| Relationships |
|---|
| The mRNA, DCAR_001363, is a part of gene, DCAR_001363. |
| The genetic_marker, MK007387 TP131799, is located in gene, DCAR_001363. |
| 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_001363 | DCAR_001363.mRNA | mRNA | DCARv2_Chr1:14052478..14058022 |
ATAAACTTGTGCACTCTCCTGCTTGTGTATAATAGTTGGGTGACTACTAA
ACACAACAGGGGCGCCTCTATCTTCATTTTTCCCGCCAAAACCAAAGCCC
AACTTAATCTTTTTTTCCTCCTGTACTTGAACAATTGGGTGTAGATTTGA
TTGATATACCCTAGATTTAGCAAAAGAAACAAGACCCAGAAGTTGAAAAG
ATGAGAGGAGGCACAGTTCAGATCAATTGGCATGACACTAAGCCTGTTCT
AACCCTAGATTTTCACCCCTTTTCTGGGCTGTTAGCAACTGGTGGTGCTG
ATTTTGATATCAAGGTACCAAAGTTCTCATCTTCTCTATTTTCTAATGTT
TTTATTATATCTGATTGTGTTGTGTAAAGTTTTGGTTTTAATTTGTGATG
GGTTTGGCTAAAATGTGTGTGTAATTTTTGGGTGGGTTTGTTTTTTTTGA
TTATATTAAATGGGTTTTGTTTGTTATGGGTGTAATTGTCAATTTTTAAG
CTCAATTAAATAGATTTTATCTGTAAATTCATGATTTGGCTTAACTAGAT
TCGCTCTAGTGAAGGAAGCCGAAATACTAGATCGATGCTACTTGAAAGTA
GGGTCTTGGAGGGTGGGATGTACGCTGATGTATGCTACTTAGGAACTAGA
ATTGTTGTTTTTTAGGAAATTTCGGGACTATGGTGCCATCACTTGTTCAT
GTAAACTTTAACCCGAGGAAGTTATACTGCACCTTTTAAAATTTATTCAA
TGTGTATTGTGTCACTCGCCGTTAGAACTATGTAATTATGAGGTTGGGCT
AACAGTTTGAACTCTATATAATTTGAAATAGAAGTGTTGCAAAATGTTGT
TTGGACTTTCATTGGGATTTTTAAAGATTAGAAACTCAGTATGGACTTTG
TGATGAGTTATTCTATTGGTTCTGATCTTTTCTTTCTTTATACAATTGAA
TTTTCAGCTTTGGCTAATAAATTCAGGAGAAGGGGAAAAGAAAGTCCCTT
CGGCTACTTATCATAATAGTCTTTCTTATCATGGATCTGCTGTAAATGTT
CTTCGATTCTCCCCTTCTGGTAAGAAGTTGCTTGTTTTCTCATGGATGAT
GTTATTACTGGGAAATGACGACGGCAACTATAATAACTATTGAACGCAAG
CTGCAGTTAATATTTCTAAGTTGCATGCTTATGGTGTATGTATATATATA
TATATAGAGAGTTTTACTCCAATAGAAACCTCCTTATCCTAGAAACTAAA
AACCAAACTGAAATATCACTAAATCCTAAAGCAAATACCACTAAATTTTT
AAACAACCCCATCTCCACCTCCATCTTCATCAAACCCACCACCATCTTCA
CCAACCCCACCTCCACTACCACCACCTCCGTCGTCGCCTCCTTCATAACC
ACTACCACCTCTATGCCGCCCACCCCCTCCATAACCACCACCTCCATCTC
CATCTCCACCTCCACCTCCATTATTTCTTTAACAACACAACCTCCACACC
TCCATCTTCACCAGGCCCATCTTAATCGCCGCTTCAACCTCCTTCAGATT
CGTTCATACTTCTTTCTCCACCTCGACTCAACTTCAAAGGCGGAGCCGCC
ACTATTCCGGCAACGCTCCAACCCCCTACTTCAAGCCGCCCAAAACCTCC
GCTACAATCATCTTTCCTCCATCTCCACCTTCACCTCCGCCATCTCCACC
ACTATCACCATCATCTGAATCAAAAACGTGAACAGATCTGGAGATTCTAA
GCTGGAACAGATCTGGAGATTAAGTTATCACTAATTTCTGCAACACATAT
CACTAAATCCTAAAGAGAATATCACTAAATTGTACTGAGAATATTATATA
TATATAGGGTCTTACTCTGGTACAAACTTTCTTAGCGTACAAACTACAAA
CTAAAATAAAAAATCTCTAAATCGAATCGAAATATAGTACATATGGTATG
CAAATTGATCGTTGGGATATGAATAAAAATTCAGTGAAGTCGGATTTTGA
AAAAAGTTTACCAATTAACGGGAAAAATTAATTTAAAAACGGAGGGGATT
AGGTGGGAGTGTGTGTGTGAGGGTGTATTTGAGTTGTGTGTGGTTGCCCC
TGCGGGGCCGTTAGATTAAATGCATCCAATGGCTGAGATTAAGGTTTGTA
GTTTGTACACTAACTTAGTTTGTATTTGAGCACTTCCCTATATATATATA
TATATATAAACTTTTGGTCTGATGAATATGAAGCATATGGGAGACACGAC
ATCCTGGTTTACTTGTATGATTAATGAGAGGCATGTTAACTATGATGACT
ATCAAATGCAGTTAATATTTTTATTTTGCATGCTTATGTTATATATTTAA
AGTCTTGGCCTAGTGGATACCAAGCAGTTGGTAGAATTGATTATAAGCGA
TATCCTAAATTGCTTGTATAATTGATGAGAGGCATGACTTTAGGTATTAA
TACTTTAAAGATTTTAGTAGTAGTGTAGTACCAAGGCAAAGATTCGAGCA
GTATCAAATCAAGAAGTTGATAATATGTGTCATATTGAATGTTCTTATTT
CAATTGACTTTCTTGGTTTAGTAGGGATTAGTAATTTATAACAAGCTCCT
TTTACCTTTTTTCTTATGACAGAGGTAGCCTCTATCCTTTTCAAAAGTTA
TAAAAGGATGGTTAAATATGCGGGGTCTTATACTTTCGTACGAAACTTTA
AGTCACACTACTCTAAGCTATAGACATTTCACAACTTTTTTAGGTTCAGA
TTACTAGTATGCACAGAATTTCAGACGTGTCAAAAAGGGTTGGTATTTCG
CAACCAAACAAATCAGTTGATGCCAGTGATGTTAATTAGATGAGAATTGC
TTATATCACTCACCTCAGTTTTTCCTTGAGATCTTAATTATTTTTTAAAA
TCATACTTGAATTATTTTATTGTTCTTTTTGACAGGTTTCTCTTCATAAA
ACATGTCTTGTATGCTATAACTTGTAAATTGTAGGAAGTTCCCACTGTAT
CAGGGAAGGCGTATCTGTATAAATTTACTATCTCCTACTATTAAGTGTTA
AACATTTGTATTGGTCCGATGGTTTATTGGCATGCAATATAAGAACTTGA
CTTTGTTCCACACTATATATAGACCTCACTCCCATCTTTCAAATTTATCT
TCCTTATATTGTTTAGTCTGCACACTTATGCATTTAGTTGTCACACTTGC
AACAAATATAGGGCTTCTGGGGCTGTTTGCTCCTGATTTCTCATCACTCA
CGAGTACTGGCATTCTAGCTTCCTTAGTCTTTTGGTCTTCTACCTATATG
ATCCTTGCTTGGTTGATATAATTTTCTATCATCTGATAATTAATTACANG
GTCGGAAGAAATTAATGTCATGCTTCACTAATTTGGAGCTAATATATTTG
TAACTTATGCAGGGGAAGAACTTGCCTCTGGTGCTGACGGTATGATTTGA
TTTACTTCATTTTCAAGTTTCTATTACAATAATAATCAAACAATGTTTTT
CCTTAGTTAATGTAATTGAGGTATGCTATTATAGGCGGTGAACTGATCTT
ATGGAAGTTACATTCCAGTGATGCTGGTCAATCATGGAAAGTCCTAAAGA
CATTATCGTAAGGCTTGTCATATTTATATAGAACAGTTTATGTCAAGTTT
AAAGTTGCCTCAAACTTTTAGTTAACATTTTCTGGGCTTGTTGAGAATAA
TATTTATGATATATTCAGTTGCTAGACTTATTAGTTGGCAAGTGTTTGCT
GCACAGGTTTCACCGCAAGGATGTCTTGGACCTTCAGTGGTCTACTGATG
GGGCATTTTTAATATCTGGATCTGTAGATAATTCTTGCATAATATGGGAT
ATGAACAAAGGTGTGCCTTCCTGTAGCTTATGATGTGCTCCTGTTGCCAT
AAGCTAAATTATATGTTCTGCTCTCTTTAGGTTCTGTTCATCAGATTCTG
GAAGCTCATTGCCATTATGTTCAAGGCGTGGCATGGGATCCCCTGGCCAA
ATATGTTGCCTCACTTAGCTCTGATAGATCGCTTCGGATATGTGTCAATA
AGCCAACTAAAGCAAAAGGAATCGAGAAGATGAACTATGTTTGTCAGCAT
ATCGTTACTAAAGTGGATCTTGAAGTTGTAGATAATTCTAAGGTTAGAAT
TTATTTTACCACTTTCCACAAGGCGAACTATATGTAGATTCATTATGATT
AAAGATTTACTGCTGAATGCAGTCTGCCAAAGGCCATCTTTTTCATGACG
AGACACTGCCATCTTTTTTCCGGAGATTATCCTGGTCACCTGATGGATCA
TTTTTACTTGTGCCTGCAGGTAACACCCTATTTCTGGTTATTTTAGCTAC
ACTCTGAGATCTCTGTTTCATACCCCTTCAGTTATTGAAAGCTAAAAGCA
CCTGTATATTTATTTGCAAAAGATGTTTTTGATGTGAAATATTTTATGAT
TGCAGGATCCTACAAAATTTCACCTGTTTCAGAACCAATAAATACTACTT
ACGTTTTCTCTCGAAAAGAACTTTCTAGGTAAGATACCGACAAACAATTT
CTTATTTTAATTTTTTTAAGACTTGTTAGTAATTAGTCTGTCACAATAGT
TACGTTGGTATTAAGTCCAAGTTGCTTATAGTGTCCGCATATGTTTCTCT
GTTCGAAAGAGATCCTTGGAGGTCAATTTCAGCAAAAATTAAGCATGGGT
CTTGTTAAATGTTTTCTGATTGTCGTAGATCTTCAAATTCTTATGATTTG
CAGACCAGCTCTTCTGCTCCCTGGTGCAAGCAAACCTGTTGTTGCAGTAC
GCTTCTGCCCTAAAGCCTTTAGTCTGCGTGGAACCACTGCATGTAAATTT
ATTAATTAGATTTTTTATTGTTTTTGTTTTTTGACAGCTAATTATCAAGT
CTATCTCTTTAAAGACTTGTCAATAATTCCACTGATTTATTGTCTTGTGT
GACTTATGCAGCTGCATTCTTCAAGCTTCCGTACCGCTTTATTTTTGCAG
TTGCTACGTTGAACTCTTTATACATTTATGATACAGAAAGTGTTCAACCA
ATAGCAGTATATGCTGGACTTCACTATGCAGCTATAACTGACATCTCATG
GTAAATATAATATTTGATGAATTGCAGCATGCCTATTGTTATCACTTGCT
GACAAGCAAGAACTTGCATTGCGTTGATTAGATTCTGACATTGTTGTTTG
TTTTAGGTCACCTACCGGCAAATATCTCGCAATATCTTCCCAGGACGGTT
ACTGTTCTTTAGTAGAATTTGTGGATGATGAGCTAGGGTCCCCCATCTAT
TCATCAGGTAACTTGAAGTTTATTGTAGTTATGTTTTTGTTAGCTTCGAT
TAATTTCCAATTTTCAGCTATATTTTCCTCTTATGATCTCCTCTTGGCCC
TCCCTCCTGTTTTTGTTTCATGACACCACTTAGAGGATAAAAATGACACA
AGTAATGAGTTTACTCCTACAAAGAAACCCGAGGATGTCAGGATGACGGA
AGCAACAACACGTAAAGATGAAATTTGTAGAGATGCTGAAGCAGAAAATG
GTGCTGGGAAACAAGCAATTCCAGCTGAGAAGAGTGAAGATAACCAAAAA
TTGCCTGCAGAAACTGATGCAGTGAAACAACCATCGCCAACTGGAGACAC
TAATGAGCAGAAACAAGAGTCGCCAAAATTAGTGAATACAGCCACTGAAG
GGAAGCCTGCCAGGAGGCGAATAACTCCGATGGCAATTGATTGACCACAG
GTCCCCATGTCCACATCCAATTTTGTATATCTTCACTAATTCTATTCCCA
TCCTAGAAGTCAATCTACCCTTGTACTAATATTTCTTCAAATCA