- 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_018681, is a part of gene, DCAR_018681. |
| The genetic_marker, MK004782 K2226, is located in gene, DCAR_018681. |
| 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_018681 | DCAR_018681.mRNA | mRNA | DCARv2_Chr5:32111720..32118659 |
ATGAAAACTACACATTTCTCATGGCTTTTCTTGACATTTTTGTTCCAAAT
CAGCTTGTTTTTGTCATTGGCTTCTGGCCAATGCCTGGACTCTCAAAGAA
GCTTGTTGCTCCAGCTAAAACAGAGTTTCTCGTTCGACTCTTCGTCATCA
ACCAAGCTAGTTCAATGGAATCAAACCACAATAGATTGCTGCCACTGGCA
AGGTGTAACTTGCAAAAAAAGTAGCGGCCTTGTTATTGGCTTAGACCTCA
GTAACGAGGGCATCACTAGTGGAATAAACAGTTCCAGCACTTTGTTCAGA
CTTCAGTTTCTTGAAAGATTGAACTTGGCTTCCAACAGTTTCAACAGTAC
AGAAATCCCATCTGGTCTGTCTAATCTCACCAGTTTAGTTTATCTGAACT
TGTCAAACTCGTTTAGCGGTCAAGTTCCAAATGTATTTTCGCGTATGCAA
AAGTTGGTTGTTCTGGATCTCTCCTATTCTTACTCCTTAAGGATAGAAAA
TCCAAAGCTGAGCATAATCGTTCAGAATCTTACACAACTTTCTGAACTTT
ATCTTGATGCTGTAGATCTGTCGAGCCAAGGATCTGATTGGTCCCGTGCT
ATATCATCTTCATTGCCTAATTTGAGAATTCTGAGCTTGACAGAATGTCA
TATTACCGGTCCTATACATCCTTCATTTGGCAAGCTTAGGTTTCTTTCAG
TGATTGAACTTGATGGAAACAATCTGAATTCGCCAATTCCAAAATCTTTT
GAGAACTTGAGTGGTTTAACAGCTTTAAGTCTTCATTCTTGTAATATGAC
TGGAGTGTTTCCGCAAAGGATCTTGCAGATACCAACTCTCCAGACTCTGC
GCTTGTCGTACAATGAATTGCTCAAGGGTTCTTTGCCAGAGTTTCCGCGA
AATGGATCCCTCCGGGAGTTGTTCCTCTACAATACTAACTTTTCAGGTGG
AGTGCCAGAGTCTATTGGTGACATGGCCAGGTTGTATGAGATAGATTTAA
GCCAAAGCAATTTCAGTGGAAGAATCCCACAATCAATGGCAAAGCTTACT
CAGCTTGTTCGTTTGAACTTTGCGTACAACAAATTCTCAGGTATTATCCC
ATCATTTGGTAAGTTCAAGAACTTGACATATGTAGATTTGTCTAATAATC
AGCTATCTGGTCCAATCCCGTCGACTCATTTTGAAGGCCTTGATAATCTT
GTACATATTGATCTGAGTTTCAATATTTTCAGTGGAAGCATTCCATCATA
TTTGTTTGCTTTCCCATCATTGCAGAATTTTTTGCTTCATTTCAATCACT
TTGATGGTATTCTGAGTAATTTTTCCAGGGCTTCGTCTTCTCAGTTGAAA
ACACTTACTTTAAGTAGCAACAAGCTCAATGGACCTATTCCATCATCCTT
TTTCGAGCTAAAAAAACTAGAATCCCTATCTCTGTCTTATAACAACCTTT
CTGGAACACTTCAACTTGAGAGATTTCAAAAACTTAAGAACCTCAACGCT
CTTGATCTTTCTCACAACCGGTTGTCAATTACAACAAGTCCGAGCAACTC
TAGCACATCTCTGCTTCCCCGCATCTACTTGTTATATTTGGCTTCTTGCA
ACCTGAAAAGATTTCCTGATCTAAGAAACCAATCAGAGCTTCAAAATTTG
GATCTTTCAGACAATCAAATTGGTGGGGAAGTACCAAACTGGATATGGAA
TATAGGCCAGGGATCTCTCTCATCGTTAAATCTTTCTCATAACCTGTTAA
AAAGTCTCCAAGAACCTTATGTTCTTCCTAAATTAAGTTACCTTGACTTG
CACTCTAACCACTTGACTGGTAAAATCCCTTTACCACCTGCAATCTATGA
GTACGCGGATTACTCTTCCAACAATTTCAGTTCTACGATTCCTCCTGATA
TTGGATATAACATCAGTGCTGCATACTTCTTTTCTGCTTCAAGGAACAAT
TTGACAGGAAGCATCCCTGAGTCCATATGCAATGCTAAAAACCTTGCAGT
TCTTGATTTGTCATACAATAGATTGAACGGGAAGATACCTTCATGTTTAC
TTCACAAGAGCAAAGTTCTTGAAGTATTGAATCTTGGAAATAACAATTTC
ACCGGCAATGTTTCCAAAACATTTTTTGAAGGGCGTGGTTTGAGAACCCT
AGACCTGCATGCAAATCAGTTGGGAGAGATTGTGCCGACAGCTTTGCCTA
ATTGCACCTCCTTAGAGGTGTTGAATCTACAGAATAACCATATAAATGGT
ACTGTTAGGAAATGAATCAGGAGCTGCTGATCAAGTGTTAAAGTATTTAA
GTAAAATGCTTTACGAGATTAGTCTTGTAATGTTTCAATCTACTCAAATA
ACAATCCTATTTTACAGGACTTTGCAAGTTTAAAGTATTTAAATAAAATG
CTTTACGAGATTAGTCTTGTATTTGATTAAAGTAAATTACTTGAATGCAG
TACAAATAGCACATTATATACAAATAACTTTGGCATCAACCTCAGCTGCA
GCAGAAGCAGAATGTAGTAATAATCAACAGGTAATGTACAAAAGTGGAAG
CACCACTGGTTCCACGAACCTATTGGAAGTTTAAAGTTATGCATAGTTGG
ACGATATTAGTACTAGGATGGATGATCCGCGGAAGTCTTGAGATTGGACT
GCGGCAGAAGTTTATGAAAATGTGACATGTAAATGTGTAGTTAGTAAAAT
TTGGGCTCCTATACATCGAAAGAAAGCTCAACCATATATCACAAAAAAAT
CAGGACATAAATAATGATAGGCCGTACATATATTAAATACGTTAGAAAGC
AACACACAGAAGATGAAGGATTCCAATGACATAGAAATTTGAGAATTGGT
TGCAACCTGCAGAACTGAAACGTGGCCTCCAAAGGTACCAGATGGAAGAA
TCCTGCTAGAAAATTCAACATTCGTATAATGACAGTATGGACTAAGATAA
GTGGCGGCACATTACGCGTTACCAGACGGAAAAATCCTGCTAAATAAGAT
TGTGTTATAAAAGATGGTACAATATGATCCAATTAAGGTTTCCTCCAAAC
ATTTTGAGGTATTAGAGAGTTCCTAACGTAACATGATGTCTGGGTTACCT
GCATGAGTAAGGTAACAAATGTGACTTGAGGTTCTAATTTTGCTGTGGAA
GATTATATATGTTGTCTCGACGGATATGCCATGTTGGCTGAAAGAATATC
AGTACGATAATATCAGAAGCACACAATGCGTTTGACTTTTAAATTTTTAA
AAATGATTTAAAATTTTAAAGCTAAGGTCCTGAAGAATCTTATGTAATTT
CTGGCACTAAGTTTACAAAATATCGAACAATTCTCAAACTTCAAATCATC
ATTTTCATTGTCATGAATTTAATATGGAGTCTGGCACCTCCTATTTGTTG
ATTGTTTCTTTGTTTTGGTAAACTCAATATGGAGAATTTAATCAAAATTC
TAAGCGTGACAAAAGGGATATAATACTTTTTGCCCTTAGTCGTGTAATTC
TAAGCCTTGAAGTCTTGAACGTAGTGTATAAACTAATATACAGAACAAGT
GGAAGAATAACGTATCTAAAACGCCCACAAGTTCACATTGACCACAAGCT
CATCATATGACCAATTATTTTTCATATTTTTCTTTCTGAATAATACTGCA
TGAACATAATCAAGAAGTGTGGTGTGTGGATGCAGAAATATTTTTATATG
TTTTGAGGCTTTCGTAAGAGTGTGCAATGAAAAATCGAGATTTTTCTTGG
GTTTTCTTGATACCCTTGTTCCAAATCTTGTTGATCACTGAAATATCTTT
AGTTCATGGTCAATGTCTGCAGAATCAAAAAAACCTTTTGGTTCAGCTAA
AGGATGGTTTGGAGTTCGACACTACGGTGTCAACGAAGATTGTGCAATGG
AATAAGAGCACAGAAGATTGCTGCAAATGGGAAGGGGTGAGTTGCAATAC
AAGTTCTGGTAATGTTATTGGCCTTGAACTGGATGGAGAAGCAATACAGG
ACGGGATATATAGTTCAAGTAGTCTATACAAATTTCAGTATCTTCAGAAA
CTGAATCTGGCCAACAATAACTTCAATTCTACTCCAATTCCGCCTGGGTT
GTTTAATCTTACAAGTTTGACATATCTGAATTTGTCAAACTGTGGATTTG
CTGGACAGATACCAGAAGGATTTTCCCGAATGGAAAGGTTGGAAATTCTT
GATCTATCTACATATTTTTTATCTAATAAAGCTCGGCTAAAAATTGAGAA
TCCAAATTTAGAAATGATTGTTCAAAATCTCAAAGGGCTTACTGAATTGT
ACTTGGATGGTGTCAACATGACAACTCAGGCAAACAGTTGGTCCAAGGCA
ATATCATCTTCACTTCCCAGTTTGAGAAAGCTAAGCTTGAAACGTAGTTT
TATATCAGGTCCTATAGACCCTTCTCTTGGAAGGGTTCGGTTTCTTTCAG
AGTTGTTTTTGGATCAGAACAATCTGAGTGTCACAGTTCCAGAGTTTTTG
GCAAACTTTAAAAACTTGACAGTTTTACATCTCAGTTCTTGTAATCTGCA
GGGGATATTCCGTAAAAGGATCTTACAAGTACCAACACTAAACGATCTTG
ATCTGTCAGACAACAAAGAACTGCAGGGTTCTGTACCAGAATTCCCCCAA
AATGGTTCCCTTCTGAAGTCGTTGGTGCTCACATTTACCAATTTCTCAGG
AACGTTACCAGAGTCTGTTGGGAACTTACGGTTGTTGTCTAGGATGGAGA
TAACGAGTTGCAACTTCGGCGGAATGATTCCAAATTCTATGGCAAACCTC
AGATTCCTTGTTTATTTGGATTTCTCACACAACAATCTTAGTGGTCCTCT
TCCATTGTTACAGAAGTCCAAGAACCTCACCTACTTAGATTTCTCCCATA
ACAGATTATCAGGTACAATTCCTTCCACGTATTTCATAGGACTTGACAAT
CTTGTACATGTTGATCTTGGATTCAATGCGTTTATGGGGACAATTTCTTC
ATCATTGTTCGCTCTCCCATCATTGAGACAGATTAAGCTTTCCCAAAATC
AGTTTGGTGGTTTACTCGCCAATTTTTCCGAGGCTTCGCGGTCACAGTTA
GATACACTTGATTTGAGTAGCAACAACTTAAATGGGTCTATTCCATTGTC
TTGGTTTGAACTGAAATGGCTGAACATTCTCTCCCTGTCCTCCAATCAGT
TGACTGGCTCATTGCAGCTAGACACCATTCATAAGCTTGCAAATCTAACC
AATCTTGACCTGTCGTACAACCATTTGTCAATTGAAACAAGTCACAACAG
CTCAAGCGAGACTCTGCTCCCCCAGTACAACACATTTAGATTAGCTTCAT
GCAAGCTAAAATCTTTTCCTCATCTGGGAAAGCAAATAAGATTGTCTGTA
CTAGACTTATCAGACAACCAAATTCGTGGAGCAATACCAAACTGGATTTG
GCCAATTGGATATCTCACGTATTTAAATTTGTCTCGAAATCAGTTAGTGA
GTCTCCAAGAACCTTATGCTTTTCCAAGATTAAGTGTACTTGACTTGCAC
TCTAACCAACTGACCGGAAGAATCCCAGTACCACCTGAAACTGCTTCATA
TGTGGATTATTCAGACAACAATTTCAGTTCTTCAATTTCTTTGGATATTG
GCAAGAATCTCACCTTTGCTTTATTTTTTTCTGTTTCAAGCAACAAGCTG
ACTGGAACCATCCCTGATTCCATTTGCGAAGCTACTTATCTTCAAGTCCT
TGATTTGTCTAATAACAATTTTAGTGGAGTGATACCACCATGTTTACTTG
GACAGAGACTGAGAGAGTCTCTTGCTGTACTAAATCTTGGGAATAACAAA
TTCAGTGGACACATCAACGGTACGTTTGGGGAGAACTGTGGTTTAAAAAC
ACTGGATCTGCATGCCAACAATTTACAAGGGAATGTTCCTAAATCTCTCG
CCAAATGTAAAATGTTGGAGGTGTTGAACCTGGGGAGCAACCAGATAAAT
GATACATTTCCATGTTTCTTAAAGAATTCTTCCAGTTTGCGAGTCCTTGT
TCTGCGATCAAACCAATTCCATGGAAACATTCATTGTCAGGGGCCAACGA
GCCATTGGCCAAACCTTCAAATCATCGACATAGCTTCCAATAGATTTACA
GGCAAGGTACCAGAGAATTTTTTCTTGAATTGGACATCAATGAACGGATA
CAAGAATGATGCAGGGTCAGAATTCGATCATTTGATTCGTTTCAAGGTCT
CAGAGCTTAATAACTTCTACTATCAGGATAGGGTGACGGTAACAGTCAAA
GGATTAGAATTACAGCTTCTGAAGATTTTAACAATCTTTAACTCCATCGA
CATATCTTGCAATCAGTTCGAAGGAAATATACCAGCAAGTTTGGTTGAAC
TCAAAGAACTCCATCTTCTGAATATATCAAACAATGCACTGACAGGCCGA
ATTCCATCGTCAATTGGAAATTTGAAACAACTGGAAGCCTTAGACTTGTC
AGTGAACAATCTAAGAGGAAGGATCCCGGTGGAGCTTGCAAAGCTAAGCT
TCCTTTCATATTTGAACTTGTCATATAATCAACTGACTGGAAAAATTCCA
CTTGGGACTCAGCTTTCAACATTTGACGAAGGATTTTTCAGAGGGAATGA
GGGATTATGTGGGAAACCATTGAACAGAACATGTGCTGAACCTGTACCTG
AAGCTGAACCATATAATCAGGATTCCAGTGACATGACGGTGGGAATTATG
ATATCTGCTGTAATCGGGTTCTTTGTTGGCCTGGAAATCGTTGTAATGCC
TCTTTTCTATTACAAGAACTGGAGAGCATATTACTTTGAACATGTTGATC
GAGCTCTTGCTAAGATACTCCAAAAGCAGTCCCCAAAGCGGAAAAATCAG
GCACGAAAAAGACGGAATGGAATTCATAGGGCAAGGTAG