| Relationships |
|---|
| The mRNA, DCAR_014397, is a part of gene, DCAR_014397. |
| The genetic_marker, MK008733 85036.36281, is located in gene, DCAR_014397. |
| The genetic_marker, MK009573 4_22176369, is located in gene, DCAR_014397. |
| 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_014397 | DCAR_014397.mRNA | mRNA | DCARv2_Chr4:22174152..22182045 |
ATGCAAAGAATGCGGAACCAAATTGAGCAATTGCAGGCTGAGTTGCTTTA
CATTCATGGAGAATCTGGTAGGCCGTTCGAGGAACTTCTGATTTTAAAGC
AGAAGATTTCTTTGCTTGAGGCTAGCAATGCAGAGCTACAACGGCAGCTT
CAAGAATGTCGGATCAGCTCTAAGCATCTCTGGCAACGAGCTATTGATGA
TCAGGTAGAAAAGGATAACCGGATCATGAAACTTGAATTGGCACGTAGTG
GTAAATCTTGGGAGGAGATTGACGCTGATCTGAACCAGAGAGATATTGGG
TTGGTTAAAAATTATGTGACGGAATTAGAAGGTGAATTCCTTCGAATACA
GAAGTCGAATACTTCCGAACACCATGAATTTGCAGGTTACCTTAAATTTG
ATGTTGTTGGGTCTGCTCCAAAAAAATCCCTGTTCGATCAGTCGGACACA
GAAGCTACAGATACTGATGGTGAAGCTGAAATTGAAAATACAAAAATTAA
ATATTTCTTTTGTTAAAAGAATATTGATCTTTATACTCTTATCCCTGGGG
TTGGGTTCCTTTGGGTGGCGAGTTTGCTCTTATCTCTAGGGTGGATTCCT
TAGAGTGGCGAGTATTAAACCCTGATCTACTTGTTTCCATTGCTTCCGGT
GTCAATTGTGCATGATAAATTAGGCGATAGCAGTTGCTTTTTTGAAAATG
GGCCATAAGTAAGTGTAGGAGTCTTGGAGAACATCCCAGAATTTTATATC
TGGAGCAATACAGGTTCTTGCCGAAATACACATGAGTACATGACCTGTTT
TAATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNAACCGGATATGATCCAGTATCGTATTTCTATTTTTTA
ACCGGGTAGTTTATGATCCATCGAATATGAGCCGGATATGATCCACTAAC
ACTAAGTATCATTATTATTTCAGTTGTTCAAATAACTATCATTAGTCTAA
GTAAACATAATATTATAAAGTATAATAATTTTAAATTAAAACTTATAGTT
ATATATTGATATATATCATTTATTAAATATATATGAAGATAATAAGTATG
ATCACATTAAATAAATCATATTTTATGAAGATATAAACTTAAATAAGATA
TTAAAATTTTATAAAATGATAACTATTTACTTGCAAATATGATGGTGTTA
AAATATAATATGTATATAAGTTTGAATCGAATATGAACCGCGGATCATAT
TCGGTTATTCGGGTAGGATCATATTATGAAAAGTTATATGAGCCCGGATC
TGAGCGGGTATAGGTGTGCTCGTATCCGGGATCATATATTATACGGGCTT
AATTTTTCCGCCAGATTTGGATCGTTTTCAAAACGTATATGAGACATGTA
TCATATTTTCGAGCCGAATATGAGCCGAGACACCGGATAGTCCGTATCGA
TTTACAGCCCTAATCAAGAGAGAGACATGTAGTTTCTCCTGCATGATGCT
TGTATATATGATTATGCATTTTGGGAGCATATTCATTGTATTAACATAAT
ATTGATTGCAGATCTTCGAATTAGTTTATTAGTAGGAGGCGATAGTATGG
AAAGTCAGTTTGAAGAGTTGGCACAGAACCCCGATATCATTATTGCAACC
CCTGGTAGACTCATGCACCATTTGTCTGAGGTTGAAGATATGTCACTGCG
