATTTAAGC
CCTTTAATTATAAAAGTTGGTGTCAGTATCACAGCCAATGTCTTTGCAGC
AGTTAATCAATGAACCAACCCTATGTATCTTCCTTAAAGCCTCCCTCTCT
TAAACAACCACATATAATAATTACAGAAAAATTAGCAATATTGTTACTGA
TATAAATGAGGTAGAGATGCTGCAATTTTCCCTCAAAAGGGTTTATTTTC
TGAACCCAGATTACTACCATTGCATTTAATCGAAAATATAAGGTTCTACT
TGTGTGCACCCTTCTATTTGTATTCATGTCTTCAAAGATCGTTCTCTTTG
TGCAATTTTTGAGCTTGTTTTAATTGGTTAAATTTTAGATGTATTCTTTA
CTCAAATATCTTACATGCTCTGTATATGAACCTTACATATAGCTGCTATA
TCAGATATTGCTGTCATCTTGAATGTGCTTAATAAAACTGTGGTTAACCT
ATATTCTCTATGGTGTAGCTGGAAAGAGAGGTAAAGGACCTGACTCTGCA
ACGAGATTCTGCTAAATCTCAAATTCAGGAAATGCTAAGATGTATTGGAA
ATGATGGGCATCCATTGACAAGGGTAAACATTGTTTTCATTCATATGGGA
CTCACTGAAGTTTCTCTTCTATCTTGACCCGTATCCATTGTTAAGTTCTA
ATTCTATGTTCCAACCTTCCAGGTAGTTCATAATCACTACCCCCACTTGC
GAGTTCAGGATTCACCAGATGCCGGATACCGAGTAGAGAATAATTACTTA
ACAGCAGTTCCTCACTCTATGGACGTTGCTTCCAAAACATTATGCACATC
TCCCTTTTCTGATAGACAGGATGTTAATGCACTAAATTATAACCACAGTT
TTTTCCCTGGTTCTTCTGAAGATTTGCACCCAGACCCATGCCGAAGACCG
CTGACCAGTACTTCACAGATCAGTGAAAGTGATTTAAGCCAGGATCTGGA
TGATTATGATGGTAAGAGTAATTGTACATCTGAAGATATATGCAAGGAAG
TTCGGTGCATCGAAACAGAAGATTTCAGTAAGAATAATCATCCGGAATCC
AGTCAATTATCTAATGCCCATGACATTGGAATATCCGCTACTATTGTTTT
GAAAAATGGAGAGACTGCAAATGAGGAATGGGTATCACCTATGTCAAAGT
CAGATGAGGTATTAGTCTCTTTGCTTTCGAAAGAAGAAACAGAATCTATT
GCACCCTCTTTAAAGACGAATAGAGAAGCTCTAACATTTCCATGTAGTGA
AGATAGACAAGTGGCATTACCATATATAGAGGATAGTAAAATAAATTGCA
TTTATGATACTCCTTCACCTGAAAAACGATCTCCATCTTATGACCTGGTC
AAGGAGTTTTCCAGGTCCAGGAGCCCGAGTTCAACAACAAGCAGGAGCTA
TGAATCTGGTATTTCGGCAACCTTATCTTCCCCGAGGCTGCAGGAGGCAG
TACACCTTGATGACACTCCACCAAATGGCTGTGAGGAATACCACACTCAA
AAACCTCATGCTTCTCAGAGTGAAAATTCTAGACTAAACTATGGTTCTGA
TGTTGTGATCTCATCTAGCAATGGCTCGCAGTCGCCTAACAAGAATGGTG
TTGACATTGAGCTTGACACACAAGAGCAGGGAAAATTATCTGCTGAAATT
ATTAGCGATGGCAATACATGCATTGCAAAACTGGAAACTATGTCTGAACC
TCATGATGAGCACCAAGGTTTTGACACTCTTGTAAGTCTTATCTTAGCCT
CAGTTTTCAAATAGATTCCTAAGATCTTCTAAGGGCCAGTGCATTTTATC
