| Relationships |
|---|
| The mRNA, DCAR_009052, is a part of gene, DCAR_009052. |
| The genetic_marker, MK005268 K2712, is located in gene, DCAR_009052. |
| 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_009052 | DCAR_009052.mRNA | mRNA | DCARv2_Chr3:3948982..3956686 |
AAATCTCTTGGATACACCCCTTAGGCGCGTGACTCATCATTTCACACACA
TTTATATATGACCTAAACCCCTCTCTTTTCGAATTTTTGCGGAGATCAAT
TCCAATCCTTGCTCTTCTTGTAAGCATAAAGATTTGATTCTTGCACCTTT
TTGGCTCTAATTGCATCGGTTTGTGTCGAGATTCGATTCGAATTTGTGAT
TGAGATTTGAATCTTGGAGCTTGTGGATCTTTGTGATGGAAGAATCGGGT
CAACAGGGTCCGGATCGGGTCGTGCCCGTGTCGAATTCCACCTCACCGGT
TGCTGGTATGTGTATGTGTATACATGTTATAAAGATTAATTGTTTTAGTT
AAGTCTTGATTTTTATAGTTTTCAATTTGATTGTGTGATTTTTTTGGTGA
TTTAAGTGAATTTGGGATTTAGGGTTTTTGAGAATTGGGGTTGTGGGATA
TGTGGAAATGTGTGTGGGTTTTGTTGGTTATGATTTATGAGTTTGCGGGT
ATTGGTTTTCGAGCTGTTGTGTAATTGTTATTAGTGCAGAGAATGATGTT
AAGCTATCGGAGATGGTATAAGTTAGTTTGGTAGTTTTTATACTGTGATT
CCTATTTGGCCCGCCTCCAGTATGGTGTTAAGAGTGAGATTCTGGGGTTA
TTGGGATATATCGAAATGTGTTCGTGGTTTGTTGATTACGCTATTTGTAT
GTGAGTCGTAGTTGAATTTTGTGATTCCGTATACTGTACTGTGTTTTGTC
TTTGGACGGCTTCAATTTGATGGTATGTGTGTTTGTGTGTGTTAGGATTT
TAGATTTTAAGTATTTGCATGAAGAGGTGTAAGGATCTGAACCCATGAAC
TTGTCCTTTTTTATACCTATATAATTGCTTAATTTAACTGCACCTATGAG
GTTTGGTGAGAAGTATTGTAGTGTTCATTAGTCCATTGTGTTGTACAATG
TGTAAGTAGTTTTCAAGTTCGAATGGCTTATTATTTGTTCCTTCAGTTTC
TGTATGTTTAGTTGTCTAGCAAATGATTATGATCACAACCATCGTAGCTT
TGATCTGGGTTCTACTTGTCTCTTCCTTTGCCTACATCAAATAAGCAGAA
TTATATGCTGCACTTATCAGTTCCAATTAATCTAATAAGATAATATGATC
AGCTGGTATTTAACAAGTGAGTTGCTTCTGGATTGAAATTATTATCGCTC
AATGCTGTAGTAGCTTATAGGCAACTATGTCAAGACAAGTGTAATAGGGG
TAGCATTTCTATGGTTGGAGTCAGCTGAATAATATATTATGTAGGTGGAT
CAGATAGTCACACTTTTAGTTGTTGAAAGAATATTTTCAAAGACATAGTT
ATTCCTCTCAGTTATGATTTCATTTAGAAATTTGACTTTATTTTGGTGGT
ATCCAAATTGGTTCTCTGCTTTTATAGCTTTTAATGAGTACTCAGTGACC
TATCTTTTAGTGTTTTTTTTTGGCAAACTGACCAATCTGTTGATTGATGC
AGTTGAGAGTCATTTTAGTCCTGATAACCGGATTGAACAGGTAATTAAGA
TGCACACCTGCATCTTCTTTTCACTTGTATAGTTTTATCTGAAATGTTTA
TTGTTCCTTATTGATACTTCTAAGTTTTTGCTGTCAGATATTGCAACCTA
AAGAGGATAAGGTTGTATCAGCGAGTTCTCTAAATACCACCATTGCTGGG
CCGCCAAGCATTATAACAGGCCCGCCAGAAATCTTGGCTTCAAGTGGAGC
ACTTGCCACATCCTACCAGCCCAATGCATATGCTCCGCTAGAACAAAGTT
TCTACTATGGAGGTTATATATCTAGTCAGTCCGCATTATGCTTTAAACAA
AATGAGTGGATAAATCCCAACCACTTGTAATTACTTGATAATTTGCCCTA
GAAATTCTATTAGGTATTTATTCAAAGTTCTATGGAAAAGAAAGAGTCAG
ATAGGAGTTATATCGTATTGTGACCTTTGTCTGACTGCAATCTAAATGGA
AAGGTTGTCGAGATTGGTAGTACTAGGGGCTTGATATGCTGCTCTATGTA
TCATCTTTTAAGCAGTAGTGATTAAATTGTTGTGAAAACGAGCAACTATT
GGTGTATTAGCTGACATACAAAAAAGAGTTCCGATCATAATACCATATGT
TGATCAAATGTTTGCATCGATATTTGATGACTTCCATTAATTTCTTCCTG
CTACCTTTAGTTTTAAAAAATGACCTGGTTTGAGATTTGAAGTAGTTGGA
GGGTGGTTGTGTGAGTGAGTAGTGCCATGTGTGGTTATTTTGAGTAACAG
AATGAGCATATGAAGGTGGTGATGAATTTTGTGTTGCAAGTAAATGCAAT
TTGTTCAAGATGTTTTTGTGGAAGGAGAGTCGGCTTCGAAGGGTTTCTGA
TTTAATTGAGCTGGCTTGGTTAGCAACCATTGAGTACTAATTTTGACAGC
TTTAAAAATTTTATGCCAACGCAGAACTTTCTTGTGTTTGATGATTTCTC
CTAATGTCTAATAGGCATGCTGACTTGAAACTAACTTCTTCGACTATATG
TAGCTAAATTGGCATTGGATTTAGTTTACTCTCCTGCTAGTTTAGTTAGC
AATTCCTGGCATGCCATTCTCATATTGCTTTTGGTTGATGTATTGCTTAC
CTAACTAAATTTCTCTTTGATCTTATTACTCATCTCCTTTCTTTGTTCAT
GCTTCAGGTTACGAGAACAATGCTGGTAACTGGGGGGAGTATCCTAACTA
TGTTAATGCAAACAACTTGCAGATAATACCTCCAGTGAGTAAAGCTTGTT
TCAAACAATATAATTTATTTATTTTTAAGTTTATTGCCTTTGGATTAACT
CACTAGATGTTCTTATGATCAATCATAGGCTATGTTCAACGATAATTCCT
CACTCTTTTATCCTTCCGGCTATAGCTTTGATACACAAATGGCCTATGGC
CAGTTTCCTCCTCTGGCCAGCCCAATGTCCCCATTTTTGGTTGATGGTCA
GCTGTACTCACCACATCAAATACCCATGTCGCCGAATTTTTATCCGCAGT
CAATCTCTCCTGGACTGCCCCATGTCGGATCATCTCATTCAATGTCTCAA
ACTGAGATGGCGACCCCAGTAAGTACAGGTCAAGACAGTGTTAATGATAA
TATGCTTCTTGGACCAGGATCTGGTTATTACTTGCATTTTGGATCATTTC
CTGCTAGTAGTGCACCTGCAAACAGTAGCCTTGGCTTGTACAAGTATCCA
GGAGAGTTTGGATCTGGTGAAAATCCACTAATTCGATCGAATTCCAACGA
CACGGGTAACATTTTGTCTCCGTTGACCCCAGGAGCAGTTTACACCCAGC
CTGTTGGCATACTTGGATCATATGACCACAGCCTGGCACAGGTTCGTCCT
CTAAATAGGAAATTTTCTGTTACAGTAATCTGAACCATGAGAATATTGTT
ATTAAAAATATGTTATTGCTTCTAGATGTACTCTTTTTTTGTCTTATATT
TCAGTGACCAAAGTTATTGTGTTGATGTTATATAGCACTATTATGATTGT
TACCATCACCACATTTATGTTAAAATCAATATTTAGGTGCTCTCGTAAAA
GCTCGTAATTTTTAAGAATCAAAATTGGAAGCTTATAATTTTTTAAGAAT
CAGAATTGTGAAGACAGAGAAAACAACTAAATAAATATATAATAATAAAT
ATATGATGACAATGAAAATAAAATCATACTGACATATACTATATCTTCAT
TGGTTTCTCCCTTCTGCATTTTTGTTTTTTCCTATGTAGAAGTACCCCTC
TATTAGGATACACCCAAATGTAAACCTATAAGACTATACTTTGAGTTAAA
CGTTAAAACTGCTGTCAATAACATCATGTTTGAGGGAACTCTTTGGTTCT
TTGATACACACTTTAAGTATTCCTTGGGCAATGGTTTCTGACTACAAGTT
AATTGCAATACTGATTTTATGTACATGGGTTCTTGATGTGTTGCTTGTTA
TTTTATTGGTCACTTCCATGCTTTATTATGACTTGTTTTCCTCTTTCTTC
ATGAAGTCGAGTTTGATATTTACACTACATATTAAAAGAAAGGTTGGATA
TTTACACCACGAACCTCCTTTCTATTACCCATTTGCAGGGTGGAAGTATG
CAGTTAATCATTTATCTTTGCAGTTTGACAAGTTTGTCTTTGCAATATCT
TCCCTGATCTTGAATCAATACTAAACTGCAGATTATACTGTTAGAAAAAC
TCTTGGTTTCTCATTACTAGTATGACCCGTCCAAGACAGGAAAAAAAAAA
TTGCACATGTTTTTGGGGTACACTTCACTTGAACTATATTTGAACTTGTT
AGAGTACAACTCCTTAAATCATTAGCTGGGGACTGGAGAGTTCTATAATA
AAAATTGAGTCTATTAATTAAATTGAGAAAAGAAATATATCATATGTTTT
ATAATCAAGACCAATAAAGTTTATTATTATTAAGTTCTATAAGCAGTCGA
GTATTAATTTATTAAAGTTTAACACAGTTTATGTATGGTAATTTGAATGA
TTTTTTTTTTATATGGAACTTGTTACATGAAAAATGTGTCTAAATATATA
TGATATTTTGCAGGCTTCTCAGCAGCAAATACCATTTACAAGGCGCTATC
ATAATAGTACATCTTCTAGAATGTCAAACTATGGGAACTGGGATGCTAGT
CGCTCCAACCGATTCACTCCTGATAAAGGTGGAAGAAGGGATAGGGACTC
AATCAGTATTTCTGCTGATTCACATGGCAATGCCAACGACCGTAATCGAG
GTCCAAGAGCATTGAAGCCAAAAATAAAAACTAGTACTGAAGAAAAGGCT
GCACCTGGTGTTGCAAAAGCAGGCGCATCGACTTCTGGAGTCAATCTTGA
TCTATACAACCAACCAGATTTTGTCACAGACTATGAGCGAGCCAAGTTCT
TTGTCATCAAGTCTTTTAGTGAAGACAATGTTCACAAAAGTATTAAATAT
TGTGTTTGGGCCAGCACACCCCTTGGGAACAGGAAACTGGATGCTGCCTT
TCAAGAAGCTAAGGATTCTAATAGCATATACCCCGTTTTTCTCTTCTTCT
CGGTATGCTACTTACTTTTTTTAAATCAGATTTATTAGGTATTATCTTGA
TTGAATATAAATCATAATTTGTATAATCACTTAATAAAATTATAAAATAT
GGGTATGTGGATATACATGGTGGTTCATCAGTTCTGCTCATCAGAAATCT
GATTAAAAGCAACACCGACTACGGATCCTGGGGATTGCCTAGTTGTATTT
GTGAACTTGCACATATTTACAAACCAACCTGCAGTTGTTTGGATCTAATT
TGACTAAACACTCCCTATCAAAGTTTTGTAGTGTGAATCATTATTTGTTT
GGTAAGTGTAATGTGATAATATTTTGCCTTACCGTATGCTAGAATAAAAC
AGTGTGTGGTGAATGGTGATTCAAATTTCATATATAGGTTTCTCATATTG
ATCTTTGATTGGACTTAGAAATGAATAATCTTCAACTAAGATCTGTAGTG
ATTATGTTATTGCAGTACTCTCTGTTCTATAAAGAGGCCATATCTATCGT
TAGAGAAGTTAGAAACTCTTAAATGTAGGTTGTGTCATGGATTAGGATCC
AAAACACTTTTCTCTTCTCTCAGTGGTTGCGCTTAATCTGTTATACTGAA
TCGGGTTTCTCAACTTTGCTTTCCTACATCAGAATGTTTATATTATTTTG
GAACATAAGTATACTGGATGTGGTAAATATCAATTTGTGTTAAGCTCTTA
TGTGGGTTGTACAGTTTAAAGACTACTGCATAATTGGCAGGCTATTAACT
CTTACATTTAGGTGTTTGTGGAACAATCGCTTATGTATGTTTTTTAAGTA
TTTGAATAAATCGTCTATATTTAAGCAAGATCTATATTTCTTGTTTAATA
GTATTTCCATATGACTTATTTAAACAGGGCATTTATTAATTGTTTACTTC
ATTTCTTATTAATTAAGGAATTCATACTGTTGAAAGATGATAATCAATCG
GATAAATAGTTATCTGCAAGACAGGAGTGTACTCGATGCAAGTCGTTATA
TTTAAATACCTAGGAAGAAGCTGAATACTTGACTCGTTGTTAAAAAGATA
GGCAAATGAATTTTGTTTGATGAAGAGTTGCAATGTATGAAAATTAGATA
TTGCACCAATTTCTCTATCTGTATATGTTTGCATTTATTTATGTTCGTGG
TTCACTTTGTTCTAAGCCACATTTTTAATCACTATTTATACACTTTGCAG
GTTAATGCTAGCGGGCAGTTCTGTGGTGTGGCTGAAATGACTGGCCCTGT
CGATTTTGAGAATGATGCAGATTACTGGCAGCAGGATAGATGGAGTGGGC
AATTTCCTGTCAAGTGGCATATAATAAAAGATATACCAAATGGTCGATTT
CGCCATATTCTTCTGGACAACAATGAAAATAAGCCCGTCACTCACAGCCG
AGACTCTCAGGAGGTACGTACCAGTTAAAGTTTTGTTTACACTTTACAGT
TACTCTTTGTTCTTACAAGTCTATTTCTTTTTATCGTCAACTGTTATTAC
CTGGGGGGAAATTGAGAAAAACAAAAGGATGTGTAGCAGTTTTTTAAGAT
TTGTTGGTCGGTTCAATGTGTTGGCATTTCTCATTTAATCTTTTCAAGAC
CATGTGTTTCTTATATTCTCAAATCTCACCCCTACACACATCTCTTCCTT
ATAGCTACCTGTACTTTTAGGTGGCGAGCCACCTTAAGGGGCTCTGAGTC
AGTTGATTTGGACTTTGGTAGTAAGGTGTATTATTTTCCTAGATAGTTTA
TGGCTTTATACTGTTTTCATTAGCTTTTGAGATACACTTGCCAGTCCGAT
TGCTGATTTAGCCTTTTTATTCACCAGACTTTTCTACTGCTACCATACTT
GTTGAAAAGCCCTATCTAAGGATTCGAATTATTCTACAGCAAAGCGAAAT
ATTGTTCACTTTATTAAGTTAAAATTACCTGTTTGGGCATCTTTGTCCAC
CATACCTACAATATGATGATTTCAACACTCCGTGTTACACTATTACTAGA
GTCAAAGTTTTACTCTGTAATTCTATCCATATGTATTGAAGTCCACCTTT
TTAAATTTGAATATCCCATAGTTTGGTAATTATATATAAACAGTGCCCGT
TTGGATACTTAAAATAATGACTTACGACTTGAAGTGTTTTAAAGTGACAA
GTCCAAGGTAAAAATTGTTTGTTTGGGTAATTTTGCATTATGACAAGTGA
TAACTTAGTAATAAAAAATAAATTTGATAGCTTATCTATTTGAATGGTAA
TATTGACTTTTATCATTTAAAAATATAAAATTAAAATAATTTGTTCAAGA
AGTACCTCTTACTAACTTCTGGCTTTAAGCCAGTTTCTAGCTTATTTTTA
ACTTTAAGTCAGTTTCTGACTTGTTACAATGTACCATTCCATTAAATCTT
TTAGGTCCTGACTTCACCAAACAGACACTTTTTAACTTCCAAGTCAATAA
TGACTTTAAGCTCAAACAAACAAGCTGAGGTTATATCATCTGTTCTGTTT
CGATTTTTGACCTCTGTTTATTGTCAGAATTTGGCCTTTTCACTTTGATT
GAGCTGATCTTGCAACATTTGTTACGACACAAACATGATATTTCTTCGTA
ATTTTGTTCAGGTGAAGCTTGAACAAGGTCTTGCGATGTTAAAAATATTC
AAAGAGCATGAAGCTGATACATCAATGTTGGATGATTTTGTTTATTATGA
TGAGAAGGAGCGTTCGTTGCAGGAAAAGAGAGCTAAACAGTCAAGTCCGG
GCAAAATACCTGATGCTTCAATAACTCAATTATCTGAGAACCTGGCTGGT
ACCCTTCATCTGAAAGTCATTGAAGACAAACAAAAGTAATTTGTGGAGGC
GAAGCCAAATTAATAGGTGGAATTGATGTAAGCTGGGTTTTGGCCATTTA
GGGATAGAAATACTAAGCAGCCAAATGTTGCTACTTTAAGCAAAGAAAGC
AATGAGAGGGAGTATTCTGCTTTTGTATTTTCTGGTCAATTAAGTTCATC
TGTACACTAAGTTTCTCTATCTTTCACCTTCACCTTAGTTTCTTTTTCTT
TTTTACTATTAATGAGCATTACCCCGGCTATCTGGGTATTCTTGGCTAAA
GATTTGGGAGG