| Relationships |
|---|
| The mRNA, DCAR_026742, is a part of gene, DCAR_026742. |
| The genetic_marker, MK005066 K2510, is located in gene, DCAR_026742. |
| 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_026742 | DCAR_026742.mRNA | mRNA | DCARv2_Chr8:29172830..29180084 |
GATTACTAGGGAGAGAGAGATTAATAAACAGTTCTACCTGAATTCACGTC
TATCCATCGAAGCACACACAGGTGAGTAGTGAAATCACACACACACACAC
ACACAAAATAAATTCAAACTTCCTGTTTATTTAGGTTGTTAATATATGCT
TTTATTTAATTATACTATTTGTCTAGGTTTTCAATTGGGATTTAATTATA
CTATTTGTCATCTTCTGATTATACAAGTGATCCAATAATCATATGTATCA
ATTTCTTGTTGTATTAGATTTTGAAAAGTTATTGGGATTTCATTCTGTAG
ATTTGGTGATTATATAGGTGGAGTTAAAGATTTGTGTATATATTGAGAGG
GTCTAAGAGATATATAGCTTGAGGGGAAGAAGGGATTCGAAGAGGGAGGT
ACTGGGATGGGGAGCACGAAAACTGTGGGCTCGACGACACAGGTGCATCG
TCGTGATCCTTATGAGGTGCTGAATGTGTCGAAGGATGCCTCGGAGCAGG
ATATTAAGACTGCGTATAGGAAGCTTGCGCTAAAGTAATCTCTCTAAACC
ATTAACTTGTTTGATGTTTTTGTATTGGAATTTGCGGATGTTTGGGCGTT
AATTGTTTTTCGTGGTGTACGGGAACTTTGGGATCATTCGTCGATAGAGA
TTGTTGCTTTATTGCTTATGCACACACGGTGAATCTATTTAAACTTACCT
GGTCATTGCCTTGTCTATAAATTAATATATGTTCTCGAAGTTAGATAGAT
GTGTACCGTGTTTGAAAAAATTCCTGATGAAATATCTTTGAGGACTGTAG
TTATAGCTTGTTAGTAATTGTCCAAGAAAGCAAGAAAAATTGTCCGTTCT
TGATTTCTAATTATGTCATCAACTGCTACATACTTGGAGGTAATGGTTTT
ACATGTGTACAGGTATCATCCTGACAAGAACGTCGATAATCCTGAAGCTG
CAGGACTTTTTCAGGAGGTTGCCTATTCTTACAGTATTTTATCTGATGCA
GAGAAAAGAAGGCAATACGATAATGCTGGATTCCAGGTAGTTTTCTACAA
AATAAACACGCATCACTTCGTTTGTATATTCTGAAAATCTCTAGGGAATT
CGTTGCTTTAATATCGTATATCCGCTTTGCTATCATTAATATTTTCATGT
GGGATTGATTTAAAACCATTCTGACAGGCTCAGGAAAGGAGAACCTGTAG
AGCTGTTTTTTTTGGACAACTGTAGGCAATAGCCCAAATCCTGGACCAAG
AGTGAAAATGCTTATTGTAGGTTTTAGACAATGCATATTCTAGGTTTTAG
ACAGACACATCATTTTGAGAGAGGTTTGATTTAAAAAATTACTAAAAGAT
GTGCTTTTCACATGGTTGTGTAAAGTCTGTGGCCTATAAGATGAATTAAG
AATGAAAGTAAGAACTTATCTAGTGTCTCTACAAGATATTGTAATTTTAT
GGCCAAATGTAGATATTCAATCCTTCAAAGTAATTACAAATATACAGAGT
AGTATATTTAGGTTATTTTAAGTCAAATCATGTATAGGAGCCCTATTATT
ATATGTAAGATGCAATATGCAGAAATTGGTTTTAAAAATAAAAACAAACA
ATGACAGTATGCAATGGTTTTTGATACTTGATAATGTTGTACACGCCTGT
GAACTTTTATTTTAGCACTGCGTTCTCGAGTTTTTCTGATGAAGAAAAGA
ATAGTATTGAAGTTAAGAGAAAAGAAAGAAAAACAAAATGTTTCTGATTA
