| Relationships |
|---|
| The mRNA, DCAR_026088, is a part of gene, DCAR_026088. |
| The genetic_marker, MK006294 K3738, is located in gene, DCAR_026088. |
| 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_026088 | DCAR_026088.mRNA | mRNA | DCARv2_Chr7:33061803..33068845 |
ATGTCTAAAATCGAAGAAGACTCTTTTTCAAGCCAGCCCAATTCCCAAGA
AACCAAGAAAAAGAAGAATTTGAGTGGTGATGGTGATGAGAATGGGAGTG
ATGTGGTTAGGAGAGTGAGGCCTGCTAGAGCTTGTACGCTTCGGGCTGCG
TTGAAGGTTTATGAGGTGGAGGAAGATTGTGGTAGTGAGAGGAAGAAGAG
TAGGAAGAGAAAGGAGAGGTCTTTGTGTAGGGAGGAGTCTCCGGATCAGT
CCCCGCCTCAGGACGAGCAATGTAGTAAGATTGTGACACCGTTGGTTGCG
GAGCCAACACTTTCTCAGCTGCCGCGGTGGAGTATTAGGTCAATGTGGGA
GTTGGGTTCGGTTCTTAATTTTTTGAATGTGAGCTGAATTTAGTGTAAAG
TTTAAAGTTTTTGTGTTGAATTTTGCTGTTTGGTGGTAATGTGTGTTTGT
GATTGTAGGTGTTTAGGCCGCTTTTGAATATCAAAGTGGAGTTCTCGATT
GAGGAGCTTGAAACGGCTTTGATTACACCGAATAATACTTTGGCTGATAT
ACACATTCCTTTGTTGAAGGTTGGTGTTTTTGTCCATTAGCTTATTTGAA
TGTGCTTCCTTGTGATGTAGAAATGCATGCTCTTCTTGGTACTTGCTTTT
AATTAATATTGCATGTTCATTATAATGTGAAGCTACATTGTTTCTGTCCA
CATTTCTTTGTTGTAAAGTCCATATAGAAAGCATGTAGTTATTGTTAGTT
TAGGATGTGGTTTACCACATCAAAGTTGCAAAAGGCAATGCAGATCTTAT
GTGTTCAAATTTTCGAAGTCTATGAATTTTCTTACTTTTCACTTTAATGC
TCATAAAAATCAGTTTCTTTACGATGCTGTTCAGCTAACGACTTTTAAGG
TAAAGACTTCTGGCCATATATTTGTTAGGACTGTGAACTCCTGCAGTTCC
AAAAAGGATGAAATTTTCTTTCTTCTGCTGACACCTTGCTACGTTTCTGT
TATACCATAATTACTTTTGACTGTGCCGCATAAAATAGGCAAATCTGTTA
GCCCATTCATTAATGATTACGACTTATTAGACTTTGTTGTGAAAAGATTT
TGTTGTACCGCATTTATATGTTCATAATGTAAATTCTTCAATAGTCTATC
TACTAGCTTGTGTAGTGAATATTCTAATTGCTTCTTTTCTTTTTTCAATC
TGTATGTCCATAATATAGGCTATCCCACCTATTGCTCGAATGACGCTTGG
ACACAATACTTGGGTCACTGTTCTTTGTAGAAAGTTAAGGCAATGGTGGC
ATTGGGTAAATACTTGAGATTCTTGAACTTAACTCCTAATTTATTTCCCT
ACTGATCCTATTATGGATATTAATGAGGTTGCTCCTGTACGCAGGTTGCC
GATGGGGAGCTACCAATAATTGCATCTCATGGGTGAGTATCTTGCATATA
TCTAAACATTTAGATTTTTTTGGATTTAATATGTGACAAGGTTTCCTTGC
ATTGATTTGGTAGATCTGAGGTTGAAGCATATAATAAACTTGATCCCGGT
