| Relationships |
|---|
| The mRNA, DCAR_023609, is a part of gene, DCAR_023609. |
| The genetic_marker, MK002939 K0383, is located in gene, DCAR_023609. |
| 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_023609 | DCAR_023609.mRNA | mRNA | DCARv2_Chr7:3147657..3154921 |
ATGGATAAAATTTGCTGTGATTGCATGATGACTATTGCAGACTCTTGCAT
TAGTTATCATTGTCAAAGATGTGGTAGGATGTTGTGTGACAATTGTGTGC
AGTCAAATGGTTGTTTTGGAGGTGTTGCATTGGAAGATTCTGATAACACA
TATGATGCTGGCGTAATTGGTTATTGCAAATTCTGCTCTCATATGAGTAA
TAGGAAAAAAGTTGGAAAAAGGCTCATTGAAAAAGTTCATCCTGCAGAGT
CTCCACGACAAAGTTTTGAACCACCATCTCCTTGTTTCAATGAGAGATGC
GATGACTGTGCTAATCAGGATTTTGCTAGATGCAGAACTCATTACTCTCC
AAGCAGGTACGAAAAACAACCTGTTCTCAAGACTAGATCTCAGAATTAAT
TTGATTAATAAAATAGTTTATTTTAACTAAGCACAGTTGATCTGTTATTG
CTAAATAATGGTTCAGGTTCAGTTTATTTACCACAATTAGCTTCTGTTTG
TTTGCTTCTCTTTTCATTTATTATTATATTTCTGCCTTCCATCATATTTC
TGTCTATCACTTTTGGTAGCATTCTCAATGATGATTGCCTATGAGAATCA
TGATCTAGGGATCACAGAAACGTTTGATATTAAGTTTTATTCTAAACATG
ATCTTAAGTTATCCCATGAATCAAATTTATCATTTCTGAGATCATCCCAT
AAAGATAAATTAAGAGATGGAGTAGATGATATTATATGAACCCTTTCAAA
TGTGCTAAAAAGTGATGAAATCTTTCGTTACGAATAAGGCGATGATATAT
ACTCCATCCGTCTCAAATTAACTGTATTGTTTGACTTTTTGTGGTTAAAT
TGATCAAACTTTGACTGATATATTGGGACGGAGGGAATATAAACTCGTTA
AGTTGTATATTTCTTTCTTCCCTCAGATTACATTTGGTTACTCTAGACAT
CAAGATCTCAATTACCCTTGTTCATCTTACGAGAACTTGCTTCTGCTTTC
GTCAATAATCACACCGTGCTTATTATTGTAGGAGTGATGGATATGATAGA
GAGGATTCCACCAAAACCTTCTTCAGTTCATTTTTTGATGATACATCAGA
TATAGATTCAAGTAGTATGAGCGCTAGACATGAGTTTTACAATAATAAGT
CAGTTGGATCAAGTCCAATGGACAGTCCCTGTAGAATCCATAATTTTGAT
AAGACAGGGCAATCTGCAGAGCAGGAGCAAGTTAGGACCGGAATGTCTCA
GAATGATGGCCCCTTCGATCAAGATACTTCAGCTGTACCAGAAAGGCCTG
ACACAGGTACCGAGGATATTGACCATACTTGTGAAAACGAGGATCTTTTA
TTGGCATTTCAGGATCAACAGCACTTAAATTTGGAGAACAATGGTCTCAT
CTGGTTTCCTCCTCCTGCTGTTGATGAAAATGATGAGAGAGAAGATAACT
TTTTTGCTTATGAGGAAGATGAGGATGACATTGGGGAGGTAACTCCGATG
TTGTCATCTGGTGAATTGAATAGCATGCTACCTGAGAAGGAGAGAGATTG
TGGCCAAAAGGAATCTTTAAAAGCTCTCGTGCAGGGGCATTTTAGGGCGC