TCTTTCTTATATTCTTTAAATTTTTATTTGAGAAGAAAGTGAAGATATGT
AAAATGATTAATACATTTATTGCTATAACTGGTCTTTATTTCTCAATCTT
CTCATATTAAGAAGAAACTTTTAGAGTGTAATTAGCCTATATTTCACCTT
CCTTTCTTTTCCTTTCTATTATTTAAATATATGTGGAACATGCGAAAGAA
AATAAATAATCATATTTTTTTCCCTTTCTCCCCAAACTAAACTCTGGAGT
CTGGAACACAATGTAGAAGTTTTACAGGGGAAATTGTTGCGTATGTAAAA
TAGGCAAATCAGAGAGATGTTTTATCGGATTTGTGACTAAAGTAAAGGTG
GAAATATTTAGGGGCTGGGGTTGATAGATGGTGGAAGTTAATGATAGCTT
TAGGATAATCAAGAACACCGGTAGTGGCTTTATGTGTCCACACACATCGA
CATGTCAAATATACAGGAATCTCCTATCCCTATCATGAAGTTGTGTGTAG
TGCCACAACACACAAAGATATGTCAAATAAATAGGAACTCCTGGCCCTAC
CATGAAGTTATGTGAAGTGCTCATTCAATGTACTTCCTTAGAGCTGCAGC
ATGCTTCAGAAACACATACAAATATATGTCAAATAAATTCCTCCCTCCAT
GAAGTCATGTGTAGTGCTCATTTAATATACTTCCTTGTGGCTGCAGTGTG
CTTTATGAAAGTGAGATTGTTTTAATGGGATAAAGAGTTGACATGTAATA
ATAGGAGCGGCGTTTTCTTTTAAAATGTTACCAACTATTTTGCAGTTGTT
TGTGGTAAAAAATCTGGTCTTGTCATATATAGCTGGAAAATAATTAATGA
AACGACAAATTTAGGTTCATCCTTCTGAGTCATCAACTTTAGGATTTAAA
AAGCCACCTACAGACGCTTTACGCCCAATAATTCTAGATAACGCTTGCAT
CCTCTGTATTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTTCA
GAAAGTTGTCCTTATCATACATTTGATAGTAGATTAGCATTTGTTTAGAA
TTAGGAATTGGTCTTCCTATAATGCAATACATCAGTGAATAATTTTTTTT
GTCACAAATTGATATTTCTTCATGTAAAGATGACTTTGATATCTGTCGAG
AGGATATTAGTTTTCCTGTTCTTTTGTCAGTGTGTTAATTAAGTTATATA
TTGTAGTTTGACCGTTGTTGAATCCTATCAAACCAAAATTGCAATTTCTT
ACTCTATTAATTTCAAATGGTTTTCAATAGGCTATTGATGCTGAAGGCCT
GGAGATGGAAGTTGATCTATCTAATCTTGGAACTGTAAATACTATGTTTG
CAGCATTATTCAGGTAACTTCTTTCAGAATGTGTTAGCATTAGCTTAGAA
GGGAGTATATTACTCAGTCTCTTTATTTATTCTTAGCAAGCTGGGTGTTC
CTATTAAAACCACCATTTCTGCTAATGTTCTCGAGGAAGCATTGAATGGA
ACTGTTACAGTCAGACCTCTTCCGGTTGGAACATCAGTTAGTGGAAAGGT
ACATGTTTGCATGATTTAGATTACTCTTCAGATATTCCCTTGATGTTAAC
TTTTGAAGTTGTGAGGCAGGTAGAAAAGCAATGTGCCCACTTTTTTGGTG
TGACAATTAATGGGGAACAAGCTGCGGCAGGGATTGTTGTCAGAGTTACT
TCTGCTGCACAAAGCAAATTCAAGGTATAATGACATGTCACATGTGCATA
TAAAGTTTTATGATTTAGAATGGTTAGTTTAGCTTCTTTTTTTTTCCTGC
CCCATTACAATCTGAAGAAAATAATAAAATCTTGCAGAGTGGCATGTTAA
TAGATATATATGGATGTGATTTTGCAGCTTCTTTATTTTGAGCAAGAAGT
CAGTGGAGGTTACGGATTGGCATTACAGGTGATATATCTAATTTTGTCGA
CTATTTTTATAATTTTTGGTGTCCTTGGGTAGTTGAAATCTACTCTTTAT