GTCCGGGTGGTGATTTTAAAAGCCTTGTGTGATATTCGTGTCGAGGTACT
TAATAATTTTTTTTTTTTAATTATGTATGATTTCCTTATAACTATTTCCT
ACGGCGTGTATATCCGGCCTTCTCTTTATGGAGGCATTATTAACTGTTGT
GCTTGATATCTTCCACTGTTAATGGTCCATTTAAAATCATTTTTATAAAA
CAAAATGATAAATATTGCTGCAATGTTTTGGTGCTTATATAAAAGAGCTT
ATATATGAAAATAGATATGGGAAATTATAAGAATTGTGAAAGAAAGTAGT
GAATTTCCAAGCCACTGCTGGAAAGAAGATAAATATATACAAAGTCTCTT
AGGTTGCAAGAATATTGAGGTATAATCTAAGTATCTAAAGTATAAAAAGG
AGGTTAATTGAGCACCATGCAGATTTAAGGGACCTGGGGTTGCAGGTTAA
CTAAAAAAATTCACCTGAGTTGAGATCGTGAAGGAAGGGCTCGCATGAGC
AAAAGCTAACTTGTATGAGAAGGGCAAAGGGCAAACTTTGTTCTGAAATT
ATAATTTTGTTGAAACAAACATTGAAGTTTGTAAAACTATGATTTTCAAG
CCACACATAAATTTGTCTAATCTTTCAAGGTCTGTCAATAGATAAGTAGC
TTTGTCCTTTTTTCCAGGTAAAAATAAAGATAGAAACAGAATTATATATT
ACTAGCTTTGAGTTGTCTTTCCATAGTATTTTCCAGGGACATAATTATGC
TGTGTGCGCATACAATTCTCTATGTTTGTTGTCACACTCGTGCCCACTGA
ACATGACATGGTGTGGGATTGGGATTTGATTCCAACACTTTATTTTTCAG
CATCCCAAGATAAATTAACATAAAAGGTCTCCTCGCAACTTTTTATAAAG
AGCAAGGTTCAGGGATAACTTGTTTCTGTGTTTTTCTTTTAACTCTATGC
TACAGTTTAACATACATATTTTTAACTGTTTACATTTGTGTGTTGTAGAT
TTTATAATGTGTGTAGTAGACGCTATTTCTATAAATGCACAGTCTATATA
AAGTAAGCTTACACGCCGAGTCCCCTCACGCATGCCCAATTTCGGATCCA
TAATCAAGAATCTAATATTTTAAACTAAGAATCTGATTCTTGGATGTGCA
TTGGTGTCCAACCCCTGTAACTGAGTCCGGGTAACTATAGGTGTATATTA
TGTGTACATTTCTTTGTAACAAAGAGGAATTCATTATTAACTGATCACTT
TTTATTAATTCTATCAGAGTCATATATTCAAAACAGACTAAATATAAATA
TTGTAGTTATTAGTGTAATTATATATAGAGGCTATAAGAGGTCCGAAGTG
CAATAACCAAACAGAAAATATGAGATATGTGTATAAGTTTGAAAATGGAT
CGTCTTTTATTGGTAAGACCGTAACTCTGTCGGTGGGTCAACTAGTACTT
TGCTATCCAAGTGATAAAAACATATAAAGGTGTTGTAGACGGTAGCGAAT
AGTGAAAATGGTATATAAACCAACTTAATATTAGTTTTAACTGATAGTTT
TTCTTATTTCACAGCAAGAAGACATACGGAGCTATATAGATAATTCAATA
AAGCATGGCGTTCAGCTTTCAGTATTCCGTAAGGAACGTATTGGCGGTGA
TTCTCGTGGAATCTCCTATTGGTAATTCCTTATGCTTTTCACATTTATTT
TAAGGTTCTTTTTCAGGTCATCTTCTACCAATCTGCTTTATCCTGTTGTT
ATGTTAAAATGTGTACAAAAATGTCATTGCTTGGTAAATGGAACACCATT
GATTAGAATAGGTTTGATATAAATTGTACATTTTTGGGTATTTAATATTT
