| Relationships |
|---|
| The mRNA, DCAR_021668, is a part of gene, DCAR_021668. |
| The genetic_marker, MK004158 K1602, is located in gene, DCAR_021668. |
| 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_021668 | DCAR_021668.mRNA | mRNA | DCARv2_Chr6:20890680..20897755 |
ATGGCTGGAATGGCGAGTGGCACCAAAATAACGGATATGGGTATGGACTC
TTTGATTCACTGCGCCAGCTTTCTCAATCTTCAAGATATCTCCAATTTGT
CTCTCACCTGCAAATACCTCAATTCACTTGCTTATTCTGATTCCATCTGG
CGATCCTTCTTCAGGTCTCTCTCTCTCTCTCTCTCCCTCCTCTCTCTCTT
TCTCTCCCTCCCTCCCTCTCCCCCCCCCTCTCCCTCTCTCTCCCTATTAT
AACTGTACGAAACAATGGGTCTCACTGTTCACAACACACCTATATGTGTT
TGGTCAAATTATTAGAATAATTTAAAGTCACGTGTTTATTTTCTGAAATA
TGTACTGATGATTGCAAATTGCGTTACTAATGTTTCAGACAGAGATGGCC
TCAACAAGAACCTTCTAGCATCTCAGAACGCTCAAGTGTGAGAGAAGCAT
ACATCACTAGAAATTTTGATGTGCAGCAATTTAAATTTGTTGACCCTTTT
GCTGCTGATATTCTCACTGATGCAAAACCTTTTGACAATTTGTTCATCAA
CAAAAATGATATTGTTTTCTCACAGGTGATATGTTTTCCACTATATTCAA
CTCTTAATGGTTTTGTGATCTATTTTATTTAGAATTGGTTTTGCATTGTA
TGGCATACATGTCACAAAGACGGCTTCACAGCTTTACTAAATTGCACAAT
CTTTTTCCATTTGGAATTCCTGTATTGTTAATGTGGAAAGAATCAAGCAA
ATTGTTATTCAAGTCTTATTTTTTGTAGATATCTTGTTCGATACAGTTAA
AAAAGAAAGTCTCCACACAAATTACAGGAGATTGTAGTTTAAGAACATGG
AAACTACACTTACAAGGACACAAGTTTCTATCAATAAATAGAGAAGCTTG
AATGAGAAACAAAAACTTTGAAATAATACGTGAACGTGGGGGTAATATCC
TGATCAAGTTCCAGTTCTTGTCTGAATGCGTTCATTGTTATATAAATTGT
ATACTGTTTGTAGTACAAAGAATATAGGACGTGTGAAATCCTTTCCTTAA
TTGAAAAATAAAGCTAATTTGTGTATCTCTGTTATTAGGGGTGAAAAAAT
CAAACCCGACAACCCACATGAATTCGGCCTTTAAACCCGACAACCCACAT
GAATTCATTGTAATATTAATGAATTATCATATTTCGGTTGGGTTCTGGGT
TCTGGTTGATTATTCAGATCCATTAAAATTTCGGGCCCGGTTCCGGAAAT
TGCCAGCCCTACCTGTTATAATTAAATATGTCATCCACCTGATACAATGG
AAGTGATTTTTACTCTTTAGTTGAAGTCTATAAATGATTCTGCTCTGTAT
TATTTGTGTGGCTGTCGGAGAAGGTGGTAGACCAATCCCACTGATCTGGC
CTTATGGGTTAATGAATAATGCATCATGGTCTTTATTTGTTTAAAGAATG
ATACTGTGATACTTGAATTCGATAAAGAAAAATTAATAACATGTCATGGA
ATTTCATAAAATTTATTAATATTCATTTTACATGCATAAGATCTTCTTTT
TTTTGCATATATTACCAATTAATACGTTCAAATGATACCCGTGAACAGTC
AGATTATAAAAAAAATGAACTTGAGGATTTATTGATTGCCTGTGAGTAGT
GACGAGGTCCCTCCCCTGATCAGAGTCATGGGACAAACCATCATCATCCC
CAGTGTATATTTACTAAATATCTGAGTTTATTGATGTGATTGGATGATGT
TTTTAGCTTTAGTTTAGGGTGCTAGAGATGTTATTGATTCGTCTCTGCTT
AGTGTCGTAGTAAGATCATGTGAAAACATATATTGACAAAGTATCACTAT
TATCTTTCACATTAGTACCAGAGAAATACTACATATAAGTAGTAAATAAT
TAATATTAGAATCACTGACATGCATTAAATTTGTCTTCTTTGGAAAAACG
TTCAGGGTCCAGCAATAAACATAATGAAGATTGATAGCTTTCTAAAGAGA
AGAGAGCCTCTCCTAACGCTCCGTGATCATAGTGCTCGAGTCAGTTGTAT
GAGGTGAGACTTTTTGTCATAAGACTTTCTTGTCGTAATATTTTACTTCT
AGTTTGATATGTCCAGATATACAGTATACTGAACCTCCTCTCTTTTCCTC
CCATGAGAATCAAACTTAAAAGTTCCAAAACTGAAAGTAGGACTCGCGGG
AAATCACAGCGACGTTTTTATTAAAAAAGAAAATATTGCAAAAGGAAAGA
ATAAGAAAATTACTTGGCCAAATATAAAATTTAGATTGCGAAGGAGGTAG
CTTGTCAGTTGCCAAAATGGCTGGTAGAATGTTGCATGGAATTAAAGAAA
GTCTTTAAAAGTATCTTCTTGTTAACTTAAAAAACCGCCTTTAATAACTT
TTCTCCCCTTAAATTGCTTTTTTAAATGCATGGGTCCTCTCTCTCTCTGT
GTGTGTGTGTGTGTGTGTGTGTGTCTTTTTTAAATTGCATGATTTTATTT
TCTTGTAGGTTTCGTTCCAAGTTAAATATACTGAGTATATATATTTGTTA
ATATTTTTGTAAAATGGTTTTAGGTTTTTACACATGTTCCTCGTAATTGA
TTTTATATTTTAACATGCAAGTGTGAACCTGATTTGTGATATGGTACGTC
AATTTTATTGAAATTAACTCCAAGTATATGTATGTTTGCTATCGCCATTC
GCCAGAAAAGCAAACTGAGATTAAAGATTTTGTTTCACAATTTTATGTGT
TGGGTACTGCTAAGATTGCAAAGAGCTTCTGTTAGAAGACATTATTGTAA
TTAATAACTTGAGTTGTAAATTACAATTTTGTAAAATTCTGATGTGTTTT
GCAGATTCTATTCTCTCGATGAGACTTCTTTATTCCGTAGTGAGACACAA
AGAAATGAGAAAGTTTTGGTAACATCAAGCTATGACCACTCCATTCGCCT
ATGGTGGAAGGTATTGCGGAGTGAAGTTTATGTATATGATTGTTAGGACA
TTGAATCTAATGTTTCTCTTCTTCCACGCATGTGTAAACTTTACACTATG
TATGCTGCATTTGCAATAAATTCAAAAAACGTTATGTATGCACGAACTTG
TTCTTAAACATATCAAGATATGTGATAGATTATCAGCAAAATGAATCTCT
CATTAATGAACACAGGGAAATTGCCAGAGATGTTTCAGAGGTCACAGCGG
GCCAGTTACGACACTTTCAGATAAATTGTTGGGTGAAGGTAGTGGCAAAG
TATTTGCGAGTGGAGGTGATGATGGTACTGTTCGACTCTGGTCACTAAAC
TTAAACGGAAAGCGTGGTCAACATGCTTTAAGAGCTACACTTTATGGTCA
TGGGAAGCCATTAGTACTGATGTCAGTTGCAGGGTATGGACTTGTTTCTT
GACATTTATCTGTTCGTTCTTACCCTTGTCTATATATGTCTTGTATGTTA
ATGCTTCAATTAGTTTGCTAAAATAAGTGCGACAAAGAATATAGGTGTTT
GCATTTTCGGAAGTCCACAGCCGGTATATGAAATGTGAAATTCTGTCAAG
GAAACATATCTAATTTAATTGAAAAAGAACTATAATTACTATATAAATTT
GTTAACTTGTGTACAATATGCTTGTTTGCTGGAATTATCAAGTTTATTTT
TTATTCAATAAGAGCTATGAAACAAATTAATTATTTCGTTTTCAAAATAT
ACCTACCACTTTTAATTGCTTAGGATCAAGGATGTTGTACACAACAAAAA
CTGAAAAACTGCTTTCTTCACATATAAAAGGTGTAGCCATGCAGAAAGTT
GTTCAAGGGTGCAGTATTCCACAACTTAATCATCGGTCTGCCACACTAAA
AGTTGGTATTGTTAACTTCTAGCTTACAACCAGTGCAAAGCACGAGCGAT
CATAAATAAGTTAAATATATATTTTGAATATAAAATTTTATTTTAATTTA
ACAAGATTATATTGTTTTATCATCTTTTAAGTTTAACTTTGTTTTGATTT
AAAAAAAAAAAAGTTTAACTTTGTTTTAAAAGTTACTCTAAACATATAAT
ATTAATGAGATTCAATGTAAATAATGATTTTGAGCAGTGATGAAAGTGAG
TTTTGTAAGTATATTGTCCGTTATATGATATTAGATTGCAAGTATAATTC
TAAGTATGAGTATGTAATATTTAGGATATTAATTCATAAAAAAAATTTAA
AAAAAAATTGTTAGCAAAATTTTTTTAGGTTAATGAAAACTGATTGATTG
AATACAAAAACTTTCCAGTTTGTTATAATAGTATAGCAAGTATTTTGTTC
GTAATTGTATTTTGAAATTATATAATATTTAAAGGTTTCATACAATTTTA
TATGGACAAATTTTTTAATTGAAATGTTAGTGAGATTCAGTTTAATGTTG
CATTTCAAAATATATATAGGTTGTTCTGAGTTTTAGCAGGGATGAAATTG
AGAGTGTACGTATATCGTATTTGGTAGGACTGTGTTATTCAATTATAAAG
TTTAGGTGTATAGTTTAAATGTCATTAAAAAATAAAAAAAGTTAACCAAA
ACTTGAATAACCAAGAGTTGGGGTTAACCAAGGTCGACTACAAAAGTTTT
TATGTTTGGTTATTATAGATAGCATACAGATATGAAGTAAATAGTTTATA
CTCCTCTATCCTGAAAACGGTGCTTCTATTTTCGCTCTTTAAACTTATGT
TCCCACTTGTGCATAGGACTTACGTGGAAACAAATACAGTAGTGTATGTG
ATATTGGACTTGCTGATTTGGAACTAGCACAACAAAAAAATATTTTTATG
ATGTTATATATTTTAATTTAACCTAAATAAAGATAGACAGAGTAGCACCA
AACGAAAGAGGTTGCTCAAAGAAAAGGGAAGAACATGTCCCTGAAGGTAG
CAGTATATCCCGTTTTGTGGGCATCAAAAGCTGTAGATAGATATTACTTC
CATCCAACTTGTCATGTCCTAATTTGAATTTGTTGGTCATATTAACTAAA
CTTTGACTACAAATTAAAAATTATCTTTTGATGTATTCATAAATCAAAAA
GTTGAATCTTAGAATCTACTGAACATTGTTTCCATGATTTCTTTTTCCAA
ATTTATATTTTTGTCATATAATTTAAGTAAAATACATTATACAAGTTATT
AATTCAACCAGAATTTGGTCAGAGCGTCAAAATAAATGAGATGAAAGGAG
CACCGTACAGTTGCTAAAATGATTTTTGTAAGATCCGACTATAGCATAAC
TAATTTTTGTGTCTTGCTAACCAGATATGTTGACAACATTTTGTTTTAGC
CCTAATTAAACATTCTGTTTAACAACTTCATAAATTTGAACTTGTGATTG
AATTGCATGCATGCTACCTTTTTTTGTTTCCAGGCACAAAAGTTCTCTTT
TGGTGAGCATGTCCAAAGATTCAAAGGTATTGTCATCCTTGTAAGATTAA
TTTGTAACTTGCAGGTATTTATTCAGTTTTAGTCAAAGAAATGTACCAAC
TGGATAGATATTTCTAATTAAATGAATCCATGTGTGTTCATAATTTACAT
AAGCATAAATTGATGGCATGTCACCGCTAGTAGTGGATCTTCTCTAAAGT
CACTTTACTTTCAGATATAGTTTTGAGGCAACAAGTTTACACTGGACCTA
CAAATGCAGTGAATAGGATATATTGTTAAAGATGAAAACTGTGACTATAT
TTCTGACTGCATAATTTGTAATTTGTAAGCATAACATTTTGTAGGTTTGT
CTCTATTATATTTTTTGTGATTTTCCTACGTAAGAATTGCTATTATTTGA
GTTTTGATGTATGATGGGGAATAGTGTAATATTTTTATATTAGTATGTAG
CTTACCTAGTTCACTTCTTGATTTTTTAGTAAGCGTCATCTGACAATTTT
TATCGAAATTAGTTGAGGCTTTGGGATACCGCTACATCATCTTCGAGTTC
TTCGTGCTGTGTCGGGATGACTTCGATACCTGGTGCACCTGTTGGCCTGA
AATGCCATGAATCACTTCTTTTTGTAGCTGCTGGTTCTTCGGTTGTTGCA
ATTGATTTGAGAACCATGAAAAAGGTTTTCAGCACACCATATTATCCGCC
AAGTTTGTTTTCATTTGAAATACTTCCTTCCAAATCATTAATCTGCACTG
GTGGCATGAACAGGTACACACTAAATTTCAAGTTTTGTTATTTTGAAGAA
TACTGAATTATATGGAATCTCTTACAAAGTTTTTCTCCTTACCTTGGTTG
ATTTTTTAGCATCAGTCACCTTTCTGCAGTTAATTTGGTGTTGAGAAATC
TTTGCAATCTCAATCAAGTTTTACCCATATTAAAGGCATTTTCAGTGTCA
TAACTAAAATAATTCATCTTCCATTCTGCCTTCTTATAGGACTTGTATAA
ATATTTGGATTTCTTTATTTCAAACTGGAGTTGCTGAACTAGTTGTATTT
CCACAACTTCTTCGTTTGTGTTGGGCGTTTTATTGCACCCATCTGAAATC
ACCTTTGTAGAATGTAGTATATTCAAAAGAAAATTAGGTCTATCCAGATC
CGTGTTGTAGCAAACTTATCTTGATAGATCGTGTGTTAGTGTTGGCAGTA
GCTTTTCGTTAAGCTTTTCAATATGATTGTGTAGTCTGTAACAGAAATTT
TCAATATACTCCACAGTGCAATGCTTTGGGATATGAGAACATTCTCTGAG
ACGGTGAAAACAAAGCCTTTAGGTTTGCTGGATGGGCATATTGGTCCAGT
CAAGTTTTTGCACATGGATCGGTATAAAGTAGTTTCAGGAAGTCCTGAGG
ATCCATTTGTCAATGTTTGGGAGTCTGACACAGGTCGACAAACAAATATC
TTGGCTTGCAACCCTACTGGTGGTCTGCATTCTACCACAGGTGGTTCTGC
CATTGCTGTTAATGGTTGTGAAATAGTCACTGGTAGCTGCACTGAAGGAC
AGGGGATTATACACTACAGGAACTTCAACTATGCTACCAGTCAAGTTTTA
GCAGAAGAGAATGAAGGTGGTTCGAAGTTTTGGGGTCCTCAACATTGTAG
TGACAGTTATGAATCTGATAGCTGA