TCGTGTTACAGCTCTTGCTTGGGGAGGGTATAAAGGTGGATAAAGAAAAT
AGTGAAGACAACTGGCTTGATGTAGTTACAGCAATATCCTGGCAAGCTGC
AAACTTTGTGAAACCAGACACTAGCAGTGGAGGCAGTATGGATCCTGTTG
ATTACATAAAAGTTAAATGTATATCATCTGGAGTTCCTAGTGAAAGGTAT
GTACTCACCTTTTCCTTCTTATTTCATTTATATCTGTTAGTGCTCCAAAC
CCATCTTCATTTTTATTTTGTGGTCGATGCAGTAAATAATGTAGAGTTTT
ATTCTTAATCTGCTATCTGTTTCAATATATGCAGTAAATTCATTAAAGGA
GTAGTGTGTACCAAAAATATAAAACACAAGCGCATGATTTCGCAATTTAG
AAATGCCAGACTACTTATTTTGGAAGGAGCACTTGAGTACCAAAGAGTTC
CAAATGAGCTGGCATCTTTCGATATGCTCCTACAACAGGTTTTTAATTGG
AAATTTGGTCTATGGTATGAGATATTCTGAAAGCATGATCTTATGAACTT
TACTTTTCTTGACAGGAAATTGATCATCTGAAGATGATTGTTTCAAGGAT
AGAGGCTCACCGCCCAAACGTGTTACTGGTTGAAAAAAGTGTATCTTCAT
ATGCCCAAGAGTATCTGTTGGCAAAGGAGATCTCCTTAGTGCTGAATGTT
AAGAAGCCTCTGCTACAGAGAATAGCTAGGTGTACTGGTGCTTCTGTAAC
TCCATCAATTGATAAATTGTCTACTGCACGTTTGGGACAGTGTGAACTCT
TCCGCATAGAAAAAGTATCTGAAGACCTCGAACAAGCTAAACATCCCCAA
AAGAAGCCATCTAAAACCTTAATGTTCTTCGAAGGTTGTCCAAGGCGTTT
AGGTTGCACGGTAACATTCTCCTTCTCTCTGCCAGAAACTAATCTGCCCT
ACTGTTTAACACCTTCCAGTGTGCCTGTGATGTATGCAGTGATAAGCATA
TTTTATCTTTTACTGTGTAGTTAATTTAAAGTTTTGAGAAATAGCGGGAA
CGTTAATTTCTTTTTAATTCTAATAGAAACATGTTACTTTTGCCAGTGTT
ATCTCTTCAGTAATATTTGAACATGTGTTAAATTTTATCTAAGGGATCAA
GTTGTGCATCAGATCATCTTGCTTTTTAGTCTCAAAAAGTACAGGTCACA
TCCTAAGATGGTTCCATCACAGTTTAACATCAACCATTAAAATATTTCTA
CATATAAACAGTGCTCATGGCCGTAGTTTACGTAATCTCTATGTATACGT
TTTCTAAATGCAAAAACATTTTTACCATCCATCTTAAAGGTTCATCTTAC
AAATTGAAGGCCTTCTGATTGTTCTTTATTATTTGATTTCCTTAGGTACT
GCTAAAGGGTTCCTCTCGTGAAGAACTAAAGAAAGTTAAGCATGTTGTTC
AGTATGCAGTTTTCGCAGCATATCATTTGTCCTTGGAAACTTCTTTCCTC
GCAGATGAGGGTGCTAGCTTACCTAAACCAACTTCAAGATCTTCATTTTC
AATACTTGAAAGGACAAGTATCGACAGTGCCATTTCTGTTGTCCCTACTC
CAACCTCCTACTCGGAAATTGCTGATCTCCCAAGTTTTCATGAGGAGTCT
GCAGGCCTCAAGTTAGAACTTGAGGCAAGGGAGTCAGTAATTGAGCCTTT
TAATTCTCAATTTATCTCTTCTCCTGCCTCTGTGAAGTATGGTGTAGAAA
CCTCTGATGTACTTAATAATGGTTTACCAGCTACATTTATTTCGGAGGAA
TATAGGCCAGGTGTAGTTTCTACCGGAAGTAGAAATTTTGATCGGGAGGA
TTCCCAGCTGACCATAAACTATATGCAACCATCTGAACCCTTTAATCAGA
