| Relationships |
|---|
| The mRNA, DCAR_008779, is a part of gene, DCAR_008779. |
| The genetic_marker, MK002796 K0240, is located in gene, DCAR_008779. |
| 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_008779 | DCAR_008779.mRNA | mRNA | DCARv2_Chr3:1207853..1213242 |
CTTTAGTTTTTTCTGAAACAAAATGCCGATACAGAGTATATATGACTGAA
AGTCTAAAACCCTGACCCGATACACTAGGTCTAAACTACTGTTGTAATAG
CTTAAATGCTTCTCTGAACTCCGGCGAACGGCGGCGCCACCGGTGAATTC
AATTTGGTATCTCATTCTCATACTAACATTGCTCTTTAATTTCTAGTCTC
AATCACTTTGTGTATCACTGTGTGTAAATGCTTGAAATGTGATGATGAAA
TCGCGGTATGTAATCTCGCTATTAAGTTTGTTACGAAATGATTTGTGTGA
AGTTCCCTGAGTAGTTGCTTAATTTCACCAAATGTGGATATCGAATTTCG
AAAGCTAGAGCTTATGATTTTAATATACCTATTCTATGAGGGTTTATGGT
TTTAATTCACATTTGTGGAGGTAAGTAATGCCACTAATTAATCTATTGAA
GGCGGTTCTTGTGTGCGTCGTATAAATGTGGTGGAGTTTATATCAGTGTT
CGTAGTTTATTAATCTGAAATGCCCTGATCTGTTGCTTAATTCCAAGAAA
GTGCGAATATCAAAACTCGAGTTCTAGGGTTTATAGTTTCGCTATACATA
ACGCTAGGGGTGATTATATTTAATTAATGTGAAAATACATATGTTGAGGT
GAATTATGCAACTAATTAATTTATTGATATCTTTTATGTATCGTTCGACT
GGATGTCATGGTGGAGTTTATATCAGTATTTCTAGAAATTACATATGTCT
ACATGTTAATGGTTGGTAGTCTTGTTTGTAATGGTGTAACTAGAAAAATG
TTTAGAAGTAATGTTGAAGATATTTACATTAAGAATAATACTTCGGTCAT
TGTTGTTGCAGAAATATGAGAGGAGTTTCGTATGTTTTGTCATGTTCTCG
GCACGTTCGAAGTACGCAGTTATGTAGACCAGTCTCTAATTTCTCGTTTC
ATAGACCAATAGTTACTTTTAGTTATACTCAGTTACAGAATATGATACCC
CTGGTTCCTGATTCTCTATGCGGAATGAGGTCTTTCTGCAATAAGGCTGC
GTCGATCCCACTTGCACTTCAGGCGCAAGTGGAAAGAGAGAGGCAGAGGG
AGAGAGAAGAGAGGATCCGGATGGGGTTGGATACTGCCGATATTGATGCT
GAGGATGATGAGGATTACATGGGTGTAGGCCCGCTTATTGATAAACTTGA
GAAATGGAAGATTAAACACCCTCCGAATCCTGAGTTAGACATGATGTACG
AAGAGCCTACTGACTCTGACAGCGATGAAGATGATGACAGGTTTTCTGCT
GAAGCTAATAAAAGAAGGTCTGAAGATTTTGAAAAGAAGTTTGCGCGCCA
TAAAGAGCTTCTCAAAAGTTTCACGGACTCTAGTAACTTTCTGAATCCAC
TTCTTTTCTTTTTCTTTTTAAATGTGGTCATGTGCTCATGTTGTTGAACA
ACTGCTGTTGCTATCATTGTATTAATAATGTGTTGAAACTATGCGCACAA
CCTTTAATACTTTCAGTGAGGATCCACATCACGGTCCTCTACTCTGCTGT
AATGATTGGTTTCTTACTTTCTTTTCCGTGCAGAAACTCTAGATGAATCT
CACGAGTGGATGAACAGACTTGACAAATTCGAGCAGAAGCATTTCAAACT
ACGTCCTGAGTATATAGTTATTGGTGAATTAATGAACAGATTGAAGGAGG
CTACCGGGAAGGATAAATTTCTTCTCCAACACAAATTGAACAGGGCAATG
CGTTTGGTGGATTGGAAGGAAGCTAATGACCCAAATAATCCTGACAATTA
TGGTGCATTCCAGCATGCAGATGAAGCTGCTGTTGAAAATGAGGAATTTG
AAAAGGAACAATTGACTCGACGAGCTCAACTTAATGACGACGATGACATG
GAATTTGACAGCATGAAGGAGAGGGATGATATACTTTTGGAGAAACTTGA
AGCCATTGACAAGGAACTGGAGCAGAAGCTTGGGGACTTGGATCATACTT
TCGGAAAGAAAGGAAAGGTCCTAGAGCAGGAGATTAGAGATCTTGCTGAA
GAGAGGAACTCCTTGACTGAGCAGAAGAGAAGGCCTCTTTACAGAAAAGT
AAGTATTTTTGCTATCTTTTCAATTGTTCATATCCAAATATGATTTTGAG
TGCCTTTTGTTTTTTTATCATTGCTTTTGTACTAGATGGATGGATAAGAT
AGTATGTTGAATATGAAGCGTATGGATTCTTTGGAACTATACGCCTTCCT
TTCTCAATGTACTTACTAGGCACACTGTATATGCTCACATGCTTACCTTC
TGTAAGTTGACATTTGATCCAGTTCAAGGTTGCTCCTCACTGTTGTTCCA
TATGTATAATCTATCAGCATGAGTTGTAGTATTAAACTTGCTAAATTGTT
TTCCCTTTATGAGATTGGTTGCTGGAACCTAGTTCATATTGGATAGTGTA
CCTCCTAAGGACGTATAAAGGGGGTCTGAATTTTGCTGAATGCAATCTTA
TGGGGCATTTCTAATGGTTAAGGGGAAGTCCAATGGTGTGATATATTATA
GAACCAAAAAATTAAAATCTATCATTCCAATGGTGTTCTATATCTTGTAC
TAAAATAGCACAATGCTATACTTTGTTCTAAATGAAGAACAAAAGATAGA
TGGAGCTAAGCTAACTTAAATTGACACATCATCCCACCTCATCAGAAGTA
AAACATTAGGTAAAAAAAGTAATTCTGTATTCAAAATAGTGGGGGTACTT
GGAGAGTTGGTTAAATTTAGAACAAGATATAGAACCAAATATTGGACACA
TGTTTTATTTTAGCACAAAAAGCCACTTTTTGATGCGAAATTATAGCAAT
AGCTCCATCTATTTTGGCACAAGACATGCTCTAATTTATGTATAAAATGC
TTCTTTTGAAGGCATATGTGGTAGGAAGTAGATACAATTATAAACCAAAT
TTATGGTTAAGTGGGATGGTGATACTGATTAGGGGGTCGTTTGGTTCGCG
GAGTGGTATGGGGTTGAAATGAGGTATCGGGTTAAGGTAGTATGGATTTA
AGGTATCATATTTGATATCATGTGTTTGGTTGAGTGTTGGAATCAATATA
TTCAGATTTAAAAAAAAAATCAAATTATTTCTTTATATTAATTAAAAAAT
CTAAAAAATATTATTATTATATGTTTTTGCATCATTGATTATTGTTGTAT
TAAAAATTAATATTTAATTACTGAAATAGAGACAAAAAATTAAAATTAAA
ATTAATTCCCATACTTCCATCTCATACCCACCTCCCCCTTTGAGCATCAA
AAACCCATACTTTGAGGGTTTGAGGTATGGGTTTAAAGTTTTATTTTTTG
CAACCAAACACCAGGTATGGGTTTGGAATGAACAAAACCCATACCCGATT
CCATAAACCCGTGAACCAAACGACCCCTCTTTATTATTGAGAATGCCTTC
AAGAATCTCATCAAACTTCAAACATGTATAAATGATATATAACTGTCATG
GCAAGTGTTGTAAAATATTTTTTTGGATTGTCGAGGTATGACATCATATA
TTACTTAGCAGTTTTAGGACACGTGACTTGTATTTAACATCATCTCTTTA
CGTCATATTGGAGTGTGCATTTAAGTTTTTTTGACATGTAACTCATTCTC
ATGGTTTAAGCTAGCTGACATCACAATTCTTCAAAGTTTATTAGAAAATC
CATGTGATGAAGTCGAGGATTGGCTTTTATACCTAGAGGAAAGAAATCAC
CCCTAATGTTACTGCATGATTAAAGAACACATAGATTTATATGGCAGGGA
CCATGTCTGATGCCTCTTAGTTGTTTTTGATTTTAGCTTTGGTCAAAACT
GCTCTCAGTCTGAACTATAGTTTTGGTGACAAGTTTGGCTACATATTTCT
CTCGGTTGTTACAACTTATGGGGTAGCCAAACTATACTATTAGCTTATTT
GGGGTGGTAGACGTGCTATACCATTCTATCAGCTAATAAAAAAATTATTT
TAGGTATTAGTCATTAAAAGTTTTAAATCATGGTTTGTGTAATGTCCTCA
CATCTTTATTTTCACTATAGTCTTTATTATTTGCCTTTAACAGGCTTTCT
TTGTTCTGTCCGTTATATTGTACCTGGAAGGTTTTTTTTTTTTTGTCAGG
GAAACCTGGACGGTTTAAATCAGTGTAAGTTTACAGAAATTTAATTTGCC
TCTGTCCGAAGTATATTATTGGGATAACCGCTTTTGGGTCCTATCTCATA
TTTCAAGCTAAACTTAAGTCTTTCAAAGAGTATCCCTTAAAAGCATACAT
AAAAGATCAAGTGATGAATTTAAAGTACTTTTAAGTTTTAAGTGTATCTG
AGTGTTTTAGTTCAAGGCCTCTTAATTTCTTACATCAGTTGGTTATTCAC
ATAGTTTCAGACACTGACTATTACTAAATGTCCAAGTTAATAAGTCTTTT
GCCTTAGTTTGGGGCAGTGTTTGGTTTCAATTCTTGATGTCCAAATTAAC
CCAAGGGTCCAACTGCAAAAATAGTACTACTATTGAAATTTAAAATTCAG
CTGGACTTGGTTTAAATTCACGATGTCCAAATTAACCCAAGCTTACAATT
GCATATTATTATAGTTCTGCTATTGAACTTTAAAATCCAGTTGACTGTTG
ACAAAAGTCAAGGTAATCAAAGATTTTAACTTACGAGCACAACTTAGCAT
CCCAACTTATGGTATGGCGATTCACACTTAAAGGTACAGGTGGGCCGCTT
TAAGTAAATTGTTGATGAGAATTTTTTAGATGAATGCGGAGCTTCTTTTC
AGATAACTGGACAGAGAGGTCAATTATATCTGAAAAAAGAAAAAAAGGAT
GTTAAATGATTTTGTTTGTCTGATTTTTTTTTTGTTCATCTCTATTAAGG
GTTACTTGAGATACCTTCTGGCGATCTCTATGTGCGCTATATTGAATTAT
TAATGGAGTATAAGTATGCTTACATGTGTGTGTCTGTGAATATTTATTTT
CACTACTGTTGCCATTGACTTTGTGAACTTGTTGCAGGGTTTTGACGTGA
AACTTATCGATGTTAGTCGAACTTGTAAAGTCACAAAGGTAAAACTTGCT
CCTCAGTCTCTTCCCATATCTAATATTTAATTTGCTCATTTTACAATCGC
TGTTATAGGGAGGAAGAATTTTTAAATACACAGCAATGTTAGCTTGCGGT
AACTACAACGGCGTCATTGGTTTTGCAAAAGCAAAAGGACCAGCAATGCC
CGTTGCTGTTCAGAAGGTATGTTTTTTTTTAATGCAGTTCATGATTTATT
AGCTTACAATATAGCTACAGCAGGTTATTGGATATTCACTATAATATGCA
TGGTAATTTAATCATCTTATATGTGAATATTAGTCCTCGTGTTGCATGTG
TGCTTAATAAGAAGAGTTGATTAGGTAATTTGAAGGGCTTCGTTTTTCTT
TCTGGTATCTATGTAGTTTTGTCATATTACATCTGATTAGATGCATAGAA
GTGTTAATCTAATACTATGTATTTATCAAACTTCCAAATGACTATATGCA
TAAATGTTTATGTTAATTGAAATTAAGGAATCCACTTCTAAGTGGATGTG
CACTTTAGTGTGATGTATGAGAATTGTTCTACAGTCGCTAACCAATTTTT
ACAACAGGCGCATGAGAAGTGCTTTCAGAATCTACACTATATAGAGCGGC
ACGAGGAGCACACAATTGCACATGCAGTGCAAACATCATATAAGAAAACT
AAGGTGACTTATAGTTCGACACTTTTTGATTTTTTTTTCCTAAATTGTGA
GGGAAAGCCTTTTGGTTTCATTATCGTATAGAAATTGCTGAACTGTCTAT
TTGTTACACTCTAGGTTTATCTTTGGCCCGGCCAAACTTTGACGGGGATG
AAAGCAGGCAGGATTGTACAAACTGTGTTGAATCTAGCTGGCTTGAAAAA
TGTGAAATCTAAGGTATGGAATTTGAATTGTGGCTTGATCATGTTTCTTG
GCATAATGCTATTGTTTTGTAATATATATTTAATGTAGGTTGTTGGATCA
AGGAATCCCGATAATACAGTTAAAGCTCTTTTTAAGGCTCTAAATGCAGT
AAGTACATTTAGCATAGTTTTAATTTACACAATTATTTGAACTCTGTAGT
ATCTGTTGATAATTTTTTTCTCTGCTTCAAATTTCCAGATTGAAACCCCT
AAAGATGTTCAGCAGAAGTTTGGACGGACTGTCGTTGAGTCATACTTGCT
GTGATAGGTACGCGGGAGGCTGTTAATGGTTTACTGATAAAGCAGTCATC
AATTATTCCCCTTTGGCATTACATGATATTACTTCCAGTTTTTTCTTTAT
ATGTCCTTATTAAGACCGCACCATTATTTAAACATTTAAAGGGAGAAAAC
TGGCTTGCTTACTATGAAACTTTAATATAATCGAAGAAATCATGGTCTTA
ATTTTGATTAATCCTAGCAACTAAATTATTGAAATTTTTGAAGGGAAAGT
GGAAGCCCCCATTTTTTTGGACCACGGCATAAAAGCCAGCTCGGAATACA
TAGTCAGCATACGGGGTAGAGGAGAAAGTTTGACCTGCTGGTGACCAAAT
TTCATCTCTGGAATATCAAGTTTTGATGTTTTATCTTATATATAATAAAT
CCCAGC