| Relationships |
|---|
| The mRNA, DCAR_000844, is a part of gene, DCAR_000844. |
| The genetic_marker, MK010643 1_5061656, is located in gene, DCAR_000844. |
| The genetic_marker, MK002898 K0342, is located in gene, DCAR_000844. |
| 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_000844 | DCAR_000844.mRNA | mRNA | DCARv2_Chr1:5055422..5064449 |
ATGCATTTACGTCTTTTCGGTAAGTGGCTGCAACCATTTTCCTCAACCTC
AATCTAAACTTAACAAAGGACTTCTGTAGGAGTGTAAGTCAGTAACTTCA
AGTCATGGTACATGTTGAAGGGGGAGGTCAATGTCGATACATATTTATAC
ACACATATGACTATATATGTATATTTGTCTATAACTGTGATTACTGTTTT
ATATAATTTTTAATGGATTGCTGATTACTTTTAAAGTTTTAAATGTATAT
TTATTCTCTTGTTGCTAGAGCTTGCGAGAGATGCACTAAATTCAGAGGGG
TTCTCTGTTATTGGAGGATATATGTCGCCGGTAAATGATGCATACAAGAA
AAAGGTATGTAACTATGTGTATTAGAACATAAATTATGCACTTTGTTCCT
ACATGTGAATATGAACAAGTTGAATATGTAGTTAGTGGCTGAATGTTCTT
CTCCGTATAGGGTCTTTTATCAGCTGAACATCGGATCCCAATGTGTAATC
TTGCTTGTAGAAGTTCTGAATTCATAATGGTGGACCCTTGGGAGGTCTTT
TTCTTCCCCCAACTTTCTATCTCTCTATCTAGATATAATATATCTGTGTG
TGTGTCTTTTTATGAAAATCATTACACAGGTTTTTGGTCACTTGTTTTTT
TGTCTTGCATATATAATAAATTATGTATCTCTGTAGTAGGCAAATCAGAG
TACCTTTCAGCGGACATTAAGTGTTTTATCCAGAATCAGGAGTTCATTGT
GTGATAATGGATTGGTACCAAGTGGTAAGCTATAAACTTTCCCTTGTTTT
TCACCCAAAGTCCTAAATTGAAGAACCAGTTCTCTATGATTGAGAAAAGC
GTGGTCCTTAAAAAATTTGTATTAATAGCATAAGGTATCACGTATAGGTC
AATTCAGTCTGTACTCTGTACTCATGTTAAATGTTTGTAAAGTAGTACAT
TAACTTCGTCTATGTGAGATAGGATCATAGGAATCTTGGCTCTAAGCTTT
TTATATTCTGTACTTCTGTGTTTAAATTATCTTTGATCATGTTATATCTC
TACTGCTTTTTGGCATATCTTTCTACAGATCATGCTGCAATTAAGTGTTA
CATGGCTGATCTATGTATTTATATATTTCCATGTGTTATACTTGTACACA
AGGTCAGCCTTTTTAAATTATTTTCTTAAAGATAATATTCAAGGGTTATA
AGGACATTGATTAATTAGGCAATGTAGACTCTTTTAAATGAAACTTCAAA
TGTATTATTAAACTGTTGGAGCAAGATAGTTATATCTCTTGGTTGGGCTT
TGGCTCCCTCAGTGACAGAATGTAATTTATAGCACCTAAGCAGATATAAA
ATATCCAAATGTATTGCTTAGTCTACATCCCTGCCTTGTGATATTCCTTT
TCTTTTCTTTCCTAGATTGTACTACAATATACTGTTTCTGTGTTTTAGAT
GTTAGTATTTTCTTTCTTTGCACTCAAATTTATTGGTGATATATTGTTTT
ATCTTCTGCTTCTAGCATACCTTAAAGTCATGCTTATCTGCGGCTCTGAT
