| Relationships |
|---|
| The mRNA, DCAR_029951, is a part of gene, DCAR_029951. |
| The genetic_marker, MK003439 K0883, is located in gene, DCAR_029951. |
| 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_029951 | DCAR_029951.mRNA | mRNA | DCARv2_Chr9:18183621..18191031 |
TAAATATTAAATCAGTAAATTAAACCGATTGAGATTGCGGATTTGTACCA
ACATGTCTTTCTAACAATTAAAGTCCAAAATAATGGTAATTGTATGTATA
ATATCCCCCACCTGACCTGACCGCCCAGCCAAAGACCACAATAACAATCT
CTCTCACACACTAACACACCTTGAAAAAACACGCACATGACAATTATCTC
ACCACCGCCATGCCGTCATCAGCTATACCTTCATCCTGGTCTTCTCACAA
CCGGCCGGAATTGCTAATTGCTCGCCTGAGATCCGCCGGAGAAGGCAGAC
TCAAAGCTTTAAGAGAATTGAAGAACCAAATAATCGGCAATCGCACCAAA
AAGCTGACGTATATCAAGCTCGGCGCTGTTCCTTCCGTCGTCGAGATTCT
AACCTCCGCCGTTTTCGACACCTCCGGCGATGTTCATTCAATTTTAATTC
AGTCGTGTGCTGTTCTCGGAAGCTTCGCTTGTGGTGTTGATGCTGGTGTT
AAGGCCGTGCTTGAGGCCGGAGCTTTTTCGCATTTGATGATTCTTATTTC
CCATCGTAATGATAAGGTTATTTTATCATTTCATTTATTTCATTATTGTT
GCTTTTCAATCAGGTTAAAGTTATCTGATTTTGTAATCAAATGTTAGTTA
ATTTATTCATTTCATTCCATTTTCCTGTCTTGTTACTCATTGAGAATTAG
GTTGAATTGTCGATTTTCATTTTGTATTAAAATGTTAGTTAGCGGTCCAT
GTGTGTATTTGTTGTTTTGTTTGGTAGAATGATGATGATGTAATGGGATA
TATTTGATTTGTTTTTTAGCCCTTAGTTTGTATTGTAAGGTTGTTGCCTA
TTGGATTAGGCTAAAATATGAGATTTTGGGAATATGTGGTAAATACATTA
GCTGAATTGGATTTTAGTCTTTATTAGCCTTTTGTTGTAAGGTAAGTGAA
TTAGGTTAAAGATTTCAATTTTGTTGGTGACTATGTTGTGTTCGAACTTC
GAACATTACTATTTAGGAATATGAATGAAATAGTCTGGAGGATTAGGGCA
TGTTTATGTATTTTTCTTGCCCTTTTTGGTGGAACAAGTGATGATTATAA
GGTAATACATTAATCGAATTGGATGTTTGTCTTTATTACCTTCTGTCGTA
AGGTAATTAAATAATGGTTAGATGTCTGGCTAGTGGTTCTAGTGTTTCGA
AAACAAGGGAATCGAGACACCTGTTTTGAAGATTTTGGCACGTGCAAGAT
ACCACTGAAAGAACTAAAGTAATGAAGGATTGGTAAAAACGAGGATAAAT
TAATTGCGGTACATCTTTAGTAGTTACGAACTCTAAAAAATCTTTATGAT
ATGTTGTCCTTAATTGTAATGGTTTTGAATTGTAAAATTCCCTAAAATAT
TTAAACTTTATAGATCTAACACCAAACAATGGGACATTTTACATGAGGTC
TTTAATGCAATTTGTGATTAGCTTGTTGATAATTTACTTTTAAGGGTTGC
CTTTCGTACGCATTACTACCAAATATTATGGTTGCTGTATTCCCTTGTAT
TCACAAATTGAAGCAGTGGATTGCTGAAATATGGAAATATTATTTGGATT
TATAATTTGGGTTTAAAATTATGATCTTGTTGTGCACTGACATTATAGGA
TCCCCATTTGTGAAGTGCAAGATTTTGTGCACATTATATCTGTTTATGCA
ATTTGACGTGCTCCAGTATATATATGAATTTCAAGGATATGACAATTTCC
ACATGTTAACGATGGCAAATTTTCATTTTTAGACTAGGGAACCACATATA
TCATTTTAGTTATTTTATATATGGAACCTCTCTATCGGATCTTTGTGATA
AGCTATTAGAGGCTGGATGTCTCGTATCTTTCACCTTACTGATGCAAAAT
ACGGCTGTGCTTGTTCTTACTGTCCTTTAATATTTTGCAACTACAAATTG
TTGTTTTATTTATCAAAGAAAGCTTTATTCTTCATGGCATCTTTGGGGCT
ACTTACTAAAAGTTGGACAGTTAATGCTCATTTCACCTATAGCATGTCTT
TTACTTTATGTGTCGTTAAGATGGTTTTGTTTGTGTTGCAGGTTGTTGAT
GCCGCTGCTCGTTCCTTACGAATGATATATCAATCCAAGTTGGCCCCGAA
GTACGACTTTCTTTATGCAAAAAACATTGAGTTCATTTTATCATTACTGA
ATAAAGGGAATGAAAATGTTACTGGACTTGGTGCTAGTATTATTACACAT
TCCTGCTGGTCAAAGATGGAGCAGAGAGCTCTCAGTGATGCTGGAGTCCT
CAAGAAGCTGGTGTCCCTTCTTCGAGGTTCTCTAAGCCAGAGGGATGCTA
GCTTAGAGTCATTAGCCTCGCTTATCAAAGATAATCCAGAGGTCATCTCG
AAGTTTGTTGGACCTGAAAGTGGAAGAGCTTTAAGTGCTGTGACCGAGTT
AACAAAAGATAGATATCCTCGGACGAGGTTGCTTGCTTGCATGTGTTTGA
TTGTAGTACAAAGCTCTTCTCCTGCCTCTCTTCAAGTTGCAGGAATTAAA
ATGAAATTGATAACGATTTTGCTTGAGCTTATGGATGACCCTGGTGAAGT
TGGGGATGAAGCTGGCTTTGCTTTGTCAAGTTTCATTTCAGAATCAGAGG
ATCTGCAGAAATTAGCATTTGAGGCAAATGTTGTTGATAGACTATGTGAC
CACTTGCAGAATTGTTTATTACAGACTCGCCGTTATCAAGGTATATTGCT
TGCATTGGCTGGTCTATGCTCAAAACTGGAGTGCTGCAGATCGAAAATCT
TTTCACATAAGGTTTGTTTTCTCAGCAAAATAATTAACTTGACAACTGCC
AATTTTATGCTGCCGTAGTTTCCCTCATTTTATTTGTAAATGTCTTCTAG
TTTAATATTTTGATTATTACAATCTTGATATCCTGGTATATTGACAATTG
GAAGTTTACGTACGGAAGAGAACTGTATAGCTTTTAATTGATCTTATTAA
TATTTCTTGTGAAAATAGCTATGTACTGAGTTTCCTATTGTCTATTTGTC
TTCTGCATTTATCATCGAGCTGTTCTCAGTGTCAGAAATCAGTGGATAGA
TAGGCTACTAAAGAATATGTTATTAAATTCTTTTTCCGTAGTCTCTTCTG
AGGCCTATGTTAGTTGTGTCTTCTAAGCATTATTTACCAAGTCTCCGCGA
CTCTCCATACTTGCATGTTTATATTTGTAGTTTTGAGTTAGGTGAACCAG
GGATTGGATGTTTACCTCTAGAACTCCTGACATGTACATATTGTTCTTAC
TTTTTTTAGACCCTCAGCGCAAGAGATTATAAATTTTTTCAAATGAAACC
CCATATATGTGTAATGTAAAAATAGCTATGCAATGAATTTTCCTTTTGCC
ATTTCCTTTCGTCATCCAAGTAGCAGTGGATCAATAGGCTAGTAATTACA
TATCAATGAACTCTTCATTCCCAGTTTTGTTAGAGGCCTACATTAGTTGT
CTCTTGTAAGCTTATATAGCAAGTAACAAGTTTCCGTGACTATAAATTTG
CATGTTCCTATGGCTAGTTTTGGGTCATAAGACAGGGATGGGATGTCCAC
CTCAAGAACTCCTTACATGTACAAATTGTTAATTGCTCATTCTTTATTTT
AGACCATTCGAGGACAAGATTAAATGACCCTCAAACTGCAACCCCATAGT
AGAGTTGGAAATTAAGAACCTAAGCAAGTCGGTTGGAATCTCTGTAAATA
GTTAAAGGGGAAGTTGTACTTTTAATTGGTAGCACCTATTCTTCGCACAA
TAGTTGTATAAGTGGGATCACAGAGAAGTTTTCCGTGCAAACTTGGCGCA
TAACTTCTTCTACCGATGCAGTATTATTATGAGGGGCAAGGGGAAATGTC
CAACCCTAGCAAGGTCTGCAAATTGCTCAAAAAAGCCGGCAACTTGGAGT
GCAAGCTTAAAAGCTCCAGTGTTGTTAGTGAATGCAATAAATGAAACTCT
GCAGATTTAATTATATCTTTTTTTGTTGAACATAAATGCCAATTCCATAA
AAGACATTCTGGAGCTCCAAGTATATCACTATTGCTAGATGGAGAATTTT
TCTGTTTTCCTTAATAATAAAATGACACGTATTCTATTGCATATGCCCTC
TCAAGTCCTTTCTTTGTAACGCTGCTTCAACAATAGATATGAACGATAAT
CTCTTTCAAATCCCTACTGAAATTTTGTGGGAAATTTCTGTGCTATTGGT
ACACTGATACGCCAGTGATGTGCTAAATTTCAGTTCCACGCTGGCTTTCT
TTACGGCAAAAGTTTGTCAAAATATGTGATACTCATATAGCTTCAACAAA
GTATGGGTAACCTAAACCTGCAACAAAGTGAAAAAACAATATAGCTTCAC
CCTCTATACAATATCTTAAATACCTGTATATGTACTGTAGTTTTTGTGTA
GATCTTATATTGTTTTATTAATTTAAATCTGTCATTGCTATACTTCTGGA
TAAACAAAGTAGATCAGCCACTGCTGTATAGAATTACTGGTTTTATCGTG
GGAACAACTAGTTATAGACAGTCCTGATATACTCATATACTGATATGTGC
ACTTAGTCTCAATGAATGCTTAAAGTGTAGGCATTCAACTTGATAATTGA
TGCCTTAAATCATGAAAGATCCGAAGTACGTGTGGCAGCATGCATTTGCT
TAAAGAGTCTCTCTCGCTCAGTCCAGGTATGTAAATAATGCTAAAATATT
CAGTTTGTGCCTATAAAATATTGACCTTATATAATTTTGGCTAACATCAT
GTTATTCCAGCATCTGAGTGCAGGTCACTTTAAGACAGAATTAATCATTA
TGCCTTTGGTTAAGCTCTTGTGCGATACTTCTACTTCTGAGCAGGTGTGA
CATGTTTTCCTTGGAAAATATTTTTACATGGAGCTAGCTCTACTCACTAT
TGACAGTTCACAATATAGTAATTTGGGTTACCTAGCCTCTTTTTTCACCT
TGAGTACACGTGTCTGACATTGGTTTGTACTTTGTACTATGGATATTAGA
CATTTCATTTTAGACCACAAATATGCAAAATTTTTGAAGAAAGCACCTGA
TCCGACACTCGATCTCTTATCCATGTTGGACACTTCCAGCAAAGTCCTGG
CAACATTATGTCATAGATATTAATTATTAAGCTGACAACTACTGTTCGTC
CTTCCTTTAGAATAAGATCTTTATCCAACATTTTTTTTCTTTTACATGAT
CTCATGTTTGCACCCACATTAGAATTATCACGCTCGAAAATCCATCTTAT
GGGGGACATGGAACTATTATTTCCTTAAGTTGTATTTAACTCTCATTTCC
ACCAAAAAAACAATACTGCCGTTTATCGAAATATTTTATGTTTAATAATG
TGAAAAAGTTAAAGTTATGAAGTAGGGCTGATGTTGACAGTGCATTCCTG
CAGCATTCGACTCTAAAGAATAATTATAGTGTAATGTTGTCTGTTTCTTC
AGGTAGCAGCCCTTGGTGCTATTAGCAACATAGTGATAGATTTTGCTATG
CACAAGTCACTTCTCGTTAAATGTGGCGGTGTCAAGCAGCTTGTTCAGCT
ATCAAAATCCATGGACTCAACTATCAGAGTAAATGCTGTTTGGGCTTTGA
GAAACTTAATGTTTCTTGTGGACAATACATGCAAAGAAGGAATTTTTTCT
GAGCTTACAGCAATGACATTAAGAAGCCTTATATGTGGTAATTATCTTTA
CTTTTTATGTTAATTGCTAATTTAATTTTATGATACATTATATGTGCTAA
TGCACAACTTTCTGTGTATCTAGATCCCAAACCTTCTGTCCAGGAGCAAG
CTCTGGGCCTTGTTCGGAATTTAGTTGATGGATCTGTAGATTCTATCGAG
TACATGTTTCTCGAGGACTGTCTCTTACTCAATACTGTTGGAAGGCAACT
GCTGAGTGCTTCTAAGACTGAAGTTCTGATTCAGGTTGTCAAATAATTCT
TGAATACACCTTGCAAACACCACTTGTTTATTTGTACAAAGGAGGATATT
AATGGTCAAGTTGGTTTACATTGCATATTTAGTGGAATTTGACATTAAGG
TTGCACAGCTGTTGCTAATCTTTTATTTATGGAGCTAAAACATATGAGTG
TGTGATAACTACTAAAAAGCTTATAAAAACTGCTTAATAGAATATGAATA
CCATGTACAATTGATTAGTATATTTAGTTAGTGTACACGAGGACCCTGGA
ATTCAATGCCTGCTCAATAGAGTGTAGGCATATTTAGTTGTGCTATTAAT
AGTTAACTAATCCAGTTTCTGGAACCACTTCAGAATAGAAAATGACTGTC
AGTGTCTGTCTGTGCTATTGAGTACTCTCGAGAGTTGGAGTGATCTTTGG
TTTCCTAGTGCAATATACGCAGCGGAAGGAATTAGATTTAATATGTATTC
ATTTTATGTTAATTTAGAGATACAGTCAGTAGAATAACTGATAGATTTGT
TTCTTTTATTTTAGTTATGGTAGTGGATTGGTACAATTAAGTGGATAATT
TTTTTTTTGCTTGATTATGGTAGTGGATTAGCAGTAAGTAGATATTGATT
ATAAGTAATTTACTTGTTAGTAGGATTTTGTTTGTTGGTTAAGTACTTAA
GTTTAAGGTGCTCCTTTTAGTCCTATACAAGGAGATGTTAGTTGATTTGA
ATCATGTATCTTGAAAATTTATTTCTGAACTTTCTATGATACCTGTATGC
TTGAGATCTCCTTTCTTTGGGGACTGGAGAAGTTTCCCTAGTATGTGAAG
TTTCTGTTACTTCCACTAGTCTTTTACTTGATGATCCTCCTTCCCTTGTA
CTCTCGCTCTGTTCTCTTTACTGAACTAAATTGTTGTATTAAAATAGTAT
TACTATAACAGAAATTTGGCTATTAGAAATTTTTGCATGTTCACATCAAC
ATAAGATATAAGTGCTGTTACAAATGTTGACAACCTAGAATCAGGCATGA
TTCCATATTTAAATTTGGTGGCTTATATGCAATTAGGAAACTAATTACCA
TTATGCAGTAGGTGTAGGAGGTTGACAAAGCCAATTCTTCTCCTTATCAG
TACAGTTTTGGTGTACATTTTCACATTTATGAATTGAGTTTAGGTTTCAG
CACTGCTATTGAATTCTGATAAATCAAATATTATGTGGTAACTTTCATAT
AGGGGATGTTTGTCCTTTGCAACGTGTCTTCTGGGAATGAGTTTCACAAG
GAAGCAGTTATGCACCAATTAATGACACCAGCAGACCCTGATACCTTGTC
GATTGTGGTCAAGTTCTTGCAAAATAGTGATAGCCAATTACGCGTAGCTG
CTGTCTGGGCTTTGGTAAATCTTACCTCTCCCAGCAGTCCTGGTGCATTT
GCTCGTGTTGTAAGATTAAGAAATGCTGGTGTTGTTCAACAATTAAAGAC
TATGGTCACTGATCCGTGCTTGGATGTGAAGGTGAACATGTCAATAATTG
ATACGTTTTTTAATTGCCTGTTCCATATTTTTTGTCTGATATATATGTAT
TTGTTCTCTCAGCTTCGTGTGAGAACAGCACTGGGGCAGACCATGACTTT
TGATGCCAGTGTGGTATGAATCAATTTTCCTATACGCTAAAACATAATCG
TCAACAAGGAGTGTAATTCAGAATGGCATAATTACAGCATGGTATGCCTA
TGCTAGAGATTTATCATGTCACCGTTCATGATACGAGAGCTCAGATGTAT
TTCTGTACTGTTGTAATAGTGAGTGAAATCTGATTATTTTGTTAGTTTCA
CCACCTCCTGC