- 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_015681, is a part of gene, DCAR_015681. |
| The genetic_marker, MK011764 4_9130424, is located in gene, DCAR_015681. |
| The genetic_marker, MK009558 4_9130542, is located in gene, DCAR_015681. |
| 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_015681 | DCAR_015681.mRNA | mRNA | DCARv2_Chr4:9128537..9135169 |
ATGGAGTACATGTCACCTGAAATCATTCTTGGGAAGGGTCATGATAAAGC
TGCAGACTGGTGGAGTGTTGGTATTTTGCTGTTTGAGATGCTCACTGGGA
AGGTTAGTATATTGCAAAATTGTTTACATAAATCCATCTATTTTTCGGTG
TTTATTACATGCCGGTGTAAACATACTAGTTGAAATATTTTTGGTTCATC
ACATTAGTCAAAGTCAAGGTCTCAAATACATGTATATGGTCCATTGGTCC
TCGATGAATTTGTCACTAGATATGTACGTCAATTATGTGGATATATCATG
ATATTGATATCGAACACTCAGTCACAGATGCATTCACGGCGATCGAAACT
GTTTAGGTAAATCTTGTGTATCACACACTGTTTTATTTATTGTGCACTAA
GCTGGGAGTCTTCACGGAAACAGTCTCTCTACTTTAAGGANTCTATCGTC
AAGCTTTCCCATAAGAATATGCACGTATGCGGTAACTATAATAAAAGCAT
GAACTTAATGCCACAAAATAAGGCGGTCAGTACAACTGGAACTTATATGT
ACGTGTACAAGTAAACTCAGAGGTGGTGGCCGGTAAGCCTGAAATTATGG
TGGGTAGAAGACGTGTGTAATAAATTATATATCAAAGTTCAAAGAGAGGT
GCATTGAAAAAGTTAATATCTAGGAACATGCATGCAGGCTAAAAGAATTC
ACACAGGTTTTCTTATGTGACAGTAGTATGAAAGAAATGATAACATGTGA
GTAGCTCCAGAAAATAAGGTAGGCCAGCAAGCTTGTATTAAAAAGAGTGC
ATGTCACAGACGATGTTAGTGTGTTTTTTGAAGCCTATAAATAAGGCTCA
TCTATTAGTATTGTAATATATCGAGTGAAATATTTGTGAAAGGAAAAGAG
CAGAAGCTCTGTGTCTTGTACCGGAGAAAAAGGTTGTAGCCTGTTTTATA
TAAAATAGAGTCGTATTCCTGCTAAGTGAAACAAATAAGTGCGGTTGAGT
TTATCTTTAAATTAATATTTTTTTTTTAAAGCTCATTACGTTTCCAACAA
GTGGCATCAGAGTTAGGTTATGTTCTGAACATTTTATTTTTTTTGGAAAA
AAATAGATTTTTTTCTTAGTATGAAACAATTAGTGCTGGCAAAAAGGATG
AAAAATCATAAACTCAACTCTATTGATATTTTTGTTTGATTTTGAGTGAC
CCAACCATATTTTTAAATTAATTTTTTAAAAAAATCAGATTTTCAAACCT
ATATTTATTATTCTATCTTCATGATCATTAGTTTAATTCAAAATATTTGG
TCCAAGTTCCCATTTCCTGATAAAAACTTAACGGGCAGAAAAGATAAATA
ACCATAGCTTATGCTCAATTTTGTTCAAAGAAATCCCCGCTCTTTTCCTT
ATAGAATTATAACCGACATTTGATGAATAAAAGGTAGTTTCATGTTAATA
TAATGTAAAAAAAAAAATCACAGTTTGTAGAAAACATACAGGGTGACTTT
CATGGTGTGGAACAATGGAGTACATGTCACCTGAAATCATTCTTGGGAAG
GGTCATGATAAAGCTGCAGACTGGTGGAGTGTTGGTATTTTGCTGTTTGA
GATGCTCACTGGGAAGGTTAGTATATTGCAAAATTGTTTACATAAATCCA
TCTATTTTTCGGTGTTTATTACATGCCGGTGTAAACATACTAGTTGAAAT
ATTTTTGGTTCATCACATTAGTCAAAGTCAAGGTCTCAAATACATGTATA
TGGTCCATTGGTCCTCGATGAATTTGTCACTAGATATGTACGTCAATTAT
GTGGATATATCATGATATTGATATCGAACACTCAGTCACAGATGCATTCA
CGGCGATCGAAACTGTTTAGGTAAATCTTGTGTATCACACACTGTTTTAT
TTATTGTGCACTAAGCTGGGAGTCTTCACGGAAACAGTCTCTCTACTTTA
AGGATAGGGGCATGGTCTGCGTACATCTTACCCTCCTCAGACCCTGCTCT
AAGCGGGATATACCGAATATGTTTGGTTTGGTTCGGTTTATACAGGGCGA
CTTCATTTTAAAAAACGAACAGGCCGAGGATATGGTGGCAGACGTAAAAA
AAACTCGAAGGGTCCGGATTAAATACTAATAAATATAATCATATCAATAT
TGTTTTCATAAAAATTTTACTTTTTTTATAATTATTTATGTATAAAACTA
TATGTTAAATATTATATATATGTAGCCAAATCATGTAAACATAATTGAAC
CCAGGAAATTAATCCCAAGTAAAAATATTAGAGTTAGAAAACAAATTTCA
CATATTTAAGAAAAGGGAAAATAGATATTTTCGTCACTCAACTTATTGTG
TATTTAGAAACCTATCAGTAAATTATAAATTGTTTTCTTTTTGTCACTAA
TGTTAGATTCAGATGTTTTTTTGGTCACGAACGTTAGGTTTGGATTTGAT
TATTAACATTATGTTAATTTTTTAGTATTATAAAAACGTTGTGGTAATCT
GAAATATTATGGTGATCTAATATATATCTATATCTTTAAATATAATACTC
TATATGTCTCTTAGGTAGTTTGCTTTGGAGGCGAGAGTTTGATACGCATT
TTAAAACTCCTAAAAAATTTAGTTTTATAAATTATTTTATTTTTAAATAA
AAAATTATGATTGTCTATATTATATATTATTTTATAAAAATCAAGGTTAG
ATGTCATTTACAATTATTTATAGTATTGTACAAAAATATAGACGAATATT
ATAACAAAAGTAGACAATAGACAATTATAGAATTTCTTAACCTTGATTTG
AGGTTTATATATATGATATCTAAATTGGTGGTTGAATTCTATAAAAATAT
AGAATCACTTAACTCAATTTTACTTGAGAATTGATTGTAAATGATAAATT
ATTTTAATTCATTGATTTCAGATTGATGATTTATTGAATATTTAGAATTC
TTATTATAATTCTTCCCGATTTTACCGCTCATTTATGTTATTATTACTCT
CTTCATCCATCTCATTTATTTATAGTTCTTTCCCACCCTTGGCATGTATT
ATGTGGTTCCCACTTCTTATGAAACATAGTTTATAACATAATTTTGAGAT
TTTTTTTTTGTGTATGAAAATTCAAACGTTAAATTTTTATTCTGGAAAAA
AATTTAAATAATTTATGAAACTAAATTTTTTTTATTTTTTTTTGAAAGAA
AAATGCATTTCATTAAACTGAAGCCTCAAACTCTAAAGCCTCCAACAGTA
ATTCAGGATGAGACGAAAACACAGTGAAACAAGCGTTTAAACAAGGAAAA
CGAGCCAACTCATGGGCAACCTTAAAATGCGTGTCAAACTCTTGCCCTCC
AAGATAAATTGCCGAGGACACATACGGAGTACTACATATAAAAATATAGA
CACATATCAGATCATCATAATATTACAAACTATCACTATATTATAATAAT
GCTAAAAAGAATAACATAGTGTTAATAATCAAATCCGAACTTAACGTTAG
TGATCAAAAAGAATTCAAACCTAAGATTAGTGACATAAAGGAAAAAATAA
TAATTTAGTGATAAGTTTTCAAAACAGGAAACGTTAGTGATCAAAAAAAA
TTCAAACCTAAGATTAGTGACATAAAGGAAAAAATAATAATTTAGTGATA
AGTTTTCAAAACAAGACGGCGAAAAAATTTATTTTCCCTCACCAATTGGA
GATGCTTTTATACCACCAGTTAATCTTCTTGAGCCTTATTTGTAAAATAG
CTCTTTTCTTGCATTATCTTTTCTTTATATAATAAATTATTACGCAAGCT
CTTTTTTTAAAGCGTGAGATAGGATATTTTGATCTGCTCTACGTAAACTT
ACCCATATCATTAGTGAATCACTTCTTTAATCAAGAACTCCCACTTGAAG
AGTTGAAGACTTGAAGTCCACAATCACACTCAAATAATGTGAATAATGAC
AAAGTAAGAAAAGGAAGATCCACAAATTAAGTCCAGCCTCATGGTCCCCA
CCTTACTTAGATCATGACTGACGTGTACCCGTTACCCAAAAATATATGCA
GAGTAATAATCTAGCAACTACAAGCCCAGTGAAAAAATAAATAGAGGTTT
TGTTGTATATATCCTAGTCTAAATATTTTTTATAAGTATACCATACTTAT
AGTTTCAAAAAAAAAAAAAAAAGTATACCATACCTTTTTGATTATTTTAC
AAAAATATCATATTTAAAAAGAGTGTACATAATCAGTATAATCATATGCA
ATCATACTTTTAATCAAATGCAATCATATTTGCAAGCCCTTCGAAACCAA
TTAAGCATACGATATTTTTTTCAAGTAATTTTAAAAAAAATAGTATTCTT
ATAAATATTTTCAAAAATAATAAAAACACAAAAAAATTTAGAAAAATAAC
ATTTTTGATAAATTCCAAAAAAAATATACTACGCCCTATAAATACAGCAC
ATGACTCTTACCATTCATTTGATCAAGATTCATGTATAAACTTGCTCAAC
TGCATCTATAAATTCTTCTCGTTTAGCTACTGATTATTATGTACAACGTT
GAGGGATCAATGGAAAGCTTACTTGCTGCAACAAATTTCATGTTTCCATC
ACCAGCAGCTGATCATTTTGCGAAAAACAAAGAGACTGTGCATTCGGAGA
CGTGCAACTTCATGAATAATCATGATTCTCCGCAGCCACAGAGCTTGAAT
TTGAGCCGGTATCAATCTGTTCCCAGCTCATTCTTGGAAAGTCTTGTGAA
TGACAGTGCTGTTGCTGCTGATTACCGCAGTTCTAATATTGAGACAGAGA
TGAAGTTCTCTGATCCGGGTGATTGTAAATATACGAAAGGACTTGGCACG
GATTCGAGTAAGAATTTGCTTAGTAGTGGCGTGGAGAATTTGTTTAGGGG
TTTTGGTTCGAATGTAGGAGGGGAGAATATGAATCAAGTTAAGAAGGAGA
CTAGTAACGGAAGTCGTTTGTCTTTGGTTCGACAGAGCAGTTCTCCAGCT
GGATTTTCGTCGAGCTTAGCTGATGATGATATCGGTTCTGGTAATCACTA
CATCTTGTTTTTATATGTTGCTTCAAGTTTTATATCTGATGATGATTTAT
ATATTTTCTTGAATAATTATGATTGATTGTATGAACAAGGAACTACTAGT
GTGTTTGTGTGTGTGATTTGATGATAGTAACTAGATCGACGAATCTGTAG
TCGTTTTGTTTATTTCTGTTTTCATTTGTCTTTTAGTCTGGATCTCAGTG
GAATCAACATTTATAAGCTTGTTTGTGCTTGATCTTTACTGCAAATTGTT
GTCAGTAATTATCATGTATTCATGTTCCAAAATGCTTCTTGTGCTATTTT
ATTGTTAGAATTTGAAACAGATATATGTGTAGAACAGAAAATTTGTTGGA
GAACACTTTGACCTGGAATGACAGAAGATCTGGTAGAGTGTTATATGTGT
CAAAAATTAACAGGTTGATGGTTAAGACTTATGTCTACTGTTTTTCCATG
TTATGATGATGAAGTCTTCCTGTGCTATTATTACAATGATTTTGTATGGA
CTGCTAAGAACTCGAGGCCTAATAACAGGATTCACGGGGATGAACGATTT
GGGAAATTTCAGATCTTGTAATAAGACCAAGGCAGGATTAAGTTCCTCAA
CGAATAGGTTGGGTATGAACTTCTCTTCTGTGCCGTCTTCTCACTCACGG
TTCATGCCTCAAAGTGCTGCTAATGTGAATGAGAATTTCGGAACTAGTGA
ATTGTACTCGGCCAATGGACATAGTGGAGGGAATTTTAACGGTCCTAACT
TGTACAATGATCCTAACTGCAACAGCCTAAAAAGAAACAGAGATGGTGAA
GCAAAGATGTTATCCAGTTTGCCTGGACTGAACAAGCAGGTACTAACTTA
AGATAATACTGTATCCGTGATAGTTGCTTTCTCATTACTTATTTTTTTGT
CAGTCAATTGAATTACATTTTTTCTTGGTTCGTTAGAATGATGATTTCAA
CCATTACACCTCTGGTTTAGTTCACCAACTGAGCTTGCCAAGCACTTCTG
CTGAAATGGCAACGATGGAGAATTTTCTGCACTTTCAGCAAGACTCCATT
CCATGTAAAATTCGGGCAAAAAGAGGCTTTGCCACTCATCCGCGAAGCAT
TGCAGAGAGGGTAAGTCTTACTAACCAAATCAAATATGCCCCGTATATCA
CACTCAGAAGTCAGGGTATCGGGTGGTTAATATGTACCCAGACCTTACAC
CAATCACTTATATTAATTATTAATAATTGTGGTCCTCGAAAACTTTTCTG
ATTATTGAAATATTGCACCTCTTTCTTTGTTGACAATTGACAGTATCTAA
AACAATGACATCTTCAACTTGACACATAATATGAATCTGGGCTTTATGAT
TTACAGGTGAGACGAACACGGATTAGTGCACGAATGAAAAAGCTGCAAGA
TCTTTTTCCAAATATGGACAAGGTAACTTTCAAATGATTCACTGTAACTG
CTCTGTCAAGATTATAAATTAAAGTGAAATAGTCACATGATTCTTGTCAA
TCTGCAGCAAGCAAATACAGCTGATATGCTGGACTTGGCTGTTGTCTACA
TTAAAGACCTCCAAAAAGAAGTGCAGGTATAG