| Relationships |
|---|
| The mRNA, DCAR_011930, is a part of gene, DCAR_011930. |
| The genetic_marker, MK002233 ESSR-128, is located in gene, DCAR_011930. |
| The genetic_marker, MK010034 3_42059400, is located in gene, DCAR_011930. |
| The genetic_marker, MK011002 3_42059411, is located in gene, DCAR_011930. |
| 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_011930 | DCAR_011930.mRNA | mRNA | DCARv2_Chr3:42054604..42060819 |
ATGGAAGCAGGAGAAAGGAAAGCAATTAATTCTGAGTTATGGCATGCCTG
TGCTGGGCCGCTGGTCTCTTTACCTCCAGTGGGAAGCCTTGTAGTGTACT
TTCCTCAAGGTCACAGTGAGCAAGTATGTTGCCTCTCTTTACCTAGTGAA
ATATGGGCAAACTCTATAGTTTCTTTGCTTATGAAACTTATCTTAGGTTG
CCGCATCGATGCAAAAAGAGACTGATGGAATCCCAAGTTATCCTAACCTT
CCTTCCAAATTAGTGTGCATGCTTCATAACGTCACACTACAGGTATGAAG
GCTTTCATACACACATTAACTCTAACGGATTCTACTTTGTGCAATGTTCT
GTTTTGTTACATTGCACATATTGTGAATGACTTCTTTTCTGATGGTCAAA
GAGTGAAATATGTTTAGTAACTTGAGTGGCTGCTTATTTGTCTTGGATTA
GGCTGATGCAGAAACTGACGAGGTTTATGCACAGATGACTCTTCAACCTG
TTAACAAAGTATGTCGGCTACTTGACTGGACCCTAGTTACTTATAGTTAC
TGATCGGTAGAGGAAAACATGGAGCCTGACTGTAATCATATTAATAGATC
ATTATTCTTGCAGTATGACCAGGATGCTTTACTTATTTCTGACATGGGAC
TCAAACAAAGCAGACAACCGGCTGAATTCTTCTGCAAAACTCTTACAGCT
AGTGACACAAGCACTCATGGTGGATTTTCTGTACCTCGTCGAGCAGCTGA
GAAAATTTTTCCACCGCTTGTATGTGCTACACGCTTACATTTTGTTTAAA
TCTGGATTCATACTAATAGCAATATGGGCAATTTTCCAATGCGAGTATTC
ACTAGTGAGGTGATTTGTAGGATTTCACAATGCAACCACCTGCTCAGGAG
ATAGTAGCTAGAGATTTACATGACCAGACATGGACATTCAGACATATCTT
CCGAGGTACATTCCTCTATACGATACCACCAATATCCCTTCAAAGTGTTC
TGCAGAAGCTCTTATTTTCCAGATGCTGATTTTTTTGATAGCTCCGCTAG
TGTTCACTTATTCGTACTTTTATTCCCAGTATATGAAATTATATGAAGGT
TTCTGTGAGTGAAGCTATAATATTTAATGTAAATAGCTCTCTCTGGAAAA
AGGTATCCCATGACTAAGAGGCATGAGATAGATATGCACTTGACTATTTC
TTTTCTATATTAGCATAGGATACCAGACTCAGCCAGAAGTGTCCATTTTC
AAGTGTTGGACTTGGCAAAAATTTTAAAAATTTTCATGTTGGACTTTTGG
CTATAATGATTTCCAAGTGCGAGTGTCTCATTCATGTACTCAGGGTTAAA
TAAGTGAGGGTGTTGTACAAATCATATAATTTGCCTTAATCAATATTTTT
GAGGATAAAGGTGGTCTTTGGACTGCACATATTTTTTTGAAGGCAAATAA
CCACTACCATACCTATTTACGTAACTGTTTATGGTCGACAAGATTACTTG
TTTTACATAACATTCAAAGTCTCAAATGGAGTTCTTTATTCACCTTAAGA
TGTCCAAATTGTTTAAATAACATGACTTAAGTGACAAACTTTTTGTGATA
AATAAATATAAATGCGGTAATTATGCTCCATGTAGTTAAAGAGAATAATA
TGGCAAAGGAATGGAATGAAAAGTTTTAAACAAATTTGAAGAGGAACCGA
AGGATATGAGAGGGAAGATTGAAAAAGATAATAACAAGAAAGTGCAATTT
TTCTATGATGAAACTTAAATTAATTCTTAAATTAGGCGGGTTTGAGTTTT
