| Relationships |
|---|
| The mRNA, DCAR_026353, is a part of gene, DCAR_026353. |
| The genetic_marker, MK009787 7_35589231, is located in gene, DCAR_026353. |
| 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_026353 | DCAR_026353.mRNA | mRNA | DCARv2_Chr7:35589043..35596846 |
ATGTCAACTGAAAGCTTGTTCATACCAGTTAAACTGCCTCAACAAAAACA
CTACAACAATGGCATCACCTTCCCGGCTGTTCTGTCACCAAACCCTGAAA
AATTATCCAACAACACAGTTCCTTTTTCCAGTGTTTTACAGGCTATAAAA
TCATCAGCAGCAGCCCTGGAAAGTCTTCTTAGTGAAACAGGGGCGATCCT
GTTCAAGGGCTTCCCGGTTGTGTCAGCTTCTGATTTCAATGATGTTGTCG
AGGCTTTCGGGTTTCTTGAGCTGCCTTATGTTGGTGGCGCCGCCCCGCGG
AGTAATGTCGTGGGACGGGTCTTTACGGCTAATGAGTCTCCTCCTGATCA
GAAGATTCCGTTTCATCATGAAATGGCTCAGGTACATCCTGCTCCGATAC
AAACCTTCTTAAAATATATAATAAAAAAAAAAATCTTTAATGCTCCCTTC
ATTATTTATATATAATTGTTTTGAGATTAGCTAGAAAAGTCAAACAACCT
GTATAAAAAACAGAGGACCGCGTTAGAATATGCTTTCGACTTAAAAGTTA
AAAATCACTTAAATTCTTAATATAAACTACATGTTATACGATTGTACAAA
TTTCATAATGTGCTTATATTGCTATCCCTGTGTGCTTGTGTACAATGATT
GTAATAGGTACTTGTATTAATCTACTAAGAATCTAGGTTATTTGGCATGC
TTAAGCACAATTTATGAATGTAGTTTTAGCTTTTATCATAGTTGAGCACT
TTCTTGGCGCATACTGTATATAGGTATTAGGTTCTAGCAATTTTGCTCAG
TAGTGTGGTTGAATATATGGTATTGTTAGTGAATAGCACGTTGTATTTTA
GTAATTTGTATTGAAAGTGTTTCGGTTCTGGTCATATTGGGCGAAACTTA
GTGAATCCTTTGTGATAGGTACCCGAGTTCCCGGCCAAATTGTTCTTCTT
TTGTGAAGTAGAACCAGGTAGCGGAGGAGAAACACCTATTGTTCTTAGCC
ATATTATTTATGAGAGGATGAAGGACAAGTACCCGGACTTTGTTGAAAAA
TTGGAAGATACCGGATTGATCTACACAAGAGTGCTGGGAGAAGATGATGA
TCCTTCGTCTCCAATTGGCCGTGGCTGGAAATCTACGTTTTTGACCAAAG
ACAAGAGCGTTGCTGAGGAAAGGTTTGTAGTTTCGACCTTATTACTTCTA
GTTTGAAGTTCATATATTCTAGATGTCACTGGATGAAACTTCTCGGAACA
AAAACTAATAATGGAATGATGTACTAATCAATTTTTAGAAAAAAATTATA
GACCTAGTAGAGATCATAAAGTGTAGAGTAATTCACGTATATATTGGGTG
ATTAACAGAGCTGCTAAGCTGGGGATGAAGTTGGAGTGGATGGAGGATTC
AGTGAAGACTATAATGGGTCCAATTCCAGCAATCAAATACGACAAGGAAA
GGCAACGCAAGATTTGGTTTAATAGCATGGTTGCTGCATATACCGGATGG
AAAGATGCACGAAATGATCCTGTAAAAGCTGTCACATTCGGAGATGGTCA
AGCATTGCCAGCACATATTATCTACGACTGCTTGAGGATTCTTGATGAGG
AAAGTGTTGCCATTCCTTGGCAGAAGGGGGATGTTCTGCTGCTGGATAAT
CTGGCTGTTCTGCACTCCAGAAGATCATTTGAACCGCCACGACGAGTGCT
GGCATCACTTTGCAAGTGAAACGAGGTGGAGTTACTCCCACAGGCACCAG