TGTTTATACAAGTGAAGTGCAGAGTCATTGTTATTAGTATATATCCTACC
ATCTAATTTTGTCATCGTTACTGCATACTAAAAGAAAATTTGAGTGTGCT
GAAGGCTTTAATGGGTTCTCCTCAATCGCTAGATAAGTAGAAAGAACTTT
TGCTGCATCGACAACTTTCTTTTAGGGGAATTGCATAAGATTATTTCCTG
CATCATGCACTTGTATAATGATAGTGGGAACTGCATATATCACATGAATT
CATTGCAAGACCTCAACATGCATGCATGTTATCTAATATATTGTGTGTTT
ATGTAGACATTTGTGCAGATATGTATGTTTGTGAGTGTGATGTGTGTACA
TGGATGGACAAACATATATCCTGGCCGGACGTAGTGCAATATTTGTTACC
TATTTCAATAATTTTTTTTTGGGATAAATGTTTGAGAAACAGTAGGTGCT
CTTGTTTCGTAAGTGCACAAGAAACATGTTGGCAGCAACTACCCATCCTT
ATATAACTCTGCAATGTTATCCTTTTGAGGTCATTAAGCAAGATAACAAA
TGTTTTTCTATCCTTATTTTTATATATGTAAACTAGCTGTTTTTCTAATC
AATTTTGTTGTAAATTCTTTTAGGCAAATGAGACAAAAACGATGTCCAAT
ATGTGTTTGAAGAGTGTAAAAGATGTCGGCTTAGATCCAATGGAATATGA
TCTCAGTAGTCCTTCAAATTGGCCATCAGAATTTAAAAGACTCCAGAAAG
ATATAATAGAATTATGGCATACTTGCAATGTATCTTTAGTGCACAGAACA
CATTTCTTCTTGCTATTCAATGGTGACCCAACTGACTCCATATACATGGA
GGTTGAACTTCGGAGGTTGTTTTTTCTGAAGGAGACATTTTCTCAGGGTA
ATCAGACTGTGGAAGACGGAAGGACTCTTACAATTGCTTCCAGGTGAGAG
ATGTTTTTTCTTTTATTTGTTTTATTAAGGAAGATATTTTTACTTCAAGT
TATTATAGTGCAGATTATCGCAGTCAACTCACTTTATTGCTTTGTTCTTT
CGGTAAAATCATGGTAGATAAGTTCTGTAGGCATGCATGTACTTCGGAAA
TAATGGCACTGTTCTGGTTGTAAGTTGCAAAAATTTGACGTTTAATTACA
AAGGTTATAATTAGAAATAGCAGCTGATACTTTTGTACTCTGATTAATGA
AGAGATCTCCAATACACCACCTCTATATCACTTGTCTTTTATTACTTGTA
GCTTCATTAATTACTTTATTAACTCTCTGTCCATTGCTGTTATGTTTCCT
TCTGTAATAGTCTCAAGGCTATTCGTCATGAGAGGCACATGCTCAGCATC
CAAATGCACAAGCAACTCCCCCAAATAGAGAGAAAGAGTCTCTACCTTAA
ATGGAACATTCCTTTGAATAGTAAACATAGGAGAGTTCAGCTGGCCAATC
TCCTATGGACGAATTCAGGAGATTTGGACCACATTGCAGACAGTGCCTTT
GTCGTAGCTAAACTTATTGGGCTTACAGAGCCCGGAAAGGCTTCTAAGGA
GATGTTTGGTCTGAAGTTTGCTCCCTGGAGCTCCAGAAGATCGTATAGTG
TTAAGCGCAGCCTGATATCAATATTGTAAGATTGCTGCAGATGGCAAGGG
AGAAAGTGTGGTAACAATGTGGTACCCAGGGGGCTCCATTTACTTAGATA
TTTATAATATATGTATAATTGCTACCTTAAACTTTCTAGTATAATTTTAG
AGGCTGGTACATTGCTCAGGGG