AGTTTAAATTGCTTGGAATGTAATGGAGGAAGGAATAATAATTCTAAATC
TGTACCTATAAACTATTACATATTCTATTCCCTAGCAACTCCATCTCCCC
AACAGTCCAACCAAACACAACAATAGTGTCTGATACAGCTAAGCTGTGGT
TTCACAAGTGCTCATTCTTACTTTTGCAGAGTCTGTGCTCGACTCCTTGT
TTTTTAAATGATTGTCATAGAAATTTTGTTGATTAAAGAATTGTCTTCAT
GTTGTAAAAGTATTTTGAACTATTAGGGTCCAAGGGAAATACAGCTTGAT
CTTGCAGTATTTCTGCTCCCTAGTCCGCAAAGTCTGTACTTTGAGTTCTG
TTTCCTGCATATGGTGGTAAAGTGAAATGGGTTCCCATGCCTACAATTTT
TACTGCCCCCCATAATTTGGTGGTCAGGAGATATTGTCGAGATCTTTACA
ATGCTTCAGTCCCAAATATTGTTAAATTAATGAATTCCCTGCATTTGGAA
AACTACAGATTTTCTACTTTATAGTTACCGCACTTGGTCTTATCTTGAAA
TACCAATGTGTTGTTTTTCTTCCTTTTCTTCCTCTTCTGACTTGTAGATA
TTCTAATTTGTTTAGTACGTACATGCATGCATGATAGAATCTTAACCCTC
AATTTAAGCTGAAAATGTATGCACTGAAATATCAAGTATGTTAAAGAATT
TGATGTCTTCAAAGTATTAACACAATAATATATGTATATCAGGCCAACCA
AAAAGGCACCTGTTGACTACAGGTTGGAGTGTCTTTGTCAGCTCTAAAAG
ACTCTTTGCTGGAGATTCTGTTCTATTTATACGGTATGAGAACGATGTTT
TTTGCAGTTATTCTCTATTTTCACTTCCTACTACTTTTTCTGAATGTGCA
TATTTGGGTGTAGAGATGAAAAATCACAGCTTCTTTTGGGTATAAGGCGT
GCTAATCGACAGCAGCCTGCTCTATCCTCATCTGTTATATCCAGTGACAG
CATGCACATCGGGATTCTGGCCGCAGCTGCTCATGCTGCTGCCAATAACA
GCCCATTTACCATATTTTATAACCCAAGGTAATGCAGATCAGTTTGGATA
ATACGTGGTATTATGACATAAATTGAAATTTTTGAAATATCATATACTTA
TGGCGGTAAATTATACAGGGCTAGCCCAGCTGAGTTTGTAATTCCTTTAG
CCAAGTATAACAAAGCAATGTATGCTCAAGTTTCACTTGGAATGAGGTTT
AGAATGATGTTTGAGACAGAAGAGTCAGGAGTGCGTAGATACATGGGTAC
CATCACAGGCATAAGTGATCTGGATGCTGCTCGTTGGAAAAGCTCTCAAT
GGCGCAATCTTCAGGTATTGGGCATGTCACTTCAAGTGGTTTTATGTATG
GAACTGAATGTCACGACCTTGCAGAGGCCATAGTGCTATAGTTTGGTTGG
AGAGTGTTTGCAACCATATTAATGCCTCTCTACTATCAAAATCTCTGCTT
TTTGCTTACAAAGTCTTGTACCTCTCCCATAAACTGGCAGTTGGCTAAAA
ACTGCATTAAATTGCTCATGTTATCACATGTTTACCTCTCTAAACAGTGG
TTGCAACTTGGTTAATTTGCAATACATAGTTATTATTTGATTAGGCTTCC
TTGGTTTCTAACTATGGTTGAACATGTGAAACTGAGTATCACTTGTACTA
TTAACAGGTCGGATGGGATGAATCAACTGCTGGGGAACGTCCAAGTCGAG
TTTCGATATGGGATATAGAGCCTGTTGTAACTCCTTTTTACATATGTCCA
CCTCCATTCTTCAGACCTAAATTCCCTAGACAGGCAGGGTTACCAGGTAT
TAGATTTACTGTATTAACTACTGTTTTTTCTTTCTTAATTATTATAATTT
GTGTACTTGTGATTGAATGTTAATATATCTGCAATAAGAATTTTTTATTT
ACCAAATGCTTTAACAGATGACGAATCTGACATGGAGAATGCTTTTAAAA
GAGGCATGCCCTGGCTTGATGACTATGGCATGAAGGATGCTTCCAACTCT
ATACTCCCCGGTCTGAGTTTAGTCCAATGGATGAGCATGCAACAGAATCA
GCGGTTTCCAGGCACTCAACCAGCATCATTTTCTCCTGTTGTTTCTTCAA
CAGCCCTGCAAAGTGGTCTCGGCACTGATGATCCTTCGAAGCTATTGAAC
TTTCAAGCTCCTGCTTTATCTATACCGAATCTTCAATTCAACAAAGCTAA
TCAACAAAACCAGCCAGGTGGTCAAATGCAGCAGTCATCTTTGGCATGGC
ACCAACAGCAACAGATGCAGCAATTGTTGCAGACTTCTGCCAATCAGCAA
CAGCAGCAGCAGCAGCAGCAACAGCAACAACAATCTCATCAACATTCCCA
GCAGCAACAGCAGCAGCAGCAACAACAACAATCCAATCAGCCACAGCAAC
AACACCAACAAAAACAATCTATTCAACAAAGTCAACCACTACAGCTCCCT
CAACAGCAGCAACAGCCGCTGGTACAAGTGCAGCAGCCAATCCAACAAGT
GCAGCAGCCCCGTCCGCAGCAGCTGCATCAGCAACAACAAATACTACAGT
CTTCCCTTGTAAATAGTGGTGGAGTTTCCTCTAACCAGATCCCAATTCAA
AGTTCAATGCTGCCAATTAATTACTCTCAGCTTCAGCAGCAACAACTACT
TGCAGGAAATACACAATTGCAGCAAACCAACCCCATAAATAGTAGGAATT
CAATACAGATGACATCCTTACCGCAAGACTTGCAGTTTCAGCAATCTATG
GAACAAATGAGTAGACCTCAGCAGCAGCAGCATCCTCAATTACAACAGGC
TCAAATGCAGCTACTGCAGCAGAGTTTGTCACAGAGACCACAAATGCAAC
ATACATTACAGCAGAGCCTTTCAGAGCAGCAGCTACAGTTGCTGCAGAAA
TTGCAGCAGCAGCAGCAGCAGCAACTTCCGACTCCAGTAAGCCCTCGTCT
AGAGCCTCAGCTGCCCTTACAGCAACAAGCTTTTCAACAAAATCGTCAAT
CACAGCAGATGCCCATGTCTCAGCAGCAATTAAGTGGCAACAGCTTCTCC
ACATCAATGCTTCTTCCATCAGCACAGTTTCCAATGAACCAACTTCTAAG
TCAACATAAACCACTAGGAATAAATAGAGCTCATTCTGGTATCACTGAAG
GGGATGCACCTTCATGTTCAACCTCTCCATCGACCAATAACTGCCAGGTG
GCCCCATCAAGCTTCTTGAACAAGAATCAGCAGGGGTCAGGAGGATTTTT
AGATGAAACGGTGGTCGGTCCTGCTACTAATTCAATTCAAGAGCTTCAAA
GCAGGCCTGATATAAGAATGAAACATGAAATAATGAATCCCAAAGGACCA
GACCAACCCAAGTACAAAGGTATTGCTAGTGATCAACTGGAGGCCTCCTC
ATCTGCTACATCATACTGCTTGGATGTTGGTGGACTCCAAAACTTCTCAC
TCCCTGGCTTCACTTTGGATAGTGACGTTCAGTCACATGTGAAGAGTAAT
CTTCCTTTCGCAGTAAATATGGACGGGTTGACACCTGATGCTTTGTTATC
AAGAGGTTTTGATTCTCAGAATGTGCTCTCGAATTATGGCGGCACTCCTA
GAGATATTGAAACAGAGCTATCCACTGCAATTGACTCTCAATCGTTTGGA
GTGCCTAACATGTCATTCAAACCCGGCTGTTCAAATGATGTTGATATAGC
TATGAACGAAACAGGGGTAGTGAGTAGTGGGTTGTGGGGAAACCAGACTC
AACGAATGAGAACATATACAAAGGTAAGCTCTTTTGTTTAATATACAAAA
TTACATGATAAGACCATATAAAAACGAGACTAGCTCGCTGTGAAATGACA
TAGTATACTTTTTCTGTGTATTGGCAACGTTTTTAGTATCTAAAATTGAA
CAATAAATACAGGTTCAGAAACGTGGCTCGGTGGGCAGAACTATAGATGT
TACTCGTTATAAGGGTTATGATGACCTCAGGCATGATCTGGCTCGTATGT
TTGGTATTGAAGGGCAACTGCAAGATCCCCAAAGAAATGAGTGGAAACTT
GTTTATGTAGATAACGAAAATGACATACTACTTGTTGGTGATGATCCGTG
GGAGTAAGTTACAAATCAGTTTGTACAATCACTTCTGCTTTTGTTTCCTT
TTACCATCCATGATGCAATTCTGTTTACTTTCAGGGAATTTTTGGGTTGT
GTTCAGAGTATCAAGATACTATCATCCGCTGAGGTGCAACAGATGAGTTT
GGATGGTGACTTGGGTAACGTAGCAGTCCTGAACCAAACTTGCAGTGGGA
GTGACAGTGGCAATGCTTGGAAAGGACAGTATGACGATAATTCAGCTGCC
TCATTCAATCGATAA