TAGTGTGGAGTATGTGGTTTTTGATGAAGCTGACTGTATCTTTAGCATGG
GGTTTGCTGAGCAGCTGCATCAAATTCTGTCCAAACTTAGTGACAATCGT
CAAACCTTGCTCTTCAGTGCAACTTTACCAAGTGCCCTTGCCGAATTTGC
CAAAGCTGGTTTACGAGATCCCCAGCGTGTGCGACTTGATTTGGAGACTA
AGATTAGCCCTGACTTGAAGCTTGTCTTTTTCACTTTAAGGCAGGAAGAA
AAACATGCTGCATTGTTGTACTTAATTGAGGAGAGGATTAGACCTGATGA
ACAGACTTTGATCTTTGTTTCCACAAAATATCACGTTGAGTTTCTTAATG
TTCTCTGTCAAGAAAGGGGTATTCGTCCATCTGTTTGCTATGGTGATATG
GACCAAGATGCTCGCAAGATGGCTGTATCCCAATTTAGATCAAGAAAGAC
TATGCTGCTGATCGTGACTGATGTAGCAGCCAGGGGGATTGACATTCCTC
TGCTTGATAATGTCATCAACTGGGATTTTCCTCCTAGACCTAAGCTTTTT
GTCCATCGAGTAGGACGAGCTGCAAGGGCTGGTCGGACTGGTACTGCATT
TTCTTTTGTCACAACTGAAGATATGCCCCATGTTTTAGATCTTCATCTCT
TTCTTTCAAAGCCTGTCAGGGCTGCTCCCACTGAGGAAGAGGTTTCACAT
AATGTGAATAATCTCATGTCTAAAATTGATCAAGCAATTGCCAACGGAGA
AACCGTTTATGGGCGCTTCCCTCAGACAGTTCTTGATCTCTACGCAGATA
GGGTTCGGGAGTTACTGGATTCTTCTACCGAATTACATTCATTGGAGAGG
CCGTGTACTAAAGCATTTCGTTTATATTACAAGACGAAAGCAAAGCCTTC
TAAGGAGTCTGTTAGAAGAGCAAAGAAGTTGCCCCGTGAAGGACTTCATC
CAATATTCAAAAGTTCGCTAGGTGGTGATGAGATAACTGCACTTGCCTAT
CTTGAGCAGTTGAAAAAATACAGGTACATTATACATGTTATGGTTAGATG
TTTAAAATGTAAGTTTGTTTTGTATAATATTTAGACGAGGCTCTGATTAA
TATTGAATCAATCTGTTGTAAACTAGACCCAAGCAGACTATCTTGGAAGC
TGAAGGTGAAGTTGCTAAATCAAAGAAAGTAAAAGTAAGATTTACATTTG
TTGGCATGAATTTCTTTTGTGATTTATACTTTTCGAATGTGTATGTGCAA
CATAGTCTTGTCTATAGCCTGTCTATGGTTACAGACACACACATACATTA
ATATATATATATATATATATATATATTTATATATATTTATATTAGTCGGT
TGGTTCTCGATATGCTTTATTGTACTTCACTTTCTAGTGAAATTTTTTAA
TTATTACATTGATATGTTATGTGATTGAAGGGGTCTGCAAGTCAAGGGGG
TGATGTAATGAAAATGAAAAGAGCTGTGCATGAGGAGATCATTAATAAAG
AACATCAGAAACACTCCAGAGAGTGTGCAGAAAAGGTGAACTTGATGTTT
TGAACATATGAGTAGACATTTTTGACTTCATCAGCATGATAGGACTTAGT
CACATATATACAGCAACTATCGTACTCGTATTATCATCTTGTTTTGTATT
CTTAGAGCAAGTAACAAAATATATCTGTCAAACTGTTAAGCACTTGAGGG
AGCTGCTGAGTGCTGAGACAGGCTTGCAAATGCTGAAAAATTAGACATTT
GTTATTTTGTCACCGAGTTTTCCAGGGTGTGATTCTGAAGTTAGAAGATA
AGATGATAATGTTCAGATACTTGTGTCCTCCGTATAGGTCCTTAGTCATG
TGCGATTGCCCGGAGCCAACTCTAATATCTTATGCCTCTTCTCTTATTTT
ATAATTTCTGCCTCGTAGAGATTGGTTTTGTACTTTTGCCTGAATTTTCC
TGATCTTCCCTTGTAGGATCCCTTTCAATAATGTAGTGATTGTACATTTG
TATAATCTGCTCAGGGCATCTTAAAGATTAATGCCCAGTGGCAGCCAATG