AAAAACATGAACAATTAAAAGATATTGATGGCTCTAGTGAATACAATTCA
GCAGGTGATAGTCACCAGAGCATACTGGTATCTTTTTCAAGTCGCCGTGT
CCTTGATGGAACTGTCTGTGAACGTTCTCGACTCTTGCGCATTAAGTTCT
ATGGTTGTTTTGATAAGCCACTTGGAAGGTATCTTCAAGAAGATCTGTTT
GATCAGGTACACATTTCTTTTTTCTTCTCTTCGATTTCTATTCCTACACT
TACAGAGATGGGATTATTGAATGGGTGCACTTCTAATGCTAGACTTCCTG
CTGTGAATCATGCAAAGAGCCGGCTGATGGCCACATAGTTTGCTATACTC
ACCAGCAGGGTAATCTAACAATAAGTGTTAGGAGACTACCCACGGTGAGA
CTGCCTGGAGAACGAGATGGAAAAATTTGGATGTGGCACCGATGCCTCAG
ATGTACACATGTAGATGGGGTTCCACCGGCAACCCGCAGGGTGGTTATGT
CTGATGCTGCTTGGGGTCTTTCTTTAGGAAAGTTCTTAGAACTTAGTTTC
TCAAACCATGCAACTGCTAATCGTGTTGCAAGTTGTGGTCATTCTCTGCA
AAGGGACTGTCTTCGGTACTACGGGTAATGACATTTTGTTAATCTAGGAC
TTTTACTCTACAACTTTAATATCACCCTTTTTGTATTTTTATCTGGTTAG
GATTAAAATAATGCGGTACCAATATATTTATTAAATGTCTGTATGTGCAT
GTGTTTATGATTCATGAAATGTTTTTTGGTTATAACAGATTTGGGAGTAT
GGTAGCATTCTTCCGCTATTCTCATATCGATATTTACTCGGTTTGTTTGC
CCCCATTAGCACTTGAGTTTATTCCCCATTCACAGCAGGATTGGATAAAG
AAAGAGATGGCAGAGGTGAAGCGCACTCAAATTATGTGATATAATGTAGA
ATAATATTAGGACTGCATGTTTTTTGTCACACTCCTAGAAATTTATACCA
TTTTACTTTTGCTACAGATTTTGAACAAGCAAGAAGCTTTATACGAGGAA
ATATTGGGTTTACTTTATAAGATTGAACAGAGAAGTACATCTCTTGGACA
AGAATCGTCTACGAGAAATGAGTTGCATAAACACATAATTGAGTTGAAAG
ACCAGCTCATAAAAGAAAGAGATGATTCTCAGGTAAGCATGCAAATACAA
TATGTTTATACAGTAAGGCTCGGTGTCATACAAGCACAAAAAAATTCCTT
ATAATTTTATATTTTAAATATCTTGCTGATTTTCTGTTGCTTCCATGTTT
TCTGACAGTGCATATATCAGCAATTTAGCAAAGATAGTTCAGAACTAGTC
CCAGCGACAATGGATGTTTTTGACCTTAATCAATTGAGACAATCACTCCT
GATTGTTTCACATGATTGGGAGCACCGGCTTAGTTCATTAGATTCTCTCA
TTAGCTCCAATGCAGGGTTACAAGATTTGAGAAGTGTTTCGTGTATTAAT
GATATTAGTCTTTCCTGTGACCGTGATAATGATGGTGTCTCTGATCTGGT
TTTGAAATTGCCAGATTTCCTCCAGAAAGATATACCGTACACACAAGACA
GAGAGCCTGAAAAATCCCTGGTTGATTCTGGTGTTCCTAAAGTTAACATG
CCGATGTCATGCAAGACTAAGAATGAGACATTGACACACTTGGATGGGGA
ACCTACAGTCAACAAGACGCTCTTGGATCGTGCTCCCTCAGCTGCATCTG
AATTGTCTGATAAAATTGATTCTGTATGGAATGGTACAGCAGACAGTCCG
TTGAAATTGCCTTCTTGGAGATTGCTATCACCAGCAAGAGTTCAATCCAT
TGATTCTGCTATAAGTATCCAAGAAAAGCTAATGAAAGGATTACCGCCCT
CATCATTTCATTTATTAGCAATTAGATCTTCTCACGCCTCTGGGGACTAT
GCAAACATGTCTAGAGATCCCTTACTTAATGTACAGAGGACTTATTCTCA
AATGTCACCTCTTGAGGCCCAGAAGTTTAACCTTTGGAACACCTCACACT
CATTTAACTCGTCTGCATCTCTTTTGCCTGAAGGGGCACGATTGGTACGT
CGGCAAGATGGCCAGACAGATTTGACCATTGTTGTTTATGACAATGAACC
AACTAGCGTGATTTCATATGCTCTCAGTTCCAAAGAGCATAAAGACTGGA
TAGCTGATGAGCCTTGTGAATTTGAAGAAGCCTGGAATGCTGCTCAACTG
AAGCGAGAGAATTCTGTGGCTTCAACCATTCCAGCCTGGCAGTCTTTTGG
TTCTGTGGACTTGGATTATATCCACTATGGAAGTTATGGTTCTGAAGACG
TTTCAACAACCATTAGTACTATGCTTACAGATACAACCAATAGCAGTTCC
CATTTTAAAATTGCTTTTGAGGATGATAACCCCAGTGCTGGAGGAAGGGT
AAAGTTTTCTGTTACCTGTTATTTTCCAAAGCAATTTGACGTGCTCAGAA
AGAAATGTAGCTGTAGCCAAATAGATCTTGTACGTTCTTTGAGCCGCTGC
AAGAGGTGGAGTGCACAAGGTGGAAAAAGCAATGTGTACTTTGCAAAGTC
TTTGGATGAAAGGTTTATTATAAAGCAAGTCACGAAGACTGAATTAGAAT
CTTTTGAAGAGTTTGCACCTGAGTACTTTAATTATATGAAAGATTCCCTC
GACTCCAGAAGTCCAACATGTCTCGCGAAAATTCTGGGGATATTCCAGGT
TGCTTGCAGTTTTACACCCGAGTACTTGAATATTCTACATATATCCAGTT
ATTTATTACCGCTGTTACACAACATACATTTGTTCCTAGTGTCTTGCTGG
AGTTGGGTAGGTGGCATTGATACTACCTTGCTTTCTCTAATCTTGATTTT
CTCTTACTTTCAGGTAACCGTCAAACACTTGAAGGGTGGAAAGGAAACAA
AAATGGATCTGATGGTGATGGAAAATCTATTTTTCAGAAGAAATATTTCA
AGAATCTATGATCTTAAGGGCTCTTTACGATCTCGTTACAATTCAGATAC
TACCGGAGTGAACAAGGTGTTGCTTGACATGAATCTCTTGGAAGCATTGC
GAACAAATCCTATGTTTCTTGGAAGTAAGGCCAAGAGAAGCTTGGAAAGA
GCAATTTGGAATGACACATCCTTTTTAGCGGTAAGAGAATTTTATCCAAC
TACATATAACAGATTCAATATTTTGCAATTTATGCTACCGGAATAGTAAT
GTGTTAAAATATATAGTCAAGACCCATAATATGCTTAAAGATATTTTATG
CAAAGTCAAAAAAAAGCTTCAAGTGCATTACAAAAAGGGAATGGAAATGA
AAAACTCATGATGTTTACGATTTATTTGTACTTTGATATCTTGATACCTT
GAACCTTGATGCATCTGTAGGGTGCCCATTTTATTTCAGAAAAGTATTGG
CCGTTTTTTTTAAGTCGGGCATAACTAGATTTTGAGATCGGCATTCTTGT
GCTGTGCAGTCTGTAGACGTTATGGATTATTCTTTGCTGGTCGGAGTAGA
TGAAGAAAAGAAAGAGCTGGTGGTTGGGATAATCGATTACATGAGACAAT
ATACATGGGATAAGCACCTGGAGACATGGGTGAAGAGCTCTGGAATACTA
GGAGGTCCAAAGAATGCTGCCCCAACTATCGTGTCGCCGAAACAATACAA
AAAAAGATTTAGAAAAGCAATGACAGCTTATTTTCTAACAGTACCTGATC
AGTGGTCAGCATAA