ATTAATAATTGTTGCATTTTGCTAAGATTTTGAGCATTATAAATTACGTT
AAGGGTTGTTAATGTACAATAGTCTGTGTGCAATTGTATTCTTGTGCAGC
ATTTAGCTGGGTGACTGGTTCGTTACTTTTCTGAATTGTACATTTTCTGT
TTGCCTTAAGAAACTAAAACCATTCATGGAAATTACATCAGACAGCTCTA
TCTCCTGTGAGTCTGTGACTGTGCATCTAATCAAAAGGAGGGGGGGGGGG
GGGGGGGGGGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNAAGACGTTGGGGGGGGGGGGGGGGGGGGGTCAGTGTTGTTACT
TGTTAGAGGGGCAGAGATTCATGCCCAGGAGTAAGGCTTGGATAGGGGCA
CATCTGTTAGAGGGGCAGAGATTCATGCCCAGGAGTAAGGCTTGGATAGG
GGCACATCTCTGCCTAGAAATATCTATGAACTTGTCCCTACTTCTAATCC
CCTAATGAAAAAATTTCCCGAATTCCAGCCATGTTCAAAGCAGGGTTCAG
ATCAGGCAGGATGGGGGTTGAAGCCCCATCCCTACCTAAAATTGGTGGGA
TATGTTTAAAAAATCTATGCAGTCAATTAATATCCATGCCGACAGCAAAT
ATGTCTGCAAACTAGTTGAAGTAGAACCTAGCAGAGATGTATAAGAACGA
ATATTTGGATGCAATAACCGTTTAAGCCAGAGATTGTACTAATTATTGAG
TTACTGCTATGATTCAATTACAAAACTTTATGCAACTACTACAGATTAGG
TAGAATTTAATAAATTTAGTATGATGGAGTTGTTATAGTACAACAAGATG
AGAAAGCTTAGTTTTTACAGAACATATTAACATAATTACTGATGAAAAAT
ATATGCCAGTTAGCTCTACATATGTGGAAAATAGCACAATTCAGGGGCTC
AGATCACTTTGGCTTTAGAGAATATTAATGTTTAAAAAGCAGATAATCTT
TCTTCAGAAGTTGGTTTTTGTTATTTTACATGATGACACAGAACTTGATT
CAGAAGACTTAGAATTTGATGTTACAGGATTCAGTGTGACTGGGGAGTGA
AACTTGAAATGTGTTCAGTGTCAATGTTAAACTATATGTTTATTAATTTT
GGTAACATATGTTCTTGGCTTCACCAATTTGCAGACATAATCATGCAAAT
GTTTCTTTACTATTGTTCTGGGCACGTGTTGGAGAACTGATGATAATATA
TAGTAAAATTAATACTGAGCTGCATGTATATTGTTAACGTTATATGATTG
TATATTTTAATAAGACTAAAATATGATAATTATGTACTCCATTGATGTAG
TAAATCACTGAATTACGAATATTTGTTGGGTGAGTTATGAGTAACTAATA
TTCTTAGGGGCGGGGCAAAACATTTGGGGTCCCTGTGCGAAATATCAACA
TTGGTCTCTTAGATTTTACTTTCATATAATTTGTTTTTAAATAAAATGAA
CTATCAAAACACATTATAAATTAGAAGCATACTCATAAAAAATCACTTGA
AAAGATAGGCTCTTCTTGCATATTTGTAACAAAATCATCAACAACACTTT
CAATATGTATAACCAACTTTTTTTGGTTAATTTCCAATATTTATATATAC
ATAAAATTTAAAATTTGGGGGGCCTTTATTTTCGAGGGCCCAGCTCACCC
CGTGCTCCCTCAGCACCGCCCCTGCTGATAATATATCTTGGTAGCTTTCA
AACTGATGATTAGGGGAGTCACATTCAATTTGTTCTTTTTCCTTGGCATG
TACTCGGTTCATCAACATTATTTGCTAATTATATGTCCATCCACGCAGGA
AGATAGTGATAAGGCTGGCAAAGTGACTTCTGCTGGGATGTATTTCTTAC
ATTTTCAAGTGTACAGGATGGATTCAACTGTCAATGCGGTATATAATTAC
ACTGACATTTCGTAATATTCTCCCAAGGTGATCTTCATCTAACAGCTTAG
CATCTTACGATTTTATATATGCTGGTGCAGTTGGCAATGGCCAAGGATCC
