| Relationships |
|---|
| The mRNA, DCAR_001898, is a part of gene, DCAR_001898. |
| The genetic_marker, MK001045 GSSR-046, is adjacent to gene, DCAR_001898. |
| 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_001898 | DCAR_001898.mRNA | mRNA | DCARv2_Chr1:21989123..21996619 |
ATGATTCCCAGCAGCGAAGACAATGCAACAGCCACACCGACGGTGGTGAT
CAACAATCTCCGCTTCACATACCCCGGCATCGACGGCCACCCACCACCCG
GTTCAAAGCCACTCATTCAAGATTTCTCTCTGACTCTCAATCCGGGTCAT
CGCTGTCTTCTCGTCGGAGCTAATGGCGCCGGTAATCTCTTAATCCCTCT
CTATTTTATCTCGCTCATTGTATTCTTTTGATTAATGGTGTGATTTTGTA
ATAATAATCTAGGCAAAACTACGATATTAAAGATTTTAGGAGGGAAGCAT
ATGGTGGACCAAGATATGGTTCGGGTCATGGGTCGATCCGCGTTCCATGA
CACTTCTTTGATTTCATCTGCCCAATTGTGTTATCTCGGTGGAGAGGTTT
GTAAATTGTAATGTACTAAACATTTTTTGCTCATTTCGCTGTTTTTTGTA
TCGAAAAAATTTCATACATTTCTATCAGTAGATGGTAATGCTGTGAATTC
TATTTCGCTTATATGGTGTAGCAAACTTCTTAAGTTTTAGAATTCACCCG
GGATCTTTTGTCATCTAATGCAAAGTATTTAGAAAGTTAGTTATTATTCT
CACCTTTAATGAACATACATAGGAACTTTCATTGTTTGTCGCCAGAAAAA
TAAATCAGATGTAATTCTATGTTTTTGTTGTAGAAATGCATGATGATGTA
TTAGAACAGTTTGGGTCTGTATTTGAATCAAGCAAGATTATATACCTTGT
GCCAAGAGTGAAGCATCTATTTACCAAACTTAAATAATAGTTGAAGCTTA
TTGAAACGGCCGCAATGTATATAAAGAGTTGCAAATTTTAAGGTACTTGA
TATTAGTAGAATATAGGACGTGTTAACCCAAGCATGAAATTAGATCCACC
CATACTAGTGACTGCTGAATGCTAGAGGTGGGTATATACAATTAGCGGGG
GAAGAAGAATAGTTCCCAGAATTATGACATTTAGATGAATGCGTGTCTCA
GACTCCACCCTGCTCTCTGGAAGTATGAGAAGGTGGAGGAGAGCCTTACA
AGTAATTTGCTAAAAAAAGTTAGGTGTGCTAGTATCTATTTCCGTAACTT
ATAGTCCTTATACAGACTATGTTTTCTCAAATGGGGTGTGGTTTCTAAGC
TAAATTGATGTAGATTTGGTAATTAGCAAATTAAAACAAGAACAAAAATT
GTTCGAGAAAAAAATATAAATTCTCATCTCAATAGGATTACCTGAAAACT
CAATGTCACTTTGTATTGATATGCCAAGTCTGGTAGATATTCAGTTTATT
GCTTTGTAGAGATTGAGCAGTGAAAATTGAATTCTGGAAGAGGCTCTTTA
CATTTGAATTAGGTAATGACTTAATTGATCAAATTCTCTTTTACAGTGGA
GGCGTGAAGTTGCTTTTGCTGGATTTGATGTTCCAATACAAATGGATATT
TCTGCTGAGAAGATGATTTATGGAGTATCTGGGGTTGATCCACAAAGAAG
AGATGAACTTATTAAGGTATTATGCGATGTATTTCTTCTTTGATTTAGGT
TGTAAGGGCTACAATCCCTTTCCATGTTTGATGACTTTGATGATATGATG
TTTTCACTTCCATGCAAAACAAGTTATTAGTTATCACAACTCTGTTTTGG
TGTTAAATTTTTTGTACTGCATAGTATGTTTCTTGATTCTCTCTTACAGC
ATATTGAGTTTAAATTTAGTAGTATGTTATAGCATTAAAATGTTCAAAAC
CAGATTACTAAGTACTGATATAGTCATATATAGTGTTAGTTGCTGCACCA
AATGTGTTAGTGGACTCTTGTTTGATACCAAAAGAGAAAGTTACGGGTTT
CCCTACTTTTAGATGAGATATGTTGGTTATATGAATATAATATCCCCAAC
TGGAAGCAAGTTCTGCAGTACAAAACTTCAACCATATTATAACCTTTCTA
ATGTAGTAGTCCTAAAATTCTGAGTTGTGGTATATGGATAGTACTAGCTT
TTAAGTTCTAACAAGCACCTTATTGTTGATATTTTACTTTTTCGTATAAT
ATAATTAGGATGAAGTGACAAGCTTAAGTGAGGAACAACGGGTTGCTCCA
CAAGGAAAACGGTTTTGGTTCAAATATGGGTTCAAAAGATGTAATAAATA
TTTTGGTGTATCTTACAATAGCATGTAACTGAAGTAATTACTACAAATAA
ATACACAATAACAACATACTTAAAATATATTTGAATTGGTTTAAAAGACC
ATACTGGATTTTTAAACAAACTTAAACCTTCTGAGTCTTATGTAGTACTT
GTTTTGGTGTTTACGTGGTATGAACTCATATAGGTATGTAGAATAATTTC
CAATATAATGATTTTTTATAATAACACTTTTATATAGAATTTAGATTCAA
TCTTCAAAACTTGAGATTACGGGTCTAAAAATGGATATTTTTTTATAAAT
TTTACACGTCGTCACATATAAATGGAAATTTTTTTTGTTATGTTTTCCAT
GTGTAAAATTTATATGTGCATGAACTTCATTTGGTTTACAAAATCTAGTT
TACCCAGCTTTAGTCTATGTTTGTTTTGAAGGATTATAATCCCCGGATTA
TTACCTTATTATATATAAAGTTCTATTGTTGTAGTCAACCACAAAATAAT
TATCATCCTGGTTCATTATACTGAGATTATGATGCCTAGTGAGAGAAGAT
ATCACACTTCATAGAAATGAACCAAAGAAATAACATTGGAATCTACTCCT
ATGGAATTTCGGTCCTTTAAATTTGGAATAAATAAATAAGATATTAGTCC
AGAGATTATAATGCCCTTGAAACATGGAATCTTGGTCCTTTATATTTAGA
ATAAATAGGGTAATACTCCTGATTCTGGAGAGTATAATGCCTTGAACCAT
ACATGACTTTAGGTTACAATAGTGTTATCTATAAGCATAAACTTTGATCC
GTGAGTTCCATGTTACTAGCTCCAATTGCTCTACTTAAGCTCCAATTTTT
TTATTTGAATTTAAGTGTTCTTCATATGCATGGCATCTTTTGTTGTTTTA
TGATTGAACTTTATCAGGTTATTAGAATCTAGTGTACCTGCCAATTAAAA
TTAAAAAAAAAAAGCATTGGTTTTAATTTTATGTGTAATGCTGCTTCTCT
AAAAACTTGGTGTATAATAGTGATATGTATAAGCAGAACTTTGGTCCCCA
GGTTCCATGTTCCAAGTTTCGATGGTTCTACTTTGGCTCCAATTATTTTT
TATTCATCTTTTAAGTGTTCTCCATTAGTAGGGCATCTCTTTGGTCGTGT
CTCTAATTTCAAATATTTAATCTTTTTACATGAGAGTAAATTCATGGAAC
CTCTATCATTGGTTTCAGTGTGGTAGGGAACATCCTCCCCACCCACCCTC
CGGGCCCCCATAAAAAAAGAAAGAAAACCCCAGCACACCTACAAAATTTT
TGGTATAATGACACAATAATATATCAATCTTTCATAAGAAGAAGAAAACT
AAAAGCGGAATTTAATTAATATATTAACACCAGTTAGATGCCATGTGGAT
ATCTGTAAACTTTATCTATAAAAGTTTGCGGTGGTTTTTTTCGTTGATGT
TGTTAGGATAATCCTCAAGGTCAGTTAGATGCGACACTTTTATGAAATAT
TGACATACTGCTCCTATATGTTTATATATATATATATATATGTGTGTGTG
TGTGTGTGTGTGTGTGTATATATGGGTGAGGTTCAAATCAGAACCTATAT
TAGAATTAGAACTTAGGACCGTAGACATCCGTCAGATTTATTTAAAATCT
ATGGCCATTATCTAAAGGGCAATTATATTAAATCATTTAATATCTTCCCT
CATTAAAGCACACATTATATTTTACATTATATTAGGTAATAAATTATATA
TCATATCTCACTATATCAGGAAATATATCACACATGATATAATTATAGTA
TACCATTGCAGTATATCTAAGTTAAATATAAAATAATCAAATCAATTTAC
AAATATAATATGGTATACCATTGCAGTATATTTAAGTTTTAGATAAAATA
ATGAATTCACTAATTATTTTCATTTTGGCTTATATCGTGTTTCTGAATTG
AATCTATTATTTTATCTATTACTTACATATACTGCAATGATATATACTAT
AGTTATGTTATTTTTGTATTAGTTCGACAATAGTGTAAGAGTATAATTTA
TATATGTATACTGCAATAGTATTTTCTTTTGTTTGAATGAATTTATGACA
TAAAAAGATATATTTCTTATATATTTTTAAATATATAAAAAATGATATAT
TGAATATATTGGTATATTGTAATTATATGTTCCTCAATAATAGTATGATA
TGATTAAAAACATATAGGATATAATCTATTTACAAAATAGAGTATACTGC
AGCAATATATAATAATTATAATTAAAACTAAAACTAGTTATGGTAAGTAA
GTCATTTTATTTAAAGTGATTAGTTAATGGTCATAAATATGTACATATTT
AATGCATATAGTACTTCGTAATTAATTGTAATTTCAATCTCAACCATATA
ATATACTTAGATCTAATGGTCCTTAGCGAGTTCTAAGTTCTAACAATAAC
TTGGTTCTATCTTGAACCTGACCCTATNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNATATATATATATATATATATATATA
TATATATATATATATAGGGCATTGCTCAAAACAGAACACCCTTAAAAGAA
GAACAAAGAAGAACACTTTGGAATCGAACATAGAATCTCATCTAAAACTT
GAATTAAATTCTAACTTTAAGCTAATTAACCATTTATTATGAATAATAAT
AGTATCTAGCATGTTTAACAACAATTATGGATTAAAAATAATATGATTCT
ATGTGATATTAGTCATGTAAAGAATATATACATGATTCCATTCTGGATTC
TGTTTTGGATTCTATTCTAGATTCTATAATATTTCATATTAATAATTTGG
ATAGATTTGGATGTTAGATTTCACATATTAAGTTTAGTTAGTCCTTAACT
ATGTAATTATAATCATAACAAATCATTTTTTATGAAAAATAAAGTGTTAT
GATGGTGTTCTGTGTTGTTCTTTTTTTAAAGTGTTCTGTGTGGAGTGCAA
CCCTATATATATATATATATATATACAAATAGAACCACTAAAATAAAAAT
TAAAATGGAAATCAAGAGAAATTATACTTAAATGACCTCACCCACCCCCT
CGTATGTCATCACCCACCCCTTACCACCACTGATTCCCAGCCACCATCAT
AGGTTCCGACTACCACCGAACTCGTCAATTTATTACAAATAGGGGGGCAT
TAATTGATTCATTAAAAATTATAATTAAAAATGTATAAATTCGTGTTTGA
AGAGTTGAAAGGACGAGAATGGTGGTGATGGGGCTCATGGTGATGGTCGG
AGTCCTCGTGGTGATGGTGATTTTGAACCATGGAGTGGGGGTGGGGGCTG
GTGGGGATCCAGGTTTTCTGGTATAATGTGAGTTTATTATTTAGTGATTA
ATCGATCTATTTTAGTAGTTCCGTGTCCTGATATAAGTTTATTATTTAGT
GATTGCGCCGCTTGTTTTAGTGATTGCGCGTCTGGTTTTTAGTTTGTAGG
CGAGATTTGGTTTGTATTTGAGCAAATGCCTATATATATATATCTGAAGA
ACTGAAATTGTGAGGGCCATAGTGTGAGAACTGGAAATCTTTATTCTCCA
GCAGTGGAAGGTAGAAAAGTGATATGTATATGTATACATATAACCTATTT
ATACTACCTCATTTCTTCATAGATCTTTTCTAAACTAGTTTTTATCATCA
CGTTCGGATTGTGATTAAGCGCGTTGTAAGTGTACATGCCCAATAATTAT
GAATCAGTGAGATATGCACATATTAGGCCAAATATGCTGCACAGAAATGT
GTATCAAACAATCTTCTATTGAAGATGTGTATCCAATTGGTATTATTTGG
CCACAGATCAGAAAAGGATATAATTGGCCTTCACCCTCAAAATCTACCAC
TAATATCAATTAACTCAATTAACCATGTAAAGATGTAGATACCAAAGAAG
AAGATGAAGTGTATTTGATTTTTTTCCTTTCTGATGATTGCTGCAAAATC
AATGAATTTATTTCCCTTGTTTTCTTTTACAGTCAATTGCAGGTGGTATT
ATCGTACCTTTTTCATCTATTTTATGGTGCTTTATTTTGGAATTTTAGGT
GTTAGATGTTAATTTGTCGTGGAGATTACATAAGGTATCAGACGGCCAGA
GAAGAAGAGTGCAAATATGTATGGGATTGTTAAAGCCATTTAAGGTAACA
ACTTCAACCGAAGTGCCTCTCAAGATCTCTATCACGAAGTCATTATAACA
CCATCACTCTTATCTGTGTAGGTTCTTCTTCTTGATGAAATTACAGTTGA
TCTAGATGTGCTTGCAAGGGCTGACCTTCTAAGCTTTCTTAAAAAGGATT
GTGAAGAGCGCGGTGCTACTATTATCTATGCAACCCATATATTCGATGGC
CTTGAGAGTTGGCCTTCTCATATCGTAAGCAATATTCTTTCAGTTATGCT
CAAGCTTGCGTTCGAGTTATATGCCTTCTATAAATTTTAAGGCATTCTCA
TTTCAGGTTTATGTGGCTCATGGGAAGCTGCAGTTAGCAATGCCTATGGA
TGAAGTTAAGAAAATCAGTAAATTGTCACTAATGGTAAGTCTTTTCTATG
TTCATTATTGATTTGATATTGTAATGTCATCTCTTTGTTTCAATTCAAAT
ATGGTGGTTTCTTACAGTTTTTGGTTATTCTTTAATGAGATTCATCAATG
ATTAGAATCAGGACTATTGAGCCTTTTTTTGCTGCATATAATTTTTTTTA
TCCTCTAGGAGGAACATATATTTGTTCAATTGAACTATCAGTGATTCTTG
TGTACTCTTTAAACATTCTACAATCCATTCAAATACTTGCATCATTGAAA
CTTAACTTTAAAATGCAATACCATAGTTTCTCAAAAATTACTGTAATATT
GAAAATATAATCTGAAGTGATCATAACTCAATCCAACACGACCATATGTA
TAACTATTTCAATTCAGAGACATGACTGCATTTACTTGATGTGTTTCTAA
TGGTTATTGGAAATGCAGAGAACTGTGGAGAGCTGGCTAAGGAAAGAAAG
AGACGAGGCTAGAAAGGTAAGGAAGGAAAGGAAAGCTAAGGGTCTTCCTG
AATTCGAAGATCAAGTGGATGGCACTCGTGTTATTGGGGATCCAGCACGT
CCAGTAAACAATGGCTGGGCAGCTGGAAGACTTAACTCGACCGTTGCTGG
AGAAGAGAATTTTGTCCTCAGTTCAAACAGAGTGATCAGACAGTAG