CTACTTGAATCTTTCAGTACTCCTAAAGTATGGATTCCCGAGCAGGTAAA
TCCAAGTCTATCATCAAATATGCAACTCAAATGCGTCTTTTTCTTGCTAG
TGGAGGCTGGATGAATGAATTTAGTTTCTGTATTGATTAGAAATTATTCA
CGTCTAAGTTCTGGTTTATGACTCCATAATCGTCCTGAAATCTGCCAAAG
CAAATGTAGCACGAAGCTAACGAGATCTTGCTAATTGAGAAAAGGTTTTA
TGTTGATTTTTCTTGATATTTTGGTCCATTGAAGTGTGGTGCGGGGCTGC
TTTTGATTTGATATCTTAGAAGAATAACACTGCTACTTAGAGAGAGAATT
AACACATTTACAAATGCAAAATCCCTAACATAATGAAGTTGTAGGAATTG
GATGGCATAGCACACAAATTACCACATTTGATAGCTTTGTTCACAAGAGT
GGTGTATAGTTCCTCCATCTGATAAACCAAGTTTATTATTCGCTGATTGG
TGTCCTCGGTTATTTAATCTCTTTTTAATTTCATCAGGATAATGATTACA
GTACACTGACATTGAGCAATGTGCATCTCTATGCTTTTAGGATATAATAC
TTAGCAACATTTTGAGCTTGTTGGAACGTGTAATCATGCAATCTCAATCA
TGTTAATTGGGCTTTCCATACACCATCAAATTGATTATAGATCCGAAACA
TCCAAAATGTTTGTATCTGTTAGTATGTGAAACGTCAACAAGTTGTCTGA
CAGTTGCTACGACTAAAACATCTATGTTGAAGACCTTAGATCTTGTGGAA
TTTGATTTCTGGAAGGAATTTGGTCATAATGTTTATTTTCAATTTATAGG
TCAGAACAATATGTAGAGACTATGGCGTAGTTTGCATCCGGCGAGAAGGT
CAAGACATTGAGAAACTTATTGCCAGTGATGAAATTTTGAATGAATGCAA
GGTAAAAAAATTGCATATATTGAAGATCTCTTCTTCCAGGCGGTTCCTTT
GGGATGAGTTTCCTTTCGTAATATATGAAAACATTTTCCATATTCTTTTG
AACTTGTGAACATTTTTATACAATTGTTTTGCATGTTTCAGAAAAATATT
TTCCTTCAAACAAGTAGAGCCTTAATTTCGGATTGTTTGTGTCAAAATTA
AACTACTTTATCTGGAATTGGCATTGCATAGAAGTTCATAAAATGACTGA
CTTTTTTAGTTTGCATCTTCCAGCAATATATGCCAAGTTTATTAATTTAT
TTTTGATCGATTCAAATAATGACACGAGTGATAGGCATATCATATTGTTT
TTCCTATATGTGCAGAGTAACATCAAAATTGTCGATGAAATTGTTCCAAA
CCGAATTAGTTCAACAATAGTGAGGTAACTAACGTATCTAAATATCTAGT
TGCTTTGATGAAATATTAATGATTTACTGGTGAGAGGGCTTACTTGTATT
CGTTGGGCTAACTCATATTTGTTGCAGGGATTGTGTTTCCAGGGGTTTGT
CGGTAAAATACCTGGTGCCAGACGAAGTAATTGACTACATCAAACAACAT
AATCTGTACACAAACTCTACATAAATTTGAGAATTTCTTGGCTGGATTGA
GAAGCGAAGAATCTTGCTTGTACAATTTAATAACTTACCCTTTAAGGGTA
AGATAATTTGGGGATGTGTCAATTATAACTTTGAAATCAGACGCCTGTTG
TGTTGGGTTGCATATGTCCACAGATGTTGAGATTACATATTGTTAGTTTA
GCAAGATATGCAATGAGATACCGGCGGTTTTCTTCATACTTTACCTGTAT
TGTGCAATAGAAAGCAAAACGTGCTGTCTTGTATTGTATTATCTATTCCT
CTCTACATAGATGTTGCGAAAATTAGGTTGTGTCTAGTGTGGAGGACTTA
CTCGCTTCCAGATTCTGCATCTTCGGAATATGTGAATCACCTTTTCCGAT
TTTGAACTTCTGCAACTAAGATACATGTAATTGCTTAGATTTGTCTATTG
ATTTAATAGATTTAATGACATAGAAAGTTTGTTAATTTGTGTTTGTCGTT
TGTGGAATTGGTGAAATAGTTATGATTTGTGAAATTAGTGATTAGTGATG
GATTAATGGCTGTATGTATATATATTAGTTACGTGTATGTAGTATTTAAT
ATCTTAAAATGCTGATACGAACATATAATACATGCAAGAGAAATCAAAAC
GAGTTAAAGGAGTATTGGGGAGGCTTGGTTCACCCCTTGCGAGAGATTTT
AGTTATAATTTACTATCAAGATTGTTCAATGTAGAATTAATTTATTGTAA
AAACTCATTATCTAGCTAACTTGTTATCAAAAATCATTTACTAGTTAAGT
CGACAGATTTTTTTAACATGTAGTAAAATATTTTGAGTTGACAGGTCTTC
TATATGCTGCAAGTCTTGTAACACATGTATTCCTCCTGACAAAAAAAAAC
ACATGTATTCCTTGTTTTCAACTGAATCTGGGTTAACAAATTATTCCAAA
AATCCGAGTAGAAATTTGGGTTAATAAATTACTCCAAAATCTGAGTAAAA
ATTAAAATTTGAATTTACGACTGCTCAGTAGTATATTTCACTCAAATGTT
CAACTAATCCATGTAATACCTTCTTTCCCGTTCCACCAGAAAAAATCCAC
AGACCAACACAATACCTCATTCTTCACTCCACTGAAATAAAATATGAGCA
AAACGAATTTTTAGACAACTCTCTTTTTCTGATCAAAGATAATATGAGGA
ACACAATTTCTTAAATAGTTACTATTATAATAATTAGGATCGTACTCAAG
AGAGAACTAATACTTAAAATAAAATCATAAAATCATTAAAATTCAAAATA
TGATACATAAATAAGACATTTTTTTTCATATATTTGCAAACTCTAACTAA
TACGAGAAATAAAGTAAGGTTTACATGGGTTCTGTATAATGACTTCTCTT
AAACATGACCCAACTAGCTAACTCTATTAACGAGCTAACAATATTTTAGA
TGAAGAACTATCACATTTTTACATTTTACATGAATAACTATCACAATTAT
TCTTATTGTTAATCACCTTTGAAATAAACTGATAGGTTTGAATTTTACAA
ATATTCGTTAATTATATTTATATGAAAACTAGATTAAACGAGAGTCAATT
ACATCATATAAAACATGGATGCTTAGCCGATTTCTGAATTTCCACTCGCA
CATTTTTATATAAGTTCAACTACTGATTATTATTTTTTATCGAGTTCTAA
AATTCGAATAAAAGAATAAATTTCACCGAGTAACAAATCACTTGTTTAAT
GAGAAAAAAGAAAACCAAATATTCTTTTCATCTCATTCCATAACTTCACA
ATATATCCCACTTTATAATATTTATGATAAAATATTTAATTCTTGGAAGA
CGACAATTTGTTCCAATAAAAAAAATTAAAAAGTCAAATATAATTTAATT
GACCAGTAAAATATAAGTTGAGGGAGAAAATTTTGATACAAAATTTAGTA
AAAGTAACTATCTCCACTTTATAATATTTATGATAAAATATTTAATTCTT
GGAAGACGACAATTTGTTCCAATAAAAAAAATTAAAAAGTCAAATATAAC
TTAATTGACCAGTAAAATATAAGTTGAGGGAGAAAATTTTGATACAAAAT
TTAGTAAAAGTAACTATCTCGACAAGAATCTGGAAGTATGGCCTAGGGTT
ACAAAAGACTATCGACAGACAATCCCTGGAACCAAACATCCCGGTGGCCT
AGTGTTCGACGGATCTAGCTCTACGACGCCGTTTCGCCCCTAATCACAGT
CAGTAACCTATTCCTGTTTCAAATCACTATTTTAATTTTGTTTCGATGCC
CAATTTAAACTTTTAATCGCATCTTAATTTAATATTCGTGTGTATGTTTC
TGTATGTATGTGTAGTTTGATTGTTGAATTGAAAACTTTGTGGATTAAAA
AATGTCGAATTAGATTAAATTTGGAGTTGAATTGGTGTAGTTGAATGGTT
ATTGTAAATTTGTGAAAGAGGGATTTTGTTCGACGTAGTTTGAGGTTGTT
AAGTTTGGGGGAATTTTGGAATTGGACTGTTTGTGAAGTTGTTTTGGTGG
GTGGTTCGGCATGTATGTTGTAGATTTAGTGATTTACAAAAGATTGATTT
TATTAGGCGTAGCGAATGGTTATTAAGTTTTGGGGAAATGTTAAATTGGA
CTGTCTGTTGAGTTGTTTCGGTACGTGGTTCGGAATGTTGGTATAACTTC
CCGAGCCCACAATTAGATGCATACCGGACCCAACAACCCATAACAGGTTG
GCCCAAAAGTGTTGGTATACATCAGTTATTTACTTGTGCTTATAAAGGCT
TCAAATACTCTTTATCTAACTGATATGAGATGTTACACACACCCATTTCT
AGATTCGATATCCTTATCGAATTTACACACAAATTTATGAAACGCGGGTA
ATGCCTTTGTCCTTACGGCCATGTAGAGCTCTTCCTGTCGGGTAGAGCTC
TAATAATATGTATAACATCCAAGCCCACAACTAGATGCATTACCGGACCC
AAACCCATCAACCCACCACAGGTTAATTCGAAAATGCTAGCAAATTGGTA
CGTAAGGTGAGGTTATTAAGTTTTTAGAGATGTTGAATTGGGCTGCTTGT
CGAGTTGTTTTGAATTGGATTGTTTGTGAAGTGTTTTAGATACATGGATC
AGAATGTTTATTACTAATTTACATAAGGGTAATTCTATTAGACTTTAGAC
ATAGCATGAGGTTCCTAAGTTGTTGGGGAAATGTTGAATTGGGCTGCTTG
TGGATTTGTTTGAATTGGACCGTTGGGGAAGTGTTTTTGATACATGGCTT
CAGATTTCTGTCATCAATTTATGGAAGAGTAATTTTATTAGACGTTATGC
GATTGTCTGAGGTTGTTTAGTTTTTGGGGAAATGTTAAATCGTACTATTT
GTAAAGTTGTTCTCTTACATGTCTGGGAATGTTGGTTGTAAATTTCTAAA
GAGGGATTCTATTAGACCTGGTACCAGGTTATTTAGCTCTTCTGATTTGT
CTTTGTAATTCCCCTATGTGATCATTTACCATTAATTGGAAGGGCAACTT
TTTTTTTTTTATTTTGATTTTTCTCTTGAATTTTGTGAATAGTGTATTAT
GAAATTGTCCTTTCTATTTGTATGATATCTTGTTTCACATTTCTATTTTT
TATTGGGTTGTTTAGAGCATCTCCAAGGGACTCCTAAATGAGCTCTTAAA
TCAAAATGTAAGAAGCGCGATCATAAATAAAGCTCTAAGAGCATCTCCAA
TGGGCTCTTCAAATAAGCTCACAACTCTAAAATTAAAGAAAATGTGAAAA
AATAGTGTTCCAACGGGGTCCTAGTGGCTCTTTAAGAATTTAAGAGTTTT
GTATCTCTCCTCTCTTTTAAAGAGCATCTAGCTGCTCTTAACTTATTATC
ATTGAATATAAAATTCACTTCCTTCTACTTCTATTCACTTTTCACTCCAA
CTTTTCTCTCAAATATTAATGAATTATGAACAGAGAGCATTTATAAAGAG
TAGGGTTGGAGTTGTCAGGATATTCAATGTATTAACTTGTTAGGAGCCAT
ATATTCTATTATTTTTTAAAGAGTGATTTAAGAGCACCATTGGAGATGCT
CTATGAGACTCTTAATGGCTCTTAAAGAGCTTCTTCCTTCTCCTCTCCTC
TATTTTAAGAGCCACTGCGTGACTCTTAATTTATTTTTAATAATAAAAAA
TTCATCCCTTCCAATTCATCAAGTACCTTTCCTACCATATTGACATAGCA
GAGTACAAATATTAAAAAATATAGAATAAAGTTGGAGTATGAAGTGCATT
GTCGGAGTTGACGCTCTAAACAATGTACTAATTTGCCAAGAGCCACAATT
TTTATTATATTTAAGAGCTAACTAGGAGACTCTTGGAGATGCTCTTGTTC
CTTTTCCTTTCTAATTTCTGCATTTTGTTGAATCAAAATCAATTGACATT
TGACCCTGACAAAGGCAGTCATGGGGATGGGGTAGAAATATTTTGATGCT
CTCTCATATATTATTTTTAACGCATGCAGTTTATTCTAGTCATCTTGCAG
AAATTGTTTCGTTATGCTTGTTTTGTCAAAATTCGCTTTTGTCTCTTCTT
TTGTTATACATCAGTCTTATTAGTTGCAATAAACCTGTTGGTCATAACTG
AAATTTGTACTCATAAAGTCTATACTCTATATATATATATTTGATCAGGT
TCCACCAGAATTATCATTTAATATTACTGGATGATGTAGATATATAGGTT
TTTGCACCCTCAAGTAAAAAAAAATTCAGTCTTCTTAATTTATTACATAC
TCTTAATTTACTGAACTTGGTTATAATTAAAAGATAAAAATAGAATCTGC
TTCGTGTTGAACCAGGTTTATACTTAGGTGCAAGACAAGACATCCCTTCT
ATCTAAGTGCTTTTTTGGTCAAGATATCACAAAATTTACGTCGACTCTTT
ATCTTACCTTGAGTATCAGTATTGTACACTGAATGCACATGGTCACATTA
GTATGGATTAATATGATGAAGTTCGACGCTTGAACATGTATATATATTGT
GGTATTCATTGTTTGTGTTTCTCTTTCTAGATAAAACCTTGTTTTAGAAG
ATAATAGTTAGCCTATGCCCAAGAAAAGAGGGTTTGCCTATCTGAATGTG
ATTAAACTTGAATCAAGGGGAGATCTTGGAGGTACCTTATGCCTTTGCTG
TACCTTGAAACCCTGTCTCCTTGACCATAATGGCTGGTAGATATCTCATT
TAATTTTAAGAAATGCTTGATGGTTAAATAACCAACGCATACCTCTATGA
TACTCCTCGAGATATGTTAATTGTATTGAATTGCTTATACTTGTTCAACT
TATTAGGTACCCTGCGTCCCTGCCCTCCACTCTCTTTAGCATGGGTGACT
TTACAATTCAGATTAGCAGCAACTTAGTTAAACAGCTCGCAGATGATGGT
GTAAAGATAAAGAAGAAAACAAGGAAACCAAAAACAAAGGCACCGCGTGA
ACAGTTCCCTGCTAAAGAACAACAAAAGCATAATGTAGATGATTCTGAAA
CACTAAAAAGTCCTAATGCTGTGGGGTGGCCAGTCCAACCACCACTGTTC
ATGCCAATTACCCCTCCTCAACTACCTGCTCAAGCGGAGATAGATGCAAT
AAGGTCTGTGCTTCAAGATAGCGAAAGGGTCCTGGAAAGATTGCAGAAGC
ATGAAGACGACATGGTGAAACAGGTTACACAGAAAGCTAAGGATCTACAT
GAGAAAGAGTTCAAGATTCCTCAGCCTAAACCTATCCCTTGCTTGGTTGA
GAAAGACGCTTGCTTGGAGTGCTATAAGGAAAATGTCAAGGATCCTCTCA
AATGTGCCAGTTTGGTAGAACAATTTTCCAATTGTGCTCGAATGGCTAGG
CAGCAAGTGAGTTCTGTGGAGAAGTAG