TTTAAATACCTTACTTTATGGAGCTGATTTTAACTGTGACAACATGTAAA
ATGTTATATAATGTTTTTTAGATCTCATATTGTGAGCTAACCTTATTGTA
TTGTGCACAGAAATATGAAATGGATGATGATATGGATGAAGTTATGGAAA
ACGTTCCTACAGCTGGCATTGAAAAGAAAGGTTTGTCCTTGGCTAACTCT
TTATCGCATGTTTCGGTCTTGTTTGTTCTATGTTTCTTGTATATTCTTCA
TCAGAGTTTTTACATGGTTAACTTTTGCATTGCTAAATCTTTATGAGCCA
CCATATTAGAGATCATTATATGAGTGGTAGAGGAATCAACTATGAAATAA
ATACCCTTAAGAAGTATCATTTGTCGCTTTTACTTTTGGTGATAGGCTGA
AAACTCCATATACTCAATTGGATTATTCAGCCAATGCTATAAAGGAGTTT
TAGTGTGGTTTCCCTTGAATTACAGCCCAGGGGAACCTAATAGCATTTTT
GTTTATATGTTGGGCATCAGAAACTGCAAACATGTACATGTTGTAGACTT
GTAGTAAGCCATCTCACCGACGTAGTATAACAATCATTTGCTACTTTAAT
GTGACAAGAATAGTAGTCCGCCAGCATATTTAAGTAATATTGTACCCAGT
GTGATGTAAAAAATAATCTGTGGAATTTCAGATGTACAAACCACGTGTTT
GGTTATTAACTTATACAGAAATAGATCAGTAATCCTCTTGTGGTTATGCT
GTTGCATTTTGACTGTGCTTAGACGTTATTGTAATACAAGTGAATAAGTA
ATGGTTTTTGCTGTTAGGATGTAATTCCTAATTAACATCTCATGTTTGTG
TAATGCTTGCAATGCTTGTGAGACATGCTCGTATACTGTGTTCATTTTTT
TATTCTTGGCAGTTTATTAATGAAAAATAAATGGGCAAAATTTGTTCATT
TTACTAGTTTCTGGTTCTAAAAGGAAGGCAAAGAGCTTCAAGGATGAGGA
GTACTTCATAAGTTCCGTGCCAACAAACCAAGTAAGATTATTTTGTCAGG
AAATAAGAAATTTTAGAGTTGAACAGAAAACCATATTATGCTACAGGCTT
GACAAAAAACTTGCCCCATCGTCTGTGTTCTGTAAAGTGATTGTGTTTCT
CCTGTATCTTTGCGTGTTTCTGAGAATGATGGTTGTAACAATTCCACCTG
CCAGAACACGTTGTTCAGTAAACTATTAACTTCTTTGTGGTTAATCATTT
CAGCATTATGAGGCAGGACTTTCAGAAAAGGGCAGCAGAGGGTTTGAATC
TAATAGGTAAAGCTTTTTTGCCTGTTTATCTACTTTATAAGCATTTATTT
ATTATGTAATTAAACTGTGCTGGCCTTTGAACTGCTATCCTATTCGAGGA
CTTGGTTGGTTTGAATTTAGTTCCTTTTGCTAGTTGATATTCAATCTGTA
TATGATAAGATATGGAACAAATGGAATCGAAATAGGTATCATTGGCGCCA
GGTTGTTAAAAGGAGTTACTTAAGATGCTGTCACGAAGTAAATCATTATA
AATGTAATGAATTGTCGTATTTATTTAAATTTTTGGAAGTTGGGCTTATA
CTTGATTGTCATGGTATTGAAGTAAATCCATATCCTTTTTTTAGGGAATT
ATGAATATGTCATTTGGATAGTGTAAAATGAAGCCCTGTTCCTAAATATA
CCATAGGATTATCTTATATGAATGTTCTTTATCTGAATAACCGTTTTGTT
GTATTTCTTTGTTTTTTTACATTTTAATGAATTAGGTATTTTATAAAGGT
TACTTGGCAGATTTTATAACTTTAGTTAAAAAGCGTCAATGATTTTACGA
AGTTTAGAATGAAAAAGGATCATGTAAGATTTCATGGTTATCACATGGGC
AGTATTGTGCAAAAATATTTTATTTTAATATAATACAAGCATATAATTAT
TTTTTTACTTCATATTTAAACTAGGAAACAGATGTGTTTATTATGTATTC
TATCAAATAAATCTATGTACATTACAGACTTGTCGACTTGTTATAACTAG
TCTTCTGGAAGGCACTCAAGTGGCTCAAGGGACTTGGCATCGTGATAAGT