TGTGCTCCTCACTCTGTATGTGCCTGACTGGCCATTGATGTTATATATAG
TTTTCTCTGAATCAGAATGACATTTTGATGCATGTTGAGCCATATATAAC
CAAACCAAACCAAACATACTCAGTATATCCCGCTTAGAGCAGGGTCTGAG
GAGGGTAAGATGTACGCAGCCTTGCCCCTACCCTTAAAGTAGAGAGGCTG
TTTCCGTGAAGACCCCCGACTTAGTGCACAATAAATAAAATAGTGTGTGC
TATAATAAGAATATAATACCTTAGCCCATGGCTTTCTTCACACGGGACTT
ACCTAAACAGTTCTGTTTGTCGACGATGGGTGATAATGATCTGAAACGGA
GATATCAAACCGGATAAGAACCGCCATTTCACACTTTCTTGAATTATGTA
AGCCATCCATGTCGATTCTCTTTTATCCACGCAAATCCTTCGATGAACCA
AAATCCGGGGATGAACCAAAATCCGGGATGACGCATTGATACGCATTGTT
GAGTAAATCTGAAGTAGAAAACATGCATGGCCTTTTCTTTCAATCTCCGA
ATTTCCACCACTTGAATTGAGTAAATCTTGATCGTTACGAGCAGTGAAAA
GGATAGAAGCAGTTTCATCACCAACAAGACACTCAGACACGCGAGTCTTC
CTAAGAGAAGGAATCTTAGATTGACCCTTCTTCAACACATCTTCACTACT
CACAACCTTAACCACAACGTTGTGCCCCTGAGTCCCCGGTTTCAAAGCAT
CCACCTTCACAAAAACCGCCTTCCTCGAGTGAGGGTGATTGAATTAAATA
TAAATTATGTGCATATTTGACTATTGCTAAAAATGTAGAAAAACGTTGTT
TACTACTCCGTCATAACATATCTTTCCTTAATTTAATTTGTGCATATATG
TTAATGTATAATGCAAACCAAGTCAGATTTTAAGGCTGCTAAACTACCAA
CGACAATCTGTCTGATCGATGAATCCTCTGATATCAGGTACTGCGTAGTT
GGAATTCAGATGTTTAACACCAAAATTTAGGAGATTGAGCCATACCATAT
ACACGTCTGGTCGATGAATTCTATGATACTTTGGTAGTTAGGATTTTATC
TCATTCCACTAATTTAAAAAGAGAAGAAGGAAAAGAAATTGAATTTAGGA
GATTGAGCCATACCATATACATGTCCAATTCATGAATTCTCTAATACTTT
GCTAGTTAGCAATTTTATCTCATTCCACTAATTTAAAAAGAGAAAAAGGG
AAAAAAAATTAATTGTTTTTGTCCTTTTTCGTTTTGAGATATCTAATCCA
ATTTTTTATATTTCAAAATTTATCAAATATAATAAAATTTTATAATATAA
AAATCAACTACTCCCGTTATTTTTATTTATTGTACTTATTTTATATATTA
AATATCAACTGGTCATATCATTACCTTTATTTTTATTACCTTTTCACTCT
TACTTTAATATATTTTTTAATTTCATTCTAACTCAAATTTAAACATTTAA
ATGGCACGAAGGGAATATAAATAATTAATTGCTAACTATTTCAAACAAAG
CATATACTGTAAGCTTTCGAGAAGAAAAAGTATCATAACAGTAATTAAGC
AACCCGGTCAGCTACCTGTCTTTGACTTTTTTCACTTTGCTTTATTTCTT
TCAAGACTTCACTGTAAATACACATTTGCACGTGAGATTAGACTTAACCT
GTGAAAATAATCGTGTGATTAGAAAAGTTGATAATGACTTTCTTGCACTG
TGTCTATTTCTTTAACTTTGCTTTATACTGTGTATTTTATTTACTTAATG
TTGGAGTTTCAACTTGCTTGTTTAATTATGATGAATCTGCCTAATTAGTG
ACCAGCTATGACATCTGTATGCATCTTTTCGTTTATTTATATGTAAAGTT
TAGGATAAGTTAGCCATTTTGATCAAAATAAAACTTTACCGTTTGTTTAA
AGAGATGAGTATATGATTCCCCTCCCTATTAATAAAATATGTCTCTTTAT
AAATTGATATATTTATTTAGAGGGTTTTCTGTTTATTTTTGTATATGATG
TGAGTTCATATTAGTGATTCGTGGTACTTATTCATTGTCAGCTATACGTG
ATAAAAAAAAGTTTATATTATTCATAATATTTATGTTCGTTATTCGTGAT
ACCTGAGCAGAAATTTATGACATCATAACACTCATGATTGTGCGTGCACA
CGATGAATTATAACTTTTAAAAAAAATTATATATTATCTGTATTATAATT
ATTGAATTATCCTCTTGATCATTATTAATCCTGATACGTAAATTTATAAA
AAAATACAAAATAATCAACCATTTAAAAATCGTTAAAATTCAGGTGCTAA
AATATTGTGTGCCTGTGGGGTGGGTAGGTGTCATGTCCTTTATTGCACAA
CTGGCAAAACCCTCTAGCCCTCCTGCAAAAAAGGATCATACAAAATCACT
TATTCACTTCCCCTCATTAATAAAATACTAGTACTACTTCAGACTAGAGT
AGCATCACTCCCAAAGTTAATGAATAATTTATAATTAATTTTCTTTTTTC
TCCCAGTTTTTCTTTTCAGCAAACAGATGTACTATCTGATTTTCTGAAGA
TGTTATTTGTAAACCAAACACTGGTGTAGTAATGTCTCCTTTTCCAGGAC
TGAAGCTAATAAAGTTGATGTTAGTAGGTTAGGATTAAGGACAAGGGGGA
TGTTTTGGGGGATTGTGCTAACAAACCTAATTAGCCTGTTAGTTTAAGAA
ACCAGATGTTACTAGATGCATGATTCTAGATAGAGGTGACACACATACTG
TAGATGAAATGAAACACAGAGTTCCTCTTGGTATACAACACTGTTGTACA
AAGTATAAGTTATGTGTCACTAGTCATTTTGCGATTTTCACGGAAATAAT
CTCTTATTTCTGTCCATAATAAATTTAAGCCAGAGTTTGAATGTTAGATG
GGTCAAAATACATTTTGTCTAATAAGTCAAGAAGCACCTGTAAAAAGTTA
AGAAAGTTAGTTTTTCTTTCAGAATTTTTACTTCTTTCTCAAACACTTTA
ATCACTCATAAGTCTTGATTTACTTCTAACTTCTATTCTACTTTTTTATT
TTAAGCAAGAAGCACTTATTTTAAACTCACTTAAACGGCCACATAAATAA
AAGATATGTGAAGTAGAATTAAATCTGGAAATATAATTTTGTATTTAAAG
TTGAAGTGGACAAATAATTCGAAACAATTTTTTTTCCAAAAATGGACATA
TAAATTAAGACGGAGGGAGTATTATCATCTCTATAACACTACTCGAAACT
TTAATCCCAAAGAAAAATAAGAGAAGTGAAATCTTCATGCATTTTCTCCT
TCTCGAACTCTACTCTAGGAGCATATTTTGTCCGTTTGTTTGTTTTCTGA
ATGTGAGCATGTATACACATACAAATACACAAGAGATGAGATAAGAAAGT
CAGCATGCATTGCTTCCTGAACCGTATAACCCAATGCAAAGGGTTGCGTG
CTCATCTTATGCTCTTCTTTCTAATAATTCCCATTCTTTCTTTTTCACTA
CCCTCCCTGTTTTAGCTTTTAATACTCATTGCAGCATCTCTCTCTAACCC
TATTGCTTTCCCCTCCTCCCCCTACCCCTAAGTCCCTAACAACCTAGCTC
ACATTCTATATATAAACATCATAGTTTTCCTCTTGTTTGTGCTTTGATCA
GTTTAAAATCTTGAGGTTTAGGCCTAGAGTTTCTGATTCTCTTCACACCT
CTGGGCTGGCTGTGTAGTGTGTGGTCCTTGTGTACTAGAGCCTTGGTGAA
GCATTCACTTTTTCATGTATAAATGCATTCAAGAATCATGTTTGGTGAAG
TGCCCAGTTGAGGATTCTTGTGTTTCTGCTAGTTTTTCTTGGTTATTTCA
CTTGGGTATCAGTTCATTTTTGCCATTCTTGATTTTTGAGTCTTGTGAGG
CCTTATGAAAAAGGGTTTGAGTTCCAGGGGCTGGGATTGTGAGGACAGCA
AGCTGGAGCTGAGGCTTGCTCCACCAGGTGATGAAGATTGGGAGATCAAG
AAAGAATGCATTACTGAAACTTGTGAAAACACCTCTTCTGCATTTCTGTC
TCTTGGTTGCTTCAATGGTTCATTTCAAGAAAACAGTTCAAAGGTTCTTG
ATGATGCAACAGTGAGTCCATGGTCAAGATCTTGCTCTCAATACAAACAA
AGCTTGGCTCCTGCTGTGGGAAAGGAATCAATACAGAATGCAGAAAAGAG
AGGATTTTCACCAGCTCCTGCAAATAATACAGCTGTTCACAAGAGCTCTC
AGAAAAGGTGCTTTTTAGATTCCCAGCTTTTTTTGTATTCCTTTTATGGT
GTTTTGTCTTTTTTCTATTAGACAGAGGATATTCACCCTATTAACTCAAT
TGTTACCTGTGGCCTGTGGTCCATACTTGAGATATTAATGATAACACAGA
GCTTTAACTGTATATATCTTCCCCATGCAAACCAAATTTTACTTCTTAGA
ATTCAAAGATTTTCATTTATGCTAGTCTTTTCTTGATTATCCGCCTCTTG
ATTCAGTGTTATCTCTTTCGCTCTTTTTACGAGATGTCGGGTTCAATGGT
GTTATATTAGACTCTGAATGATATGGAAAAGATTAAAACAGGAAATTTGT
TGTGCTGTAGATTGTGAGATTCCTCTTTTTGAAGAGTCCTTTGCTCCTTT
TAGTTTCATTGTGGACCAGTGCAGAGCTTTGAATTTCAGCTTCTCATTAC
CATTTTAGCTACATGATAATCTTTTCACCTTTAGACAATAAAATCTTTTA
CTGACCATTTGCATTGAAAGATCACTTTTTATTCACTTGTTTTGTCGTTT
GTCTTGTGACTTTATGATAATTTGTATATAAGGTACTTATTCCTCTGTTT
TCTTGCAGTACATTACTACATTAGTTAATTTAATTATTGCTTATTTGTGT
TGGTTATGTCCTAATCTTTTTACTAATGACTAATTTTATCTGTTAGTGTC
TCGTTTGAGCTAGGTTTCGGATTATGGTCTGACAACTATGTATGTGTACA
TTGTAATGCAGAATTACTTCAGCTCCTGGTCCGGTTGTTGGATGGCCGCC
AATCCGATCATTCAGGAAGAATATTGCAAGTGGCTGTGCTTCGAAGCTGC
CAACTGAAACCAAGGCAACTAATGAGGTTTCGACAAAGATTGCTGGCAAG
AGGCCAACTGAAAGATTTCAGAAAGGTCTCTTTGTGAAGATCAATATGGA
TGGAGTCCCTATTGGAAGAAAAGTCGATCTTAAAGCCTATGATAGCTATG
AAAAGTTATCTTCTGCTGTTGATGAACTCTTCAGAGGCCTCTTGGCAGGT
TATTCTGTAACTGTTATGTATTAAGTTTACCTAGTTGGCCTTAATAGGAA
AAAATGTATGTTAATTAAATTTGATGTTTCGGTAAATTGGTAATGGTTTG
AACATAGGATGTTATGGTAGGATTATCAGAAGCAAACAAGCTTAATAGCG
GTTCAGATGACAATCTCTGCTTTGAGCCAAGTATGGCTAAGTACTCGTGC
CCATGACAATTTTTATGTATATCTTCTTCTGACTTGTTCCGTCTTTGTTT
CATTGTTCAGCTCAAACTGATCCGTCAGTTAACAACATTCAGAATAGCCA
AGGAGAGAAAGCCATCACAGGATTGTTGGATGGGACTGGGGAATATACGC
TTGTCTACGAGGATAATGAAGGCGACAGAATGCTTGTGGGGGATGTACCA
TGGCAGTAAGCATCTCGCGACTGTGAATGATAAGATAGGATAATCTAATT
TATACAGAACTTCTAACTTTTCATCTGGCTACTTGTGCAGCATGTTCGTG
TCCACAGTCAAGAGATTGCGTGTGTTGAAGAGCTCTGAACTTTCTTCACT
ACTTTGTGAGTATTCTTCTCGTTCTTGTTTACCTACATTTGATCACTGAT
AGCAACAGCGGAACTGAGTAAGATTAGTCCTCTTCGGCTCTAGTAACATG
CCTATCTGTCTTCTTCTGCAGTCGGTAGCAAGCAAGAAAGGGAACCAGCT
TGA