CACTATCTTCATATGTTTAGGTATGAAGATGATCCAGTCATCGGTCATCG
TTTGTACAGAGAAATTAGAGAAATTGAGTTGACGAAAGGGAAGGGAAAAA
GTGTACAACCTATTTCTAGTTCGTGTTATCAGTGGGAGACAGTAGCAACC
AGTTTAGATGAATTTCAAGACGTTTCTGTAAGTTTATCTCGCTTAATCCC
GTGGTCTTTGTAAATTTTGCTGTTTTGACTTTTGACCTTTCTTGGCTTGT
TTGTAACTCACAAGAAATTCTGTGTGAGCAAATACACTTGAGAACACATC
TGTCGGATATAATAGTTCATGTTGCTGGATTCATTTTACTTTATTCACTA
TCATATTAGGACGTTTAAGGAATATTAAAGTTTAGATAGAATGTTGTTGG
CGACCCTATATATGAACTCCTGCCTCCTTTATGTAATTGCTACCAATTTC
TGCAGTATACTTATCTTTCACTAATATGTATTGCAATTTAAACTTCACAA
ACTAACACGTATATGCGGTGCCCATTGATAAAATTTCACCAAAATATCTG
CACATAACACAAGTTAGCATCACAAATGCACCTATTAGGACATATATGTG
GAATGAGTCTGCACTTCGCATGGACAACTCAAACCTGAAGTAAAGGATTG
GTTTGGACAAACACGTCGTAGTGTTCTTTTAGCCAAAGCCCAAAGGTCAA
CAAGTTATACAACCTTGGGCATTAGGACATGTATATGGAAATGAGTATGT
CGCATGTACAACTCAAAACCTGAATAAAAGAATTGGTTTAGACAAACGTA
TAGTAGGGTTCTGTTAGCCAAAGCCCAAAGGTCAACAATTTAACAGAATC
CAGAATTTTAGAGGAAAGATGTTCATCTACATTAATAGAAGAAAATATAG
CACAAATAAAATATAGGTGAAAAGAGGTCAAAATCAGATCTGCAAAGGGT
CAGTATCACTATTTCTGTCTAACCATATCCATGGATTCTATAGTAGTAAC
TGGAAAATTTAGACCAAGTTATTAGTTTAGAGCATTTAGTTAGAATTTTA
TACGTCTCTCGACTACTCAATCGAAGTCCACTTAGATCTTTGGATCTTTG
GTGTTCAACCTGTGCGAGGCTTGTAATTATTTGAAGGGAGCAGATCTATC
TAGGTCTTGATGGCAGGCTTTCGGATTATGACATTCATCTATGAAATTAT
AGTTTGCCCTTTCAGCTGATAGATATATGTGCGTTCTTTTTGTTTTCTGG
TTCTTGTGCTGTTTACCTGACAGGCAATGTTCTGTCTCAGGAGAAGCTTT
TAGCAAGCAAAAACAGAAACGAGTGTTCTGTTGGAAAGAAGTTACATAAT
GACATGCTTCCTGAGATTGAGAAGGTCCACAAGGTATTTTTTTGTGACTT
AGTACTGATTATTATGTTTGAAGTTATTGTTATTAAGGTAGACTTTTTTA
AAATTTTTTTTATTATTATTATCTTATTGTGCAGTATATATGTGTGGGTG
ATCATATTTGTACATTGGTGGTTGTCTTTTGTGCAGAGAAAGGAGAAAAT
GTTGAAGAAACAACATAGAGAAGCTCTTCTTCTTGATAATATGATGGGTG
TGAATGGGCTTGCACCTGGACATTCCCTTCGTGGTAGAAAACGTGTATCA
TATACTTTTGGTAAGGCTCTCGTTTAGTGGGTTTTTTTCTCTTCGAATTT
TATCACAGATTCTTAGTATTTTTAAAGAATATGTGGGTTAAGGTGTCTCT
CTGTCTCTGCCAATGTTGTTAAATGCGATATGTGCAAAGGCCCCGTGGAG
CATAAGCGCAACGCGCAATGCGAAATGCGCAATGCGAAATGCGCTGATTC
ATCGAAGACAAATAAATATACATATATAAATGATATATAAGTAGAATTTT
GTTAATTTATAGTAAATAGACATTTAACTCGTTCTTGTATGTATATCTGG
TTTGTATCTATTAGTGTCAGTTGCTACAAGATCCGTAGCTGTCTTTTTTT
ACCCATTTCCTTTTAAAATTACTCATTTTAATAAAAGCGCGCTTATCTTG
CGCTTTTGAACTGCGCATAAGCGCTCGATACACATAAAAGCGAGCGCGTC
GCATCTCCGAAGCGATGTACTTCAGGTGCACATTGCATCGCATCTCGCAT
ATGCGCGCTTTTAATAACACTGGTCTCTGCCAACCAGATATGTTACTATG
ATAATATCATAAATTACAACAATATCTTGCATATCTTTATATTCCTATAT
GTTAGATTACATACCGGCTTTTTAATATTTGATAATTCCTTGATGAATCT
TTTATATGTTGCAGATGATTATGACCGATCAATAAATGAAGCTATCAAAT
CAACAAAGTATGTTTCTTCTCACTTTTCCAATAAATTATCCGTTTTACCT
CTAGTCACTTTTTACTTGCATCTGTGGTTGACAAAAAGCAAACATTATAT
GACTTCGAATTTACATGTTTGTTTCTTCAATAGTAAATACTGACAACTTT
GAATTAAATTGTGATGGCAAGTGCTAAGTGTGTCGTGAACTCATGATGCT
CTTAAAAAACTGGCACTAACATATTGACATGAACTGACATTTATCTAATT
CATATCTCTTGCGCAGAACAAAACAACCATTTTCTGAACATCCCGTCAGA
AGAGAGGGTTTAAGACATAATTCTTCTTCAAATGGCAGTAGTAGACTGGG
CGGCCGTTCACAAAATCCTCAGCGTGATTCATTCAATGCTTTATCACCTA
AATCTCCTAATTATGTTGAAAGTGACTACGAAGATAATTCTGGACCATTA
GATCGCAGGTACATTCATTTCTTCTTACTTTCTTGTGATGCTTTTGTTCC
TTTTTTCTTCAGTTTAAAAACTTGCAACTATTGGGAACTTTTTTTTGCAG
CAATCGGCGTAGGCAGAGACCTCAACGATATTCAGAAAGAGAGTTTGTAG
AAGCGGTCTCAGATCAAGAGGCAGGCTTCGACAGTGACAATGATATAGTT
GGAGAGGTTGTGTATGACGAAGATTATTTGAGGAAACGGAAAGATATGAA
GAAAATAACCAGTAGCTCTGAAGGAGATGAAGAGTATTATTGGGAAGGAG
AACGTGCTGAAGAGGAAGAGGAAGAAGAAGATTATGAATCTTTGAGTCTT
AGTGAGGATAGCAGTGAGCGTCCAAGATTGAAGAAATTACGAGGCCAATC
TAGGAGGGAATCAAAGTCGAGGTCAGTTCATGATATCCAATCAGGTCTAA
GACGTAGTAGAAGGGCCACCAGAAACCGTATTGATTATAGGCGATTAGAT
GGGTCAGATTCAGAATACGAGTGCCTAGAACGGGAGGGATTGAATGCACA
AGACAAGCACACCAATAAATTTGAATCTGCAGAATTTTCGATGGGAGGAA
GTGAAGATACAGAAGACAATGATGAATACCAGGAGATGAAAAGTGAAGCA
CCTGTTGAAGAGAAGCCCAATGCTGTAGAAACAGAACACCAAGTACCTAC
AAAAGGTCATAGCACAGATCAAGATGAGTCGGAAGGTGTACAACAAAGGC
GTTTTCTTGATCTTAATGAACTTGCACCAGGGCCTGGGTTTGACGACGGT
CTGAATTCAACTATGAAAGATGAGGATACTGACAACTTGTAA