AATTACCAACAAAACCACACTTATGGTTTTGGTGCATAGCACTCATGGAA
AAATAATTCTTGACACATAGCACTTGTGGAAATGAGTAGGTGCTTTTGTT
TTTTTCCCGTTTTAAAATTGGATATCGTCTCTGATTACAAATCTGAAATG
GTCTTGCTATCGGTCATTGATCTTGTGTAAGGAGATATATTCCCCACATC
TCCTATTTTTGTTTCTTGGAATCAATAATTAGAAACTCTAGGTTGTAACC
TTTCCTGCATCATTTTGTTGTTGATCAATGATATAGGTTAGATGCTGATG
TTCTGGATCTAGCTGCGGATGATAATAGTGGGCTGCAGAAACAAAAGGCA
TCATATCACTGGGACAAGGTTTATAACTATATATGTTCATGTATTGATTA
GTCAATTTGGTCACTCAATCTCTCCCTTACAAATGATTTAAATTTTATGG
ATGACAGAGAAGTAAGAAATACATCAAGCTAAACAGTGGGGACCGTGTAA
CAGCTAGTGGAAAGGTAAGTGATATCTCACTTGCATGAGTCCGATGATTC
AGTTAAGGATAAAGCATCCCCGTTCACATTTGATTGGTAGAAACTTGTAT
GATACGTTCTTAGCTGAAAGGTTTAGGTGGTGATCTTATAAGGAAGCAAG
AGCCAATTTGGAGTAGATACTGTAAAGTATCATTTTTGGAAAGACCCAAA
TGGAGTATTTAGTGTCACGCTTGTAACGTTTTCATTATTGGCAACTTTTA
GTACTTACATTAACATGTGCAGGAGTGGTTTTTTCCTGGATTGTAGGTCT
AGATTATTTTCCTTTAGTTTTTTGCACAAGTAGAAAGAAGACTTGATGAA
ATCAATTAGCAAGAGCAAAGACTCGAATAATATTTGAATACGTGATGCAA
ATTATTGATATATATATAGATATAGATAATGTTATACTTTTCTCTGTGTC
TTGTTTAAAACAAAGATAATTCTGATTGAGGTTGTTACTACTCTATATTA
TTTACCAGGATATTTTTCAAAACTTAAATGTAAATAATGGTGTGCAGGTG
AAGACTGAAAGTGGCGCAAAAGTCAAAGCTAATAAGACTGGGATATACAA
AAGATGGAAAGAAAGGTCACACAATACAATATCTTCCCGAGGAACAAGTC
GTGATGGCGGTGCTGAAGAACCTACGAATATTGCAGGTAAATCCTTTTGA
ATCACCGTGGTGTCTAACTAATATGTCTTTCCTACTATAGATTTTATTTC
GGTGTTGGTTGTTATTAAGCATATTCCCCATTTCAAGTTGCATGCACTTG
GACAAAATGTGTGGCATGACTATAGTTATCAGATCTGATGGTACACTAGG
GTTGCTTAGGCACAGGTGTGCACCTCAACATATATTTCAGTGTCGAAATG
ACAAAATGTGTGAAATGAATATTTCAGTGTCACATTTATGCGCACATTTA
TGTTGCGTGTGGTTGGAGTGAATGTATTCGGAAGGAATGGAATGAAATTT
GAACTATGTTGGGGATAATTGTTAATAAATTCCATTCCTTATCCCCTATA
CTAGATAGCACACCCCCAATTTGGGAAGGAATGCTTCATTCCTCATATAC
TTGGTTTCTTTTCAAATTTCATCATAACAAACTTGTACTCACTCAATTAT
TTTTCTTCAAAACTTCCCTCCTACCTCTGTTATCTTTATTTATTTTTAGT
CATTCCATTCTATTGTCCCTAACCACATTCTATTGTCCCTAACCAAACAC
GACATTAGGATTTGTCTTCAATCATGAGTAAAACAAAATGCAATTGGTCT
CTAACATGGATTATTCTGTTAGGTGCTCGGGGGCGTATGGATAGCAGAAG
GTTTAAAGGTGGAAAACAACGGCAGTCTATACCTAATGCTCATGTGCGTT
CGGAATTGAAAAACAATGAACAAGTTCGGAAGGAAAGGCAAAAGAAAGCA
ACCAAGCTTCAACAATTAAAGAGTAATCCCAAGAGGGGTAAAAAATTTGG
TAAAGGGGGGAAAAATGGCAAGAGAGGAGGAAAGTCAAGGTAA