TGAAGCTGCTTTTTTTAAAAGGTTGGAAGGCCTGCAACCTTGTGAGGTCT
CTGAACTAAAAGCTGGCACCCACGTGTTTGCAGTTTACGGTCTGAAAACT
TCATCCTTTTATGTTTTAAGCATCCAATGGGCTCACCTACAAGAATTTAA
TATTTCCTCAGACCATATATGCTAAATGTACCATGATTAATGCAGGAGAT
AATTTCTTTAAAACTGCTTCCTACACAATCGAAGCTCTGTGTACAAAGTC
ATATGAGGATACAACAAATAAGCTCAAAGATATTGAAGCTCAGATCTTAA
GTAAGAGAAATGAGCTGCGCCAATTTGAGACGGAATACAGAAAGGTAACG
GCCTTTGCTTGGCCTTACTGATTGTATATTTTTTTACAATATAAGCTTGT
TAATGGATTCATAATTTAACATTTTGTAGGCATTGGCACGGTATCAGGAA
GTGACTAAGAGATATAGCCAGGAGAAGCAAACTGTAAGTTGTCTCCACCC
ATAGGCAGTGCACTCCTTATTTTTTTGCCTTATTCCCAGGAGATATAGCC
AGGAGACCATAATGCAGTAGCATGATTACTATAGAATAGCTCAAATTATT
ACGAGAGTACCCTTTAAATGATACAAACACGGACTTCACATCCTTGCCCT
TGGAGGAAATGGATCTTCTTTACATTTTACCCTGTTGAGGGATGTTGATG
CTCCTGACCATTATAAACCCCAATTTCGTTCCGCCATATATGTACAGTCT
TCATATTTTAAAGAATCTTACCCGACTTCCACTTTTCTTGCGCTCTGTGA
ACAGTTATTGCCTGTCTGTTTGCCTAACAGCTATGCTTTGCTGATATTGG
GTTAAATTTTCTTTCTGCTAATAAGCTGTCTGGCGGACTTAAATTCATGC
ATAGCCTAGGCCACCCCGGCTTTCTCAAAATGAGCTTTTAGTTAGACCAA
GTGCTTTACACCCCAGTAAAAACCCAAACCAGGACTTAAATGAGAAAATT
GTACATATGTTTTGCATAGAGTTAATTAAATGAAAAATGTATATTACAAT
CTTGGTAGTAATTTTCTTTTTCAGGACTTAAGTGGTAGTCTATATTATAC
ACGTGTTACTATATTATACGAATAAATACTATTATATATACCAGTAGCAT
ATCAATCAATATTCATCAAGTGACAGAATTTTCATTTATGGTTATCAAGA
ATGAAGTAATCAGTCACATAATGTAAGCATAAAAACATAATGACAATAAT
TCCTTACATATGTGATTAGCTGTTTGAGATTTTAGTTTTGGAGAGTATTG
TCCAACACTAATAAGTCAGTAACCACTACTCTGTGACGCAAAATATTAGG
GGCCAGTAATCAAAAGCAAGTCAATGACTTGAGACATACATGTGTCTAGA
CCCTAAAATAGCACCATGTTTGGGTGTACTTGGCCTCACTGTACTTGCAA
ATATATATACATTATGCATATCTATTATGTGTATGTGAATATATGTAAAT
TAAATTTTACTTAAATTCTTTGAAATTAACTGAAGTGACAAAATCTGTGG
CTCCCCCTGGTTATGCTAGACAGTAATAGCCACATTTAACGACTGATTGT
TGTATTTGCAATATTAGGTTGAAGAGCTACTGAAACAACGAGACGGCATA
CATTCTACATTCACCATAAGTAAGCCGCCCAGTCAAACTAGTGCAGATAC
AGCCAGTGTTAGCAACGGAAGTAGTAGCAAAATACCTGCTGAAAATTGTA
AAGGGGAGAGCCCCAGGGAAGATGGTAGCTCTGATGGGAAAGATAAGTCT
AGCAAGAAGAGATGGTTAAACTTCAACCTAAAAGGTTCCGCAGATAAAAA
AAGTGGTTGAAAAGAAATTGGTTGCGGATAGTCTTGTATTCCTGGAGGAC
TGGAACTCTCCATTCTTTGGCTTGATGCGATATATTTGCTGCCAGAGCGC
TCGGATTCTGTTCCTTGTCATCCATTCCCCGCCTTTGGGATTTTTTGCTC
AGG