- Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, Bowman M, Iovene M, Sanseverino W, Cavagnaro P, Yildiz M, Macko-Podgórni A, Moranska E, Grzebelus E, Grzebelus D, Ashrafi H, Zheng Z, Cheng S, Spooner D, Van Deynze A, Simon P. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.. Nature genetics. 2016 06; 48(6):657-66.
- Osuna-Cruz CM, Paytuvi-Gallart A, Di Donato A, Sundesha V, Andolfo G, Aiese Cigliano R, Sanseverino W, Ercolano MR. PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes.. Nucleic acids research. 2018 01 04; 46(D1):D1197-D1201.
| PRGdb |  |
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| Relationships |
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| The mRNA, DCAR_014285, is a part of gene, DCAR_014285. |
| The genetic_marker, MK005052 K2496, is located in gene, DCAR_014285. |
| The genetic_marker, MK009583 4_23166345, is located in gene, DCAR_014285. |
| The genetic_marker, MK009582 4_23166355, is located in gene, DCAR_014285. |
| 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_014285 | DCAR_014285.mRNA | mRNA | DCARv2_Chr4:23158659..23166493 |
AATACATGGAATAACGTAACATTATTTTTTGCATCTAATCCTTATTATAT
TTTATTATTATTAGCAGAGAAAATTGAAGATCGAACCGAAGTTAGTCGAT
AAAAATGGAGGTTTATCTTTTACTTTTATTGACGGAGGAAATTGGAGATA
AGAGTCGAAACCAGTGGACAGAATTCATAAGACTGTCGGAAGAGGAAAAA
TGCTTCGTACACAGATATACAGAATCCAACCACTTGAATCCCCCCAACCC
TTTCTCCTACCTCTAGTGAAGCAGAATGGTTTCATGTTCTTTGATCGATT
AGTTATTTCTCTCCGTTTGTATCTCTTTCTCCAATGTTGGTCTCAATTAC
ACAAGATTGTTTTCCAAGGTAGTAAATTACTATTGGAGTAGTTAGATGTA
ATACAATTATACGCATCACACACTTAAAATCGATGGAGTCCAAGTCAAAG
CCCGAGAAAGCACGATATCCGAAGCTCAAAAACCTCGATTACGATACTTT
TACTTCCAGGGGGACGACCTCTGACTTTGATGATCGCAGCTTTCGAGTCT
TGGGGATTGATGGAGAGTTTGATGCGATTTTTCAGAGTTTGGGACTCTCC
GGACCCGATGATTTTGCGATTCCTGCTGCTGATTGGGAGTCGATGAAGCT
CCGATCTTCTTGGGGTAAAAGCTTTAGAGATGGTGAATTGAGTGATAAGT
TTAGTGAGAATGTTAGGGTTACGGTTAGTAATGTTAGAGGGATTAGTGGT
GCTCGGCCTCCGGTTTTGACGCCTCCTCCTTGGGATATTATGAGGTTGTT
TGCGCCGCATGGTGATGAGAATGTGAATGTACGTGATTATGGTGATGTGG
ACAAGGAGTCTGCTAGGATTAGTAATGAGAATAAGTTAATTGGTAATGTT
GGTGACTATGATGACATGGACAATGAGTCATATTTTTCTGATGAATATGA
TTCTTCCAGTATTACTACATATTCTTCCACCACTACTGTATCTAGAACAA
CTATAAGCTCCTGGCAGAAGGGAAGGCTGCTGGGACGTGGCTCGCTCGGG
TCAGTATATGAAGGAATTACCGAGTAAGTGATTGATTATTTAATATATGA
ATAATTCTTTTATGTTTACTTATCAGTGAAAGAGGTACTTATCACAAGAT
ATAATTCCTAAACTAGTAAAAATTGTTCTGAGTAGATCGTTTTGCTCAGG
TAGCTCATGTGATCAGTGGCTTCATTTGCTATTCACTATATATATATTCA
TGTACAGTGAAATGGAATAAAATATATATTTAAATATTTGTTGTGAACAT
GACTGCTCCTTACTCCTGTAATCAGTGGTGGCTTCTTCTTTGCTGTGAAA
GAAATTTCTTTGCTCCATCAGGGAAGACAAAGTATTTCCCAACTTGAACA
GGTGACTGTTCAACCTTGTTAAGAAAAATGTGATATTCGTACTTATAATT
CTAGTTTTTTATAGAAGCCTTTTTTTTCATAATGTTATTTTGGTGTCTCC
TGTTGATATAATATTCTCGTCATCTCTTGTTAACCTGAGCAGGAAATTCA
TCTTCTGAGTAAATGCGAGCATGAAAATATTGTTCGATATCTTGGTACTG
AACAGGTATTTTCCTTCTTATGTTGCTTAAAATAAGTTCATAGTAGATAC
TGTATAATGGACCTGCAGAATAATTTAAATTTATTTTAAACAATGATATA
TAATGTATATATATAGTTTATTGATTTCTTCCTATTTATATACTATTTTT
TAACTGATTCCACTAAGACGAATGTTCTGGGATGGTGTTTAACGAGAAAA
ATTAAGTTCAAACATTAAATCGGTAATCAGAGATGATTGACACAAGTATC
TGAACAAAAAATGGAACATTTATATTAGATCCTGTCTATGTTACTCACAG
ACTCCGCCAGAATTGAGCAACATAGATGTGTCTGAGTGTCTAGCTCGACT
ATTTGTTGGAAGTTTTGCATATTATTGGCCTAAAATGAATTTTCGATTGT
CCATACTCATGTCTGAGTGTAGAGTGGTAGACATGGGTACGGAGATGAAA
ATGTACTGTCAGGGTCAGAGCTGATTTTACACAAAACATCTCCTCATCTT
GCTCTTGACTTTGGGACGTGATATCCTGGTTAGATCTGCAAAGTGATTAC
TGGTTATCTGTTGTCCGGGTGATAGCGAGTATCTGAGACCTAGCTGTGTT
TAATATCTGATTGAACATGCCACGTACAATAAATTCCTCTGACCAAAATT
TTTTTGGCTAGAATAACAGTCTAGCTTTCTAATTGCTAAGAAGTAATATG
TAGTATGTTTCTGTATTTGGTATTATTTGTTAAAATTTTGACTGAGCCTG
GAAAAGTTTGGTTAGATGGTGGGTTCTAAATTGCAAGCTTTTGTCCCTTT
GCTTTTTGCAGACTGAATCAAATCTTTATATCTTTCTTGAATTGGCAAGC
AAAGGATCTCTTTTGAGTCTCTATCAGCAGTATCACTTTCGAGATCCCCT
AGTCTCTGTTTACACAAGGCAGATATTAAATGGTCTGAAGTATTTGCATG
ATGGAAATGTTGTTCACAGGTGGTTATTAGCAGATTAATTCATGTGTTTT
TTCTGAAGTGTTTTCTACATAGGTGTGTGTTTCAGGTTTCAATGTATTCT
TTCAGTTGTTGTTCTGCTATAACTTTTTAACTTTGGGATCTGGTCCTAGT
TATAGGTATAGCTTTTCAGTTGATAGTTATAAGCATAATTTATCTATCTG
TTTTCGACTTCGCAAGTCGGGTAATCCGGTGCTAGTTAAAGTGGTTGTTA
ACTTCTATATGTCAGAATGGGCTTGACAAATTATTGAAGTCAAGCGCAGA
GTGGTATGAAGTCTCACATTCTGCTGCTTGGTTTCCAGGGATATCAAATG
TGCAAATATATTGGTGGATACTAATGGGACGGTGAAACTCGCTGACTTTG
GTTTAGCAAAGGTTCTCTCATTGCAATTACTCTATGACCTTGTTCTTTGA
TTTTTTTCATGCTCGTTTAAAAAATTAACCGCTTCTGTCTAATATGTTGT
ACAGTCTTCTAAGTTGAATGATGTGCAATCCTGCAAGGGAACAGCTTTCT
GGATGGCTCCTGAGGTATGCCTTGGCCATAAGTTTGTGTTTTGTTAGAGG
TCAGAGGTGTTCATTTGGTTGTACATATTGGACTGACCACTAGCTGAGTT
CTCAATGTAAACACTTTCTTATTCATCACACCTCAGCTATTTATCTTAGA
GGTCCGATAAAGGATTGGAGAACAGAAGTCCTCATCTAAGGCAAAAGAAG
GTCCAAGATATTGCAGCTAGCAATTATGCCACTCTACGCTTTAGTTTGAT
ACAAAATTTAAACCCTTCTGCATTAATACACAGGGGATAACCTCTTCTTT
AATTTTTCATTAACAAATCGGACATTTTACCTCTTAGGTGATAATGTTGA
GATGTTAGTTGAAAATTTGAAATACTGCAAGTATCCAACACTATTTTAAA
AGAAACTAAATATAAATGACTTGTGAGCCATTTTATGAATTGTCAGCATG
TGTTGTAACAGCCAACTCGTTGATTAAAGTTTACTTTTCCTCTATGTGCA
GGTTGTTAATAGGAGCCGGAGTTATGGGCTAGCAGCAGATATATGGAGTC
TAGGGTGCACTGTTTTGGAGATATTGACTGGTCAACACCCTTACTACCCT
CTGGATGCTGTATGTAATTTTTTTTTCAAATTAATAAGCCCTGATAACTT
CCCCCTCCCAAAATAATATCCCTCTACTCAAGTCCCAACTCCCATGCTTT
GTATGGATATTCAACATACATAGTTTTTTGCTAAAATCTGCAAAAAAAGA
AAAAAAAGATGTATAGTGAGCAGTTTGATATTTTGAAACCACTGAGTCGG
TGCTACAATCTCCCTGATCTACATCTGCTTTATTGTAAGTGGCCATTAAA
AGGAAAGGTACTCTTTCATTCCTCTCGTATAAGAGGTATATTACCCAAAC
AACCCCTATGTCCAGCCTAAAAAGCTATTTCATAAATCATACTGTCAAAG
ATAAAATTTGCATTTGATGTTCTTTTTATGTATAGTAGTCGTTTGTTGGG
AATTTCACTACAGCCTACTGCCATCATGTAGATAGTAGACAGAAAGAAAA
AAATTTCAATTGATGTTCTTTCTATGTATTGTAGTCGTCCCGACTGATGA
ATTGATCCAGGTTGATTTTTTAAACTCTCTGGGATTGTTTGGTTCGTCAT
ATTTTTAATATGAGGTATGTGTTCGTCCATTCCATGATATTCATTAAGAG
GAACGGAACTTGTGCTTGTAAAAGTTTTTGAAATGTGAATATTTTAAATT
ATACAATTCCTGTTTTCTTTATTTTATAGATACTTTATTATTTTCACATT
TGATTTAGTGGAAATAATTAAATTAAAGTACACTTTGTTTATAAATTATT
AAGAATAATGTTTAATTTTTTTGCAAGATTTAACTAATTAAAATTTATTA
ATTGTGCTAAGAAAATATTGCGTATGTATTTTTAAAAAATTATTATGTAT
TTTGTGATAATATCCATCATCCCTAATGTAGAATAGGGGTTCCATTTGAT
GTGGCCTGTGGGTCATATGTTAGATCTTATTTAACAATTAAGATATCTGA
TACGATGTTTATAGACAAGAAATCACAGGGTGAAACTGGAGTTTCATCAA
CGAAGTGAAGGCCGGAGCAGTTTTAGATGAGGAACTATTTCAGATTTGAT
GGTTTAAAATAAAATTAAAATTAGCATTAGTGATACCAATATAGAACTGA
ATCTGCTCCACAAATAATTTTTTTAAACGGAATATAATTTTTCTATATAT
TAACTGTTCCCAAACTATCATAGTACTTACAATTTATAAAGAGTTTTGGT
GTGGAAGTTCATTTCCAGACCCTTGCAATCAACAGACAAACTACACTGAA
TGTCATATTCATGGGCAGGAAGATAAATTTGTCTCATTGATTCAGTTATG
ATAGATTGCTAGTACTATATAGAAATGATAATGTCCTAGATACTTTGAAT
GGCTGCTTGCCAGAAGAATATAATACTCACTGTAGAAACCAAAAGCTATG
CGATAAAGTTACCAAAATTATCAGATGTCAAGGTAACATTTATATTTACA
CCAGAATTTGGTTGTGAAGTTGATATTAGAGTACAAGTTTTATGCTAGAG
CCTGAAGGAGCATACTTTTGTCGAGACGGAGGAGGCAGAAATTACCTCTC
TATACTCCCCATGAGTAGGCAATGTTAATACGTGATTGTGTAGAACTTCT
TTCTTTTGGATCATTTATCAGAGTATTTCTATCGATTATCTTATCATGCA
ATGCATTACAAATTGACTAGAGTTAAAATTTGACAATATTTAATATCCAT
GACATTACAGATGCAGGCAGTATATAGGATTGGGAATTGTATCCCGCCAC
GTGTTCCTGAATATATCTCTATAGAGGCACGAGATTTCATCCTCAAGTGC
CTACAAGTTAACCCATCTTCTCGTCCCACAGCTGCTCAGCTGTTGAATCA
TCCTTTTGTGAAGAAATCATTTCATTACGGAGAAGTTGTTTCAGCTCAAG
GTAAGTCTAGGCCAGTTATAAGCTCTTGGGAGAAGGGGAAGCTATTGGTA
CTTGGCTTGTTCGGGTCGGTATATGAAGGAAGTGCTGAGTAAGTGACTGA
TTATATTATTATATAGATAGTTGTTTATCTCCGTGTCAAAGAATATTACA
GAATAGCTTTTATAAACATTTAACAACAGTTAAGGTACTTATTAACAGAT
TTTCTTAAACTGGTAAAAAAAATTGGGGGAGATTGTTCTGCCAGCCGGCG
TATTTCGGATATGCTTTTAAAAAGGCCCTGGTTAATGTAGGAACACAACT
TCATCACCACTTAATAATCATGTCATAAAGTTATATTTTATCTTCTTCTT
GAAATATTAAGGATTCTAATCGACCAAGGCCAAGGGGTGATGGAGGATAG
AATTGCGAAGAGATAAATATTTGTTATTTAAAAAGTATAAAGTTGACTTG
TGTGGATTAACCACTGCAAATTCAGTATCCCAAGAGCTCCCAACTGCAGA
AGGGAGAAAAACTATGGATCTCAATTAGGCAATTCACTAGCATTCCAATT
ACCATGTCTAGGAACGGAAATGCAACGTAGTTTAAGTACTGAAATTAAAC
CCTAATGGACGGGACATAAGCAATTAGGAATTACAAATAAACTAATATTG
CAAGTGCTAGGAATATCTTGCAAGCATCAACTTCTTACCAAAAGAAAAAT
ACTTGTATATCTATGCTGATGTCTTGCTATATTGTGTAAATGCCAAGTTA
GTTATAGAAATTCGTCCAAGTATCAATAAAAAATACTGACCAATGGATCT
GGTCAGTCGAGTATTAAAAAAATTCTTCTCGCAGCTCTAAAAATATAAGA
TATCTGAAATGTGTCAATGAAGAAACCTGTTGTTGTTATTTACTTAGTTA
TGTCGTCAACTTGTACATATGCGGACAAATTGCGTATGTGTAATATACTC
ATGTCTATACCTCAATTTTTGTGATGCAGAATGGAAGTACTACTAGACTT
CCATAAAAGTGAGGGTAGTCTTCTTGACATTACAGACTTATTTAGTCTGT
TGGAAAATGGAGTGCAATATGAATTCCTCAAATCCAAATCTGTAGCAGTG
AGGAGCCTTAAGGTGATCTCCATAAGTAATTCCCAAATCCCCGAGATTCC
AGATAATTTAAGCTTCCCAGATCTCGAAGAGTTATATCTGCATTCAAACC
TTCATTTGAGTTATATTCCTCCTTCATTCTTTAAGCATATGCCAGCTCTG
AAAGTCCTAGATATGTCAGACACAAGTATTAAAAATTTGGCGCCACCTGT
TTTTGAATTGTTCGCACTGGAACAACTTATTTTGCGACGTTGTGAACTTC
TGATGGAACTGCCACCTGAAATCAGTGCCCTTACGAATCTCAAAGTGTTG
GATCTTGAAGGAACTGACCTTGTTTGTTTACCAGATGAACTCAAAGAGTT
AACTAACTTAAAGTGTTTAAAGATTTCCTTGTATGATGCTGAGAGCTACA
GAAAAAGCAAGAAAATAGTTTCCATAATCCCGGCGGCAGTACTGTCAAAA
CTCAGTCGGTTGAAGGAACTAAGCATAGTTGTTGATCCACAGGATGTCTG
GTGTAATGCTGCAATGAAGGCTATCATTGAAGACCTGCCTAGTCTGAGAA
AACTAAAAACTCTCAAGTTGTATCTCCCAACTACTGAACTTCTTAATGAT
CTCGTGGAGCTTAAGTGGAACAACGATGACTTGCCTATCTACCAAAATTT
ATCAAATTTCAATTTCATTATTGGTCCTTGTTCTCAGCATTTCATATCTC
GTCTTCCAAGTGACCTTGAGGAGGAGTTCCTGAAATTAAAGAAGTGTCTA
AAATACATTAATGGCGAGGACATCACGACTCAGTTTGCTGAAGCACTGAA
ACATGCAAATGCTTTGTATCTAGATCGTCACTGGACTATGCAGAATCTCT
CCATCTTAAAGGAATCTAATGAGTTGAAGTTCTGCTTGTTGGTGGATTGC
AATGAGATGCAAGTTGTTTTTGATGGTAGTGACTTTAATCACAGGGTAGC
TAACAAAGGAGAGAATCTTCTTTCATTGCAATACTTGGCCATTCACTACC
TAAAGAATTTAGAGGTAATCTGGAACGGGCCAGGTACTGGATGTTGCTTG
CGTACTTTGAGGGTACTGGTCCTGCATATGTGCCCAAACTTGACCACCGT
TTTCACTCCAGTGCTACTAGGAGATCTACATAACTTGCAAGAAATAATAG
TTGAGGATTGCTGCAAAATCACAAACCTAATAGCTGAAGACTCGACTCAA
TTGACATCTAAAGAAACTCTCCCTGGATTAAAAAAATTGTCACTTCTCTA
CCTACCCGAGTTGGTGAGCATATCTAGTGGCTTAAGCATTGGTTCGGAAC
TGGAAAATCTAGTCATTTATGATTGCCCGAAGCTAAAAAGACTTCCTTCC
CTGGGAATGTGCAATAAAGATTTTATAGAAATTAGAGGAGAGAGTGAATG
GTGGGATGCTTTGAAATGGAATACACCAGAATGGGATGGTGGCCAACCTC
ATTATCTACGTCGCGCATTCTCTGAACTTGACACAGACGAAGATTATCTG
GATGAGTTTGCACTGCAATATAGAAATTCACTGCGCCTCTTTGTGGAAGA
ATGTGCTGCTAATTAACATGGTAGCTTATCATTCAATCTTCTTTTATATG
TTCATTACATGTAAATGGTTCATCAGTTGCCTCCTTGAAAACTTTAATTT
GGTTGTTGTATGCACTTCTCTTTATAATTTTATGAAGATATGTTACTGAG
TATAAAAATATATTTACAAAATCATAACTACGGCAGCTGTG