- 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_021017, is a part of gene, DCAR_021017. |
| The genetic_marker, MK005428 K2872, is located in gene, DCAR_021017. |
| 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_021017 | DCAR_021017.mRNA | mRNA | DCARv2_Chr6:26575371..26580659 |
ATGCCAAAACTGAGGCCACTCATGTCCACAGTTGTGAAGATGTTAACAGG
TGAAATTGAGGTGCAAGGGAAGCTGATAGCCAAGCCGGGGATACTTCCAG
AAGCGTTTCTCAGGAGGAATATTATTACAGGAGATGCATCATCACCTGGT
TATTCTAGCATTGAGGCCTCACCAATGCGTGAGAGTACCTTCATATCACA
TGGCACTATGACTTTTTCATCAATATATAACCGAAACAGCTGAGCTTGTG
GGCAGAGGAGAACTTAAAACTGCAGTTAATACCTGACAAAAAAAAAAAAA
AAGGATTGATTTGCTTGGCAATTTTTTTTGTGTATTATTGGGGAGGGACA
CACAATTTTGTGAGTTATATTTCAAATCAAGTTTATTTTTTTGACAGCAT
GTTAAATCAAATTGGATTTTTCACTAGTAATAATCTTTAAACAGAAGTCA
CGATTCTAAAAAAAGTTATTAAATTTACAAATCTTCATTAACCCCTTGGT
TCCGCAAATGTCTTTTACAAAGGCCAAAGAAAAAGATTTGCACTCCTTTT
CAGACAGATGGAGTTTCATCATTTGACGCTGCACAAGAGACGACCTGGGA
ATGAATATTCTAGTATTAGACTTTGCCAAGTCAAAGTGACTACTTCTCAA
ATGTTTAAACTCTTCTCTTCTTTTATTTCTTACAAGCATCCACTTGGCTC
CTCAACATAGCATCCGACATCCTGGTAATGCTCTACTTCAATTTCTTGTT
TTTTCTCTTCATTTTATTATAGCATCACATTTGCTGTTACTGTTTGTCTT
CTTGGTTTCTTTTTCTCTTCATATTATATTTATAATATAATCATACAGAA
CCCATGTTTAAGATCAATGGAGAAACTTGAAAATATATTCATTTTTAATA
TTAAGTTGTTTGATTGTCAATTAAATGATGCTACTCTTTGGGGTACTTAT
AGTCAAGGTCAAGACATCGATGAGTTTTGACATTTTGTTGAATTGCCTGT
TTTTGTATGATCGTGTGAATTTTTCAGGTTTAAAATAGATTAACTTTAGA
GACCAGGTTTAAGATGATGTATTTGATTTTTATTACTGTGAATACTGATT
AGGTTTTGTAATTCTCAGTAGTCTAAGAAGTTCAGCTCCATACCTGTTTC
TTGAAACCACTTTCAAGTAAATGAATGCAAGTGATGAACTTTATCTCCTA
TCAACATAAATCCTTATATCTCTTCTGCAAGTACCTACGATTGTACGAAA
TGCAATTGCACAAAAATGGAGAATACAAGTCCCGAAACGACGGGATAGAA
GATTGACACACACTGACACTGAGAATGGAATCTACATGGCCACAGTCATA
ACTTGATTTCTTAGACCTCATTTTAGGCTTCTGTCCAATTTTTTTTAATA
GTTCTAGAGATAATGTTAGTATTTTTCCTGTACCCTTCTAGTTTGTATTC
TGTTTGGTTTATAAATTATAATATTTTATCCCAGCTCTATAATTCATGGG
GACAGACAAATTAGTGTGGGTCGAGGGGGTCTATGCCCCCTTACGGATGG
TGGCTGTACACAGTATGTGTATCTTGAAATATCAGTTGAACCAGGAATAG
GTAGGTTTGAATCTGCATCATTTCTCTTGTTTCTCCAATTTGTTAAAGCA
AATGCTAATAACTTACTCCGAATTTCAGTTGAACACGATAATTTTATAAA
GCTAGAAGGATATTTACAATTATGATGCAAATTTGGACTCCCCCTAAAAA
AATCCTGGATCAGTTACTGCTCATGGGAATACCGAACTTTATTATGGGAA
AAAAAAAAGATCATATTAGTGGTTTGCTTCCGACTGCTGGTTATAACTAG
TGATCATATGTAATAATATATAGTCAAGATTCATAATTCGTATTCTACAT
GTCTCAAGTAGAGCTGTTCACTGGTTTCCTTTCAGTATCATGTAAGATTC
CATTCCTCGAAAAAACAAAGAATTCATGACAAGCTTTCTTAGTCCAAAGC
AAACTTGTATCAAAAAGTCACAATTTAAAAATCATTAAGGTCCATGTGCC
AGTTGCATCATTGTTTTACTACACTATTGTTTCGTCCCTGCTACTCTTTG
TGTTACCATTATTATCACTTGTATACTATTTGGGCTACGATGTTTATAAC
GAGGATGTAAAATTTTAATAGTTTGTTTTGAGTGTAACATGAAATATAAG
CAAAATCACTTGATGACATATTTTTTTAATAGTTTACTTGGCGTAACAGG
GTTTAATGAGATTGTCTCTGGGACATATTGATTCACTGGTGTAATGCCTT
GCTTTAGTGCCTGTTTTGGGAAACAAACAGCTTCCCCTTTAGAGCAAGCA
ATCGATATCGAGGAAGGTACTTGGCTTTCTGTCATTGCAGTATCAAGTAT
GTTTTTCAGAGCTACCAATTTTTTTGAAAATATTTGAAATTTTTTGGAAC
CTAGTAGATAAAGAATTTATTTTTACTATGTATTGACTATCCATGGAAAA
CAAATTGCTGAGAATAGTCATATAGACTCCGTTCACATCCCATGATTGAT
AAAAATGCTTTACTGTTGTCGACCGCTATAAGCACTATACAATTTCAAGT
TCTGACTGCCTTCTTTTTTAATTCATTATATAAATACAGAGGTTTCAAGC
ATTCAGAATATCAAAATATATCCCTACAAAGAGCTTCAAATTGCCACTTC
TTACTTCAGTGCAGCTAATAAAATTGGGGAGGGTGGATTTGGTTCTGTGT
ACAAGGTATACACGCATTACATGGATCATTCATGGGCATCCTCTAGATTT
ATATATTGTTACCATTTTTATTCTGTGTTATGTATAACTTGTCAGGGGAA
GCTAAAAGATGGCACATTAGTAGCTATAAAGGTACTATCTGCAGAATCGA
GACAGGGGGTGCGGGAGTTTTTGACAGAGTTAGTTATAATTTCAGATATA
GAGCATGAAAATCTTGTTAAGATTTATGGATGTTGCGTGGAAGGAGTACA
TAGAATTCTGGTGTACGGCTACCTTGAGAATAATAGCCTTGCTCAAACCC
TTCTGGGTAATTTACTATCTAATGTCGACCTGATATGTTTAGTCTATTTT
TTTTTATCATAGAAGTGATAGTAGCCACTTTCACTTACAGGTGATGGCCA
TTGTGCCATTGAATTCAGCTGGAAAAAGCGAAAAGAAATTTGCATAGGGA
TTGCACGTGGTCTAGCTTACCTTCACGAGGATATTCAGCCTCATATCGTT
CACAGAGATATTAAAGCCAGTAATATTCTCCTTGATGAAAATCTTACTGC
CAAGATATCTGATTTTGGTCTTGCAAAGCTTATCCCTGCCCACCTAACAC
ATATTAGCACTCAAGTTGCAGGGACTTTGTAAGTTCAGGAATTCCTAGTT
TGTAGTCTTGCAGATGAAACCATTTCTTATTGAAATATTGTCTTTCTTTT
GGTGAATAACTGAATATTAAAGACCCCTTACTGTTTTCAAACATGAGCTA
TTCATAGAAGTTGTGCTTAAGAGAATTTGTTTAGTTCGACATCTTTAGTT
GCAACTAGTGTCTAGCAAATTCATTCCACTATAGGGGTTTGTTTTTGATC
CTTTATAACCTTCGTTTAGTTTCTTCGTATCATCTTCTCAAGGTGGAGTT
CCTGCATAAACAGCACTTTTCTCTTCTATAATATAGTATTTCTCCTTTAT
TGACTCTAACTCTCTCACTAAGTAAGTAGCAATATGCCTCCTAAAGTGCT
GTTTATGCAGGAATAATTTAGATGAATAATTGAAGCCTGACAAGATAAGA
TGACTAAAGTAGACAAGTTATTGGCTGTTGGTATTTTTTTTGCCTTCTGC
CTTGGCATGGCATCTGAATATGCATAGTACTATCTGGAGCATGTAACACT
GCTATTCGATTTATGTAAATTCGTTTCCAAATTTAGTGTTAATTCCAGAT
ATTGATCTTTAACTAAGAGGGCTACTATAAGTACTTCCTTTTATATACTA
CTGATTTTAATTTCAAAATTCATCTTGTTATTGATATGGTTTTTTAAAGA
GGCTATAAATGTGTGTTCTTCATTTTAGAGGCTATCTAGCCCCAGAGTAT
GCTATACGAGGCCAGCTGACTAGAAAGGCGGATGTTTATAGTCTTGGTAT
GCTGCTTTTGGAAATTGTGTGTGGAAGACGCAACAGAGACAGTCGTTTAC
CTCCCAAAGAAAAGTTTCTTCTTGAACTGGTATGGAATTTTTGGTTAAGT
AGCTTATTTAATTTTATTGGATGAATTATAGTATTGATTCTCAAAAAGCT
CCTTACAAAAAAAAAAAAAAAGATTCTTAGAAAAGCTGGAATTAGTCCAT
TGTCCTCATAATGACATCCTAGATCAGGGTTGACCCTTCAGTGTAATTTG
TCTTCGTAAAAAAGAGCACAACATGCCTATTTTCATCCGAGAAAGTTCTT
TCTTTTGTTTGCAGAACATGGCTACTCTGTCTACGTAATATTTGGTGTAT
TGCAAATCACTTTCTGTTCATATTTTGAGTATAGCTTTGTGAATTTATTA
AAAAAATTGTATATCATCATAGGTCTGGACTTGTTTCTGTATCCATGTTA
ATTGAACTAATTGTTCATCATCTTATTGTACTTGAATAAAAGGTTATTAC
TTTAAGTAAAAACTTAAAATTATTTGTTATTCGATGAGTTAATAGTTCTG
CATTCAAGTAAAAAAATTACGGGGTTATTATTCCATAGAGGTGAAATTGG
TTTTTGCAGGAGTCATCATTTCGGTGTTATTTGCTCAAAATTAACAATTG
CATGCTACCTCACAATATATAAATTTCAAGTTAGCAAGTTAATAAAGTCG
CATTTCTCTAGAGTTAGCTGGTGGTAGTGTTGGTTATACCGAAAACTAGC
ATGATAACTCCATATGTTTTCTTTTTTCCAGGCATGGGAATTATATCAGG
AACAGGATATTGTTGGTTTGGTGGATGCATCCTTAAATGGGAAATTTAGC
TTAAATGAAGCCAGCAGATATATCAAGATTGCTTTTCTTTGCACACAAGC
TGCTCCAAGGTCTCGGCCATTAATGTCAGACGTAGTAAACATGTTAAAAG
GTGATATTGATGTGAGTGAGATGGAAATATCAAAACCAGGCCTACTTTCC
GAGCTGTCAAGAACATATAAAAGTACCCCATATGAATCATCCATTGGCTC
GGGGAAACCAGATGATGTGTTCTTGTCAATGAATGAGATGTCTTGTGGCA
CCATGACTTTCACTTCCATAGAGGATGGAAGGGATTGA