| Relationships |
|---|
| The mRNA, DCAR_027121, is a part of gene, DCAR_027121. |
| The genetic_marker, MK001043 GSSR-044, is located in gene, DCAR_027121. |
| 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_027121 | DCAR_027121.mRNA | mRNA | DCARv2_Chr8:25923957..25930331 |
TGAGGTGAGGGCGCGTTTGTGACACGTATGTCCCCTCGGCGCCACGTGTG
AAATCCAACCCCAACCGTCGTGCTCATCGTACCTTGACTTTTCATCTGCA
GCACACTGTTAATAGGAGTAATTCACAGATACCCCTTTCTCTTCCCTCAA
CTTCACCCCAGCTCGCCAGGTTCTCTCTCTCTCTCTCGCTAAGTATCTTA
TGACAAATCTCTCTCTCTCAATATTCAAGTACCTTCTGACAAATCTCTCT
CTTCACACGCTCTCTCCCTCCCTCCCTCTCTCTCTCTCTCTCTCTCTCTC
GCCCCCTCCCTCTTTCTCCACACACACACAGTAGTTTATGTGATATGTAT
GTTTATGTATCTATGCGCTGTTTCTTTACTTGCTTTGACTAATTTCCCAT
TATTTTCATCGTCCAATTATGATTCTCTGCTACATAAAGATCATATCTTT
GATTCGAATCACTTCAATTTTATTTTAACAATCATTCTATTTTATTCATG
TGTTCAAGGGGTGCTTTGCACACTTGTTGTTTACAAAGATAATTAATTAC
TAAACTGCTACTGCCCCGAAAGTTTTTTATTTTTTAAGAATTCTTTTTCT
AGTAATGTCCATTTGTGGGGTTGAATTGAAAATTTGGTAATCGTAGGCAC
ATTTGTTTGACGGATTCGTAGTTTGATAATGTTTTGTTTAGTTTTGGTCG
TTGCTCATGGTTTTTGAATTTGTGTGAATGTGCACTGCTTGTGTTTCAGG
ACCGGCATACCTGCTCAAGGGTTTGGGCATTCTGCTAGTTGAATTATCGA
TTTTGTGAATGTAAAAAAATGAGTAGGACAAGAAACTTTTTGGTCGAATG
CGGGTCTGCTACTCCAAGTGAACCATATAACAGTCACGATGAGCTGTTGG
GTCTTGATCATGACATTGCACAGCTTACGAGGCTTAAGTCAGAACCTCAC
AAGTATATGAGTCGAAGATTACCGGGAAAGTCGATGTTGCCTATCTCCCC
TGTGGAAATGCTAGCGCGCCGGGAGGCTAACTTTTCTGGTCGTGGCAGGT
TTTCATCTGCAGATGGCTGTCATGTTTTGAACAGATACCTGCCAGTCAAT
GGGCCCTCTTTGATTGATACAATGGACAGCTCTGGTTATGTATCTCAGTT
CTCTGGTGATGGATCTCTTTTTGTGGCGGGATTTCAGGTATCTTTTGAGG
CATGGTTTTCATTTTGTAAAGATTAAAACTTGATGTGGATTAAGTTTGGA
TAAGCCTTTTACTCCCGTTCTCCTCAGGAAAGTCACATTAGGATCTATAA
TGTTGATAGTGGATGGAAAGTTCAGAAGGACATTCGTGCCAGAAGCTTGA
GATGGACAATTACTGACGCATCTCTTTCACCTGATCAACGTTTCCTTGTG
AGTTTATAACCATGATTAGACAATAGTTAATATGCTATGCACCAAAATGC
TGACTTAGTTTCTTTACTGTTTTTTTACTTTATTGTTAATGCCCTCAATT
TGTTGATGATGTATTGGGTTCCCTGTATCTGCTTTTACATGTTGCTTGAC
TGAATTTTTATAAATGCTAGTTCACTTTAAGGCTTTGAGCTCGCCCTTAG
TTTGAACATTCGTAGAAGGTTAAACCATAGCAAAGTAAAAATTTATTATT
ATTTCATTCTTTTGCTGGAAAGTGGAATCTAAAGCATATAGCATTTGACT
CGGCCATAAAATGCTTTATATATCTTCTGGAGTTATATGCCTAAGCAGTT
TTTAGGAATGTTTTTGGCTCCCATGACTTGATTATATTGACAATATGCCT
TGCTGACCTTCTAATAGCAGTGTCTGTCTTTTAGCCCCTGCTGGAGTAGG
TTCAAGTGTAGTTCTGTTAAAGTTTGTAGAGATTTATAAATTACATTACA
AAGGATATCACATAACTACTTCTTTGCACTGTCTCTCTTAATTCTGGAAA
TTCCCTTTCGAGTTTCGATCATGTAACCACTTGCACAGATTTATCTTAAA
AATTTGTGCCCTACATCAAGTTTTGTTATGTCATTCAATCAAGTAGGCAG
TTTTTAGTGCCGTGATGTGTTTTTACATACTATTGTGGCCAAGTCTTTAA
AATTTTAGGTTCTCCCTTTGTACATTAACTGCAGTCCTTTGAGAAAGACC
CAAGGACTTAATTATCAATTTAGGTTAAAAATATAACAGAACAATCTCTA
CACTAGATAATTAGTGAAAGAAATCCGATTTTCTGTTTGATTGTGCCGGC
CAGCTGCAATGATGAATAAAGCCAACAACTTTGCTTCGCTACATACTCAC
TTTTGTTGGAGGCCTATCTAATATTGTGCTGATGATATTTTCCATATCAG
CTAGTAGTGGCTTAAGACATATACTTAAATGATATGCTAACTCTTGCCGT
TTATGAAAATTATATTTATAGTTGGTCATATGCCTAATTATGGGCTTCTC
CTTGTTAGTTAATTTACACACGTTCTCACGCCTAAAGTAACATGTCTCAT
ATTTAACATCTAAAAGTGCAATTCTATGCTTAAAGACAGTGACAAGGCTA
TACACACTCTAATACAAGGATTCATGGTTTCCTTTTGTTTGACCCCTCAT
TAATATTTCTTTACCCACAATCGAAGTTGAATGTCTATAGCGGAAAATTC
TGAGAAATTTTTGTTATATTGCAGGTTTATTCCAGCATGTCCCCCATTGT
TCATATTGTTAACATTGGATCTGCAGCAACAGAGTCTGTTGCAAATATTA
CAGTAAGTCCTGAAAGTTCATCCTTAGATTTAATATAGAATAATACAATG
TCCATATTTATCTGTTTTAAGGTATAATGTGTTTAAGAAACATTTTCATC
ATCGAAGCTCTGTTATGCAGGAAATTCACGAGGGTCTTGATTTTTCTGCT
GGTTATGACTTTGAAGATGACGATTATTATTACGATGCTTTTGGAATATT
CTCTGTAAAATTTTCAAATGATGGACGAGAACTTGTGGCAGCAAGTAGTG
ATGCTTCAATATATATCTATGATCTTGGTGCCAATAAGCTTTCCATGCGG
TTCCCTGCTCACATGGTATTATAATTCCTGTTAGTATTTTTTGTGAGAAC
TGTCTGAATTTATGAATAATTATGTTTTATTGTTAATTTCAAAAAAAATT
ATGTTTTATTGTTATCTGCAAGTTTCACACGAAAGCGAGTTAACCTATCC
TGTAGCTGTCCTAATCCTTACAAATCCTATCCTGTTCGCAGATTTAAGTT
ACCTAATCATTTTGAAATGTAATTAGGCGATTTATTTCCTGTGCTGTTGT
GAATAGGTTTCTGACTTTCTTCATTGTGGTAATCTCAAACATACTTATTT
AGTATGAGGGATCTGTACATTTTCTAGATGCAAATCACTTGATGCAGATT
TTATGTGGTATATTGGGACCCTAGTCACGTATAGGGGTGTGTATCGGGTG
ATTTGGTTGGGTTTGGACCGTATAACTAAACCCTAACTTTTAGGTTTTTG
ATTTTTTAAACCAGAACCAAATCCAAAACCATATACATTCAAACCAAACC
AACCTGAATCAAAACGGTTTCGGTTCAAAACAGTTGCTAAGGCTATTTTA
TGTTTACTTCCTCAAAAATACAAGGTTCAATTAGTAAAATGAAACAAAAT
TAATTGGCAACAAAAATCGTAGCATTAAATTAGTAGCACCAATAACTTTT
GACAGGTTTGTGACCTGAAATGAAAATATAAAATTATAATATTATTCCTA
GTAGCAGCCAGGTACGCGGTTGTCCATAATGTTTTCCTGGTTTCCTTGAT
CATTTTTAATTGAACAAATTGCTTTGATTTGTTATTCTATATATTTAGGC
TCTATACTCTTCTGCTATACTGTAAAATAAATTATTTAATGCTTATGCTT
TTGCCTTGGATTAATAAATCAGTCTCATTCTTTGATTGTAAAGTTTGAAA
AACTATATATTATATAAACATTTTCAAGAAATTGGACCGAGATTACTAGG
CCACTGTAATTATGCTTTGTTCTGTGAACAGGGATTAGTTTTTTCATGAT
TCGGACGTGTCATTTTGCATTCCCAATCATGATGCGGATTATGATCCCCT
CCCATTGTTGTTATAGATTGTAGAGATGGCAATCGGGTTGAATCGGATAT
GGCACTATCCAAAATCAAACCTGGATTTTTTATCCATGCTCAAACCCAAG
TTGAATCCAAAAAATACCCGAAAATGAGAACCTGAACCCGATTCTACGGA
TTTCGGATCGGATTTGGGTATACCCGAAACCCGATCTTTTTCAAGATTGG
ATATGGATATACCCAAAATCTGAAACCCGGACCCGAAATTTGTGGACTCC
ATAGAATTTAACGCCTTTTGGCTTGAGCTGGTAGAGAATATTTGTGTTTG
TGTTTACAGTTTGGACAAATTATGTAGGTCATCATTGGAGATGCCCCCTC
ACTTGGTGAATCATGTTGGATTGAGTGAACCACATAATTCCTTATTTGGT
GTGATTACTTGATAGCTACCTTTCACTCAGTTTGCCACTTTTTCTACTCT
GTCAAAAACAGTAATGTAAATCTGACACTTAATTGATGACTTATTTGCAT
TTTCTGCTCCAGTGTGATGTGAACACAGTGTGCTTTGCTGATGAAAGTGG
TCATATCATATATTCTGGGAGTGATGATGGACTGTGTAAGGTAAACATTT
TATTTCTTTATTTTCTGCCAAAAGTAGTTGTTGGCATTGAACTGCCTAAG
ACTTGCTTCCTGCATATACTGCCTCTTAGCATTTGTGAATCAAATTAGCA
CAGGCTCCCATCAAAATTTTGTTTTTTGTTTCAAATTGCCAGACCATCTT
ATAAGGGGTGCTTAAAGTTTTGGTAGTCTGTCATGAGTCATGATTATCAT
AAATACTGATGATTGAGAATTATAATGCTTAATTTTCTATCTTATACAGG
TTTTGGACAGACGTTGTCTCATTAATAACGAACAAGCATCTGGGGTTTTA
GTTGGCCATCTAGAAGGTGTAACATTTATTGATAGTCGAGGTGATGGCCG
TTATCTTATCTCAAATGGAAAAGATCAGACTATTAAACTATGGGATATCC
GGAAGATGTCCTCTAATCTTTCTCAGTATGTCTTCTATCTTTCTTCTACC
CCATTGCACATGTTTGACTTTTTGTTTAAGGATTTACTATTTAAGAGCTC
ATATACTTTTTATGGCATCTCTGCTGGCCTAGCTGTTTGTGCTGTCAGCT
CACTAAATTGTCAATTAAATTTTGAATTGTCAATCAAGTTTTAAATGAAG
GTTCACAAGATGAATTATTAGCTACCACTTGTCAATTGAATTTAAGAGAT
TTGTCGCCTTGTAAGATCTGAACGTGGTCTGTGCCTCTCTCCCTACAAAT
TTTATATTATCAATCTCATTAGTTTCTTATGCAGTAATCCATATAAAAGA
AACGTAAGATGGGACTACAGATGGATGGAGTACCCAGTTCGTCTAAGAAA
TTCTCGTCATCCGAATGATATTTCTTTGGCGACATATAAAGGTCATTCAG
TTTTGCGTACCCTCATACGGTGTTACTTCTCACCAGCATACAGGTGAGAT
TGAAGTGATTTACCCTGTGTATGTTTTCAAGTTATTTTCTGCAACCTACT
TACTTAATAACATAATAACATGATATTTCTATAGAACTGTTATTTAGCCT
ATTTAGTCGGTGAACATTCTTGATTGTTACTGTAGTTTTTCATGAGAGTT
TGACTTGGCACCATTTGGTTCTGCAGTCAAGCTTTTCTTGTTGATCTGGA
TTTACCTAGTCTATTGTCCCATATGCTATTAATTGCATCTACTCTCTATG
CTAATTAGCTGAACTTCTAGTATTACTAGTACTTTCCTAATTTTAGGATT
TTATTAATCGGATTAATTACCCTAGTTTTCAAGTGCTAGTCGAACTTCTA
GTATTACTAGTACTTTTCCTAATTTTAGTATTTTATTAATCAGAATAATT
ACCCTAGTTTTCAAGTGCTGATAGTGGTATTAACAGCGTCCATTTTCATG
GATTACTCTTTATATGAATCAGAAAATTTAAAAGGGTAGGAGGTACAAAA
AAAATACTGTATGGCCGGAAAACCTTAACTTCCCTCACTTCTGAGCCCCC
CACCTCTTTTGAATGAAATAGAATCTCCTTGGTGAAGAAACCCTGCCTAA
TAGTAGCTGACTTGATGAACGATCTTGTTGAGTTAAACTCATCCATCTAA
GAAATCCCTTTTGCCTTTTACTTTGAGGCCAGTCCTATTCCTGTAGGGTA
AAATTTTTAATATCGACGCTAAAAATGTCAACAGACAAACAATTACTGAC
ACATTATATGTGCTGGAAACTAGACTTTTACTGATTTCCTGCATATTGGT
TCTGTTATAGCTTTTGCCAGTAGTCTAGTCTATTCGTCATATTGCAGCAG
ATGTGCTGCCTTTAAGATATTCTTGGATCTTTTATGATGACAACTTTCTA
GCATCAAAGGATTCTCTCTGCTAATGAATTACTTGTGTAGTTACCTGCAT
TTTTTACTTGGTGCAGCACTGGTCAGAAGTACATTTACACCGGATCTGCT
GATGATTCAGTATATATATATGATCTGGTAAGCTTTCAGTTTGGTAACTC
TTACGCTCCTGCATTGCAATTTATACTTATTTGTCATCAAGAGCCATTCA
ATGTAGAAAGCCATCCTTTTGTGCATTTTGTTCATACATGTAAAAAGGCA
AATCAGGATAAGATTTTCTTAATCACGTGATGGTCCAAACTTTTGAGGTC
GATGTAAAGTATTAAATTTAAGGGACGTGTTGGCTATATAGTCCCCATGG
TCTTGTGTAGCTGAGCTGTCCACCTTGTAAACTGGTAACATTTGTATATC
AATATAACAACGATACCCTTGACAGTAGTTTATAGTGAAATCTACTCAAC
GCAATGTGTTCATGTTATCTCGTTTGCTTTAATGGTGCTCAAATTTGATA
TATCGCCGTAATTGGTTGCAGTTAACTGGAGCTCAGGTTGCCAAACTCGA
TTATCATGAAGGTCCTGTAAGAGATTGTAGCTGGCACCCGAACTACCCTA
CTCTAGTTAGCTCTTCATGGGATGGAACTGTTGCAAAATGGGACTTCTCT
GATAAATCTTTAAACCAATCCTCTGAGACTGAGACAGTCTAGTCAAATTT
GGTGGAGCGTCTACTAAATTGTCAGCTATCCAGCAATATTGACATGTTCT
GTAAATTATGTCTAGTCTAAAATTCTAGAGCTCTGTCTCTAGACTGTGTT
TAAATTATCGAAATAAATATTTTTCTTATATTGTAATTAACGACTAGAAA
AAAGATGGTGCAGTTTTTACCTTATAATCCCCCGAGTCATATAACATTAC
ACACAGAATACATGAATACAAGCCAGTTTTATCACCAACAATTTGTTCTT